barplot method for object report_annual-class

Description

barplot method for object report_annual-class

Usage

## S4 method for signature 'report_annual'
barplot(height, legend.text = NULL, ...)

Arguments

Value

No return value, called for side effects

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

report_annual-class for examples

Generic method for calculations

Description

Generic method for calculations

Usage

calcule(object, ...)

Arguments

Author(s)

cedric.briand

Calcule method for report_ge_weight

Description

Calcule method for report_ge_weight

Usage

## S4 method for signature 'report_ge_weight'
calcule(object, silent = FALSE)

Arguments

Value

An object of class report_ge_weight-class with @calcdata[["data"]] (essentially a selection of columns and renaming from @data) and coe daily coefficients extracted from the database @calcdata[["coe"]] and prepared for graphs

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Transforms migration per period to daily migrations, and performs the conversion from weights to number is data are stored as weights (glass eel).

Description

The calculation must be launched once data are filled by the connect method. Currently the negative argument has no effect.

Usage

## S4 method for signature 'report_mig'
calcule(object, negative = FALSE, silent = FALSE)

Arguments

Value

report_mig with calcdata slot filled. It is a list with one element per counting device containing

method

In the case of instantaneous periods (video counting) the sum of daily values is done by the fun_report_mig_mult method and the value indicated in method is "sum". If any migration monitoring period is longer than a day, then the migration is split using the fun_report_mig_mult_overlaps function and the value indicated in the method is "overlaps" as the latter method uses the overlap package to split migration period.

data

the calculated data.

contient_poids

A boolean which indicates, in the case of glass eel, that the function fun_weight_conversion has been run to convert the weights to numbers using the weight to number coefficients in the database (see report_ge_weight).

negative

A parameter indicating if negative migration (downstream in the case of upstream migration devices) have been converted to positive numbers, not developed yet

Note

The class report_mig does not handle escapement rates nor 'devenir' i.e. the destination of the fishes.

Computes data to a standard format for the summary and plot methods.

Description

Merges the content of the list elements 'parqual' and 'parquan' in the data slot, and creates a single dataframe with one line per qualitative and quantitative pair. This methods allow to cross one quantity (e.g. length) with a qualitative parameter (e.g. sex).

Usage

## S4 method for signature 'report_mig_char'
calcule(object, silent = FALSE)

Arguments

Value

An object of class report_mig_char-class with slot @calcdata filled

Calculations for migration in the class report_mig_env-class

Description

Runs the calcule method in report_mig_mult-class

Usage

## S4 method for signature 'report_mig_env'
calcule(object, silent = FALSE)

Arguments

Value

report_mig_env-class with data in slot r_mig_env@report_mig_mult@calcdata

calcule method for report_mig_interannual

Description

Performs the calculation of seasonal coefficients for the plot(plot.type="seasonal") method. The numbers are split according to the period chosen, one of "day","week","month","2 weeks", French labels are also accepted as arguments. Once this is done, the seasonality of the migration is displayed using the day when the first fish was seen, then the days (or period) corresponding to 5, 50 , 95, and 100 percent of the migration. The duration of 90

Usage

## S4 method for signature 'report_mig_interannual'
calcule(object, silent = FALSE, timesplit = "mois")

Arguments

Value

An object of class report_mig_interannual-class with calcdata slot filled.

Note

The class report_mig_interannual does not handle escapement rates nor 'devenir' i.e. the destination of the fishes.

Author(s)

Marion Legrand

#' Transforms migration per period to daily migrations, and performs the conversion from weights to number is data are stored as weights (glass eel). This calculation is performed in a loop for all dc.

Description

The calculation must be launched once data are filled by the connect method. Currently the negative argument has no effect.

Usage

## S4 method for signature 'report_mig_mult'
calcule(object, negative = FALSE, silent = FALSE)

Arguments

Value

report_mig_mult with a list in slot calcdata. For each dc one will find a list with the following elements

method

In the case of instantaneous periods (video counting) the sum of daily values is done by the fun_report_mig_mult method and the value indicated in method is 'sum'. If any migration monitoring period is longer than a day, then the migration is split using the fun_report_mig_mult_overlaps function and the value indicated in the method is 'overlaps' as the latter method uses the overlap package to split migration period.

data

the calculated data. If weight are present, the columns display weight or numbers, the total number is 'Effectif_total' and corresponds to the addition of numbers and numbers converted from weight, the total weight is 'Poids_total'+'poids_depuis_effectifs' and corresponds to weighed glass eel plus glass eel number converted in weights. CALCULE corresponds to calulated number, MESURE to measured numbers, EXPERT to punctual expertise of migration (for instance measured in other path, or known migration of fishes passing the dam but not actually counted, PONCTUEL to fishes counted by visual identification but not by the counting apparatus (in case of technical problem for instance)

contient_poids

A boolean which indicates, in the case of glass eel, that the function fun_weight_conversion has been run to convert the weights to numbers using the weight to number coefficients in the database (see report_ge_weight).

negative

A parameter indicating if negative migration (downstream in the case of upstream migration devices) have been converted to positive numbers, not developed yet

Note

The class does not handle escapement rates, though structurally those are present in the database. If you want to use those you will have to do the calculation manually from the data in report_mig_mult@data.

Calculation for report_sample_char

Description

In that class, most treatments are done in the query, this method checks that data are available and fills information for year, month, two weeks, week, doy

Usage

## S4 method for signature 'report_sample_char'
calcule(object, silent = FALSE)

Arguments

Value

An object of class report_sample_char-class with slot @data filled

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Split data according to the limits set in the limit1hm, and limit2hm arguments of the report_sea_age-class.

Description

If no value are provided in the limit1hm slot, an error is returned, if no value is provided in the limit2hm slot a default upper value for salmon size is taken to ensure all salmon are either of age 1 or 2, but no age 3 are returned

Usage

## S4 method for signature 'report_sea_age'
calcule(object, silent)

Arguments

Value

An object of class report_sea_age-class with calculated data in slot calcdata

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Calculate individual silver eel parameters.

Description

This calcule method for report_silver_eel, will transform data from long (one line per size characteristic, size, weight, eye diameter, pectoral fin measurement, lateral line and constrast) to wide format (one line per silver eel). It will also calculate Durif silvering index and Pankhurst and Fulton's K.

Usage

## S4 method for signature 'report_silver_eel'
calcule(object, silent)

Arguments

Value

An object of class report_silver_eel-class with slot calcdata filled, as a list for each counting device

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

calcule method for report_species

Description

The number will be split according to the split argument passed to the class, e.g. per year or month or week. Data from different DC will be grouped. Counts are given per taxa, unless there are several stages, in which case the counts correspond to taxa + stage.

Usage

## S4 method for signature 'report_species'
calcule(object, silent = FALSE)

Arguments

Value

An object of class report_species-class with calcdata slot filled.

Generic method to load referentials

Description

Generic method to load referentials

Usage

charge(object, ...)

Arguments

Author(s)

cedric.briand

Loading method for Refchoice referential objects

Description

Loading method for Refchoice referential objects

Usage

## S4 method for signature 'ref_choice'
charge(object, vecteur, label, selected)

Arguments

Value

An S4 object of class ref_choice-class

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

Other referential objects: ref_choice-class, ref_coe-class, ref_dc-class, ref_df-class, ref_horodate-class, ref_list-class, ref_par-class, ref_parqual-class, ref_parquan-class, ref_stage-class, ref_taxa-class, ref_year-class

Examples

## Not run: 
object=new('ref_choice')
charge(object,vecteur=c('oui','non'),label='essai',selected=as.integer(1))

## End(Not run)

loads the coefficients for the period defined in class

Description

The slots datedebut and datefin have to be filled before using charge

Usage

## S4 method for signature 'ref_coe'
charge(object)

Arguments

Value

An object of class ref_coe-class

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
object<- new('ref_coe')
object@datedebut<-strptime('01/01/1996',format='%d/%m/%Y')
object@datefin<-strptime('01/01/1997',format='%d/%m/%Y')
charge(object) 

## End(Not run)

Method to load the counting devices of the control station

Description

Method to load the counting devices of the control station

Usage

## S4 method for signature 'ref_dc'
charge(object)

Arguments

Value

an object of class ref_dc with data loaded

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Loading method for DF referential objects

Description

Loading method for DF referential objects

Usage

## S4 method for signature 'ref_df'
charge(object)

Arguments

Value

An object of class ref_df with df loaded

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
 object=new('ref_df')
charge(object)

## End(Not run)

Loading method for ref_env referential object

Description

Loading method for ref_env referential object

Usage

## S4 method for signature 'ref_env'
charge(object)

Arguments

Value

An S4 object of class ref_env with data loaded from the database

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
 object=new('ref_env')
 charge(object)

## End(Not run)

Loading method for ref_list referential objects

Description

Loading method for ref_list referential objects

Usage

## S4 method for signature 'ref_list'
charge(object, listechoice, label)

Arguments

Value

An S4 object of class ref_list-class

An S4 object of class ref_list-class

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
 object=new('ref_list')
charge(object)

## End(Not run)

Loading method for ref_par referential objects

Description

Loading method for ref_par referential objects

Usage

## S4 method for signature 'ref_par'
charge(object)

Arguments

Value

An S4 object of class ref_par

An S4 object of class ref_par-class

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
 object=new('ref_par')
charge(object)

## End(Not run)

Loading method for Reparqual referential objects

Description

Loading method for Reparqual referential objects

Usage

## S4 method for signature 'ref_parqual'
charge(object)

Arguments

Value

An S4 object of class ref_parqual

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
 object=new('ref_parqual')
 charge(object)

## End(Not run)

Loading method for Reparquan referential objects

Description

Loading method for Reparquan referential objects

Usage

## S4 method for signature 'ref_parquan'
charge(object)

Arguments

Value

An S4 object of class ref_parquan-class with data loaded

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
 object=new('ref_parquan')
 charge(object)

## End(Not run)

Loading method for ref_stage referential objects

Description

Loading method for ref_stage referential objects

Usage

## S4 method for signature 'ref_stage'
charge(object)

Arguments

Value

An S4 object of class ref_stage-class with all stages available in the database

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
 object=new('ref_stage')
 charge(object)

## End(Not run)

Loading method for ref_taxa referential objects

Description

Loading method for ref_taxa referential objects

Usage

## S4 method for signature 'ref_taxa'
charge(object)

Arguments

Value

An S4 object of class ref_taxa

An S4 object of class ref_taxa-class with all taxa loaded from the database

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
 object=new('ref_taxa')
 charge(object)
## End(Not run)

Loading method for ref_textbox referential objects

Description

Loading method for ref_textbox referential objects

Usage

## S4 method for signature 'ref_textbox'
charge(object, title, label)

Arguments

Value

An S4 object of class ref_textbox-class

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
 object=new('ref_textbox')
charge(object,title='un titre',label='20')

## End(Not run)

Loading method for ref_year referential objects

Description

Selects year available either in the bjo table if report_object==report_mig_interannual) or in the t_operation_ope table

Usage

## S4 method for signature 'ref_year'
charge(object, objectreport = "report_ge_weight")

Arguments

Value

object An object of class ref_year-class with slot data filled with the available years for the corresponding report

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
object=new("ref_year")
charge(object)
 validObject(annee)
showMethods("charge")

## End(Not run)

charge method for report_annual class

Description

Method used by the graphical interface to load data and check that all choices have been made by the user

Usage

## S4 method for signature 'report_annual'
charge(object, silent = FALSE)

Arguments

Value

object An object of class report_annual-class with data set from values assigned in envir_stacomi environment

charge method for report_dc

Description

used by the graphical interface to retrieve the objects of referential classes assigned to envir_stacomi

Usage

## S4 method for signature 'report_dc'
charge(object, silent = FALSE)

Arguments

Value

object An object of class report_dc-class with data set from values assigned in envir_stacomi environment

charge method for report_df

Description

used by the graphical interface to retrieve the objects of referential classes assigned to envir_stacomi

Usage

## S4 method for signature 'report_df'
charge(object, silent = FALSE)

Arguments

Value

An object of class report_df-class with data set from values assigned in envir_stacomi environment

charge method for report_env class

Description

charge method for report_env class

Usage

## S4 method for signature 'report_env'
charge(object, silent)

Arguments

Value

An object of class report_env-class with data set from values assigned in envir_stacomi environment

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Loads additional data on migration control operations, df (fishway) dc (counting device).

Description

this method creates additional classes in envir_stacomi for later use in plot (operations, DF operation, DC operation). So unlike in most report classes where the charge method is only used by the graphical interface, it is necessary to run charge for report_mig.

Usage

## S4 method for signature 'report_mig'
charge(object, silent = FALSE)

Arguments

Value

An object of class report_mig-class with slots filled from values assigned in envir_stacomi environment

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

charge method for report_mig_char

Description

Used by the graphical interface to collect and test objects in the environment envir_stacomi, fills also the data slot by the connect method. It is not necessary to run the charge method if the choice is made from the command line using the choice_c method.

Usage

## S4 method for signature 'report_mig_char'
charge(object, silent = FALSE)

Arguments

Value

report_mig_char-class with slot filled from values assigned in envir_stacomi environment

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

charge method for report_mig_env class

Description

#' Unique the other report classes where the charge method is only used by the graphical interface to collect and test objects in the environment envir_stacomi, and see if the right choices have been made in the graphical interface, this methods runs the charge,report_mig_mult-method and needs to be called from the command line (see examples)

Usage

## S4 method for signature 'report_mig_env'
charge(object, silent = FALSE)

Arguments

Value

An object of class report_mig_env-class with data set from values assigned in envir_stacomi environment

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

loading method for report_mig_interannual class

Description

loading method for report_mig_interannual class

Usage

## S4 method for signature 'report_mig_interannual'
charge(object, silent = FALSE)

Arguments

Value

An object of class report_mig_interannual-class with slots set from values assigned in envir_stacomi environment

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

charge method for report_mig_mult

Description

For the report_mig_mult class the charge method must be run to load data on migration control operations fishway operations, and counting devices operations as data from those are displayed in the main plots. For other classes the charge method is only used by the graphical interface (shiny)

Usage

## S4 method for signature 'report_mig_mult'
charge(object, silent = FALSE)

Arguments

Value

An object of class report_mig_mult-class with slots filled from values assigned in envir_stacomi environment

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

charge method for report_ope

Description

used by the graphical interface to retrieve referential classes assigned to envir_stacomi

Usage

## S4 method for signature 'report_ope'
charge(object, silent = FALSE)

Arguments

Value

An object of class report_ope-class with slots filled from values assigned in envir_stacomi environment

Author(s)

cedric.briand

charge method for report_sample_char class

Description

this method verifies that boxes have been clicked in the user interface and gets the objects pasted in envir_stacomi

Usage

## S4 method for signature 'report_sample_char'
charge(object)

Arguments

Value

An object of class report_sample_char-class with slots filled with user choice

An object of the class report_sample_char-class with slots filled from values assigned in envir_stacomi environment

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Loads data and check that all choices in the graphical interface have been made.

Description

It is not necessary to run this method if the choice_c method has been run. This method verifies that boxes have been clicked in the user interface and gets the objects pasted in envir_stacomi

Usage

## S4 method for signature 'report_sea_age'
charge(object, silent = FALSE)

Arguments

Value

An object of class report_sea_age-class with slots filled with user choice

An object of class report_sea_age-class with slots filled from values assigned in envir_stacomi environment

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

charge method for report_silver_eel class

Description

this method is used by the graphical interface load the user's choice and get the objects pasted in envir_stacomi. It is not necessary to run this method when loading from the command line using the choice_c method

Usage

## S4 method for signature 'report_silver_eel'
charge(object, silent = FALSE)

Arguments

Value

An object of class report_silver_eel-class with slots filled from values assigned in envir_stacomi environment

An object of the class

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

charge method for report_species

Description

Verifies the content of objects when the graphical interface is used, it is not necessary to call the charge method if the choice_c method has been used

Usage

## S4 method for signature 'report_species'
charge(object, silent = FALSE)

Arguments

Value

report_species with slots filled by user choice

An object of class report_species-class with slots filled from values assigned in envir_stacomi environment

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Generic method to load additional data

Description

Generic method to load additional data

Usage

charge_complement(object, ...)

Arguments

Author(s)

cedric.briand

Loads an additional dataset this method is loaded to obtain the possible values of a qualitative parameter. Here data only contains one line

Description

Loads an additional dataset this method is loaded to obtain the possible values of a qualitative parameter. Here data only contains one line

Usage

## S4 method for signature 'ref_parqual'
charge_complement(object)

Arguments

Value

An S4 object of class ref_parqual-class with the valqual slot filled

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
 dc_selected=6
taxa_selected=2038
 stage_selected='AGJ'
 object=new('ref_parqual')
 object<-charge(object)
 charge_complement(object)

## End(Not run)  

Generic method to load referentials, with filters from the parent object in the database

Description

Generic method to load referentials, with filters from the parent object in the database

Usage

charge_with_filter(object, ...)

Arguments

Author(s)

cedric.briand

Loading method for ref_par referential objects searching only those parameters existing for a DC, a Taxa, and a stage

Description

Loading method for ref_par referential objects searching only those parameters existing for a DC, a Taxa, and a stage

Usage

## S4 method for signature 'ref_par'
charge_with_filter(object, dc_selected, taxa_selected, stage_selected)

Arguments

Value

An S4 object of class ref_par-class

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
 object=new('ref_par')
charge_with_filter(object,dc_selected=6,taxa_selected=2038,stage_selected=c('AGJ','CIV'))

## End(Not run)

Loading method for Reparqual referential objects searching only those parameters existing for a DC, a Taxon, and a stage

Description

Loading method for Reparqual referential objects searching only those parameters existing for a DC, a Taxon, and a stage

Usage

## S4 method for signature 'ref_parqual'
charge_with_filter(object, dc_selected, taxa_selected, stage_selected)

Arguments

Value

An S4 object of class ref_parqual-class

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
 dc_selected=6
 taxa_selected=2038
 stage_selected='AGJ'
 object=new('ref_parqual')
 charge_with_filter(object,dc_selected,taxa_selected,stage_selected)

## End(Not run)

Loading method for Reparquan referential objects searching only those parameters existing for a DC (counting device), a Taxon, and a stage

Description

Loading method for Reparquan referential objects searching only those parameters existing for a DC (counting device), a Taxon, and a stage

Usage

## S4 method for signature 'ref_parquan'
charge_with_filter(object, dc_selected, taxa_selected, stage_selected)

Arguments

Value

An S4 object of class ref_parquan-class with data loaded showing available parameters for one DC

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
 dc_selected=6
taxa_selected=2038
 stage_selected='AGJ'
 object=new('ref_parquan')
 charge_with_filter(object,dc_selected,taxa_selected,stage_selected)

## End(Not run)  

Loading method for ref_stage referential objects searching only those stages existing for a DC and a Taxon

Description

Loading method for ref_stage referential objects searching only those stages existing for a DC and a Taxon

Usage

## S4 method for signature 'ref_stage'
charge_with_filter(object, dc_selected, taxa_selected)

Arguments

Value

An S4 object of class ref_stage-class listing all stages available for one DC and one taxon

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
 dc_selected=6
taxa_selected=2038
 object=new('ref_stage')
 charge_with_filter(object,dc_selected,taxa_selected)

## End(Not run)

Loading method for ref_taxa referential objects searching only taxa existing for a DC

Description

Loading method for ref_taxa referential objects searching only taxa existing for a DC

Usage

## S4 method for signature 'ref_taxa'
charge_with_filter(object, dc_selected)

Arguments

Value

An S4 object of class ref_taxa-class with all taxa present on a DC (counting device)

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
 dc_selected=6
 object=new('ref_taxa')
 charge_with_filter(object,dc_selected=dc_selected)
## End(Not run)

Generic method for manual choice using the command line

Description

Generic method for manual choice using the command line

Usage

choice_c(object, ...)

Arguments

Author(s)

cedric.briand

Choice_c method for ref_choice referential objects

Description

Choice_c method for ref_choice referential objects

Usage

## S4 method for signature 'ref_choice'
choice_c(object, selectedvalue)

Arguments

Value

An S4 object of class ref_choice-class

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

 
## Not run: 
object=new('ref_list')
object<-charge(object,vecteur=c('1','2'),label='please choose')
object<-choice_c(object)

## End(Not run)

Command line interface to select a counting device

Description

the choice_c method is intended to have the same behaviour as choice (which creates a widget in the graphical interface) but from the command line. The parameters for dc are transformed to integer as the ref_dc only takes integer in the dc slots. The method also loads the stations and ouvrages (dams) associated with the counting device (dc). The values passed to the choice_c method are then checked with the setValidty method. Finally, if an objectreport is passed as a parameter, the method will do a charge_with_filter to select only the taxa present in the counting devices

Usage

## S4 method for signature 'ref_dc'
choice_c(object, dc)

Arguments

Value

An object of class ref_dc with dc selected

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
win=gwindow()
group=ggroup(container=win,horizontal=FALSE)
object=new('ref_dc')
object<-charge(object)
objectreport=new('report_mig_mult')
choice_c(object=object,objectreport=objectreport,dc=1)

## End(Not run)

Command line interface to choose a fishway

Description

the choice_c method is intended to have the same behaviour as choice (which creates a widget in the graphical interface) but from the command line. The parameters for dF are transformed to integer as the ref_df only takes integer in the df slots. DF are third in hierarchy in the stacomi database Station>ouvrage>DF>DC>operation. This class is only used in the report_df class.

Usage

## S4 method for signature 'ref_df'
choice_c(object, df)

Arguments

Value

An object of class ref_df with df selected

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
win=gwindow()
group=ggroup(container=win,horizontal=FALSE)
object=new('ref_df')
object<-charge(object)
objectreport=new('report_mig_mult')
choice_c(object=object,objectreport=objectreport,dc=1)

## End(Not run)

Command line interface to select a monitoring station

Description

the choice_c method is intended to have the same behaviour as choice (which creates a widget in the graphical interface) but from the command line.

Usage

## S4 method for signature 'ref_env'
choice_c(object, stationMesure)

Arguments

Value

an object of class ref_env-class with the monitoring station selected

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Choice_c method for ref_horodate

Description

Choice_c method for ref_horodate

Usage

## S4 method for signature 'ref_horodate'
choice_c(
  object,
  nomassign = "horodate",
  funoutlabel = "nous avons le choix dans la date\n",
  horodate,
  silent = FALSE
)

Arguments

Value

An object of class ref_horodate-class with slot horodate set, and assigns an object of class POSIXt with name nomassign in envir_stacomi

Choice_c method for ref_list referential objects

Description

Choice_c method for ref_list referential objects

Usage

## S4 method for signature 'ref_list'
choice_c(object, selectedvalue)

Arguments

Value

An S4 object of class ref_list-class

Note

the choice method assigns an object of class refList named ref_list in the environment envir_stacomi

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

 
## Not run: 
object=new('ref_list')
object<-charge(object,vecteur=c('1','2'),label='please choose')
object<-choice_c(object)

## End(Not run)

Command line interface to select a parameter

Description

Command line interface to select a parameter

Usage

## S4 method for signature 'ref_par'
choice_c(object, par, silent = FALSE)

Arguments

Value

An object of class ref_par-class

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

choice_c method for ref_stage

Description

the choice_c method is intended to have the same behaviour as choice (which creates a widget in the graphical interface) but from the command line. The values passed to the choice_c method for stage is the code. Any numeric value will be discarded

Usage

## S4 method for signature 'ref_stage'
choice_c(object, stage, silent = FALSE)

Arguments

Value

An S4 object of class ref_stage-class with the stage selected in the data slot

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
object=new('ref_stage')
object<-charge(object)

## End(Not run)

choice_c method for ref_taxa

Description

the choice_cc method is intended to have the same behaviour as choice (which creates a widget in the graphical interface) but from the command line. The values passed to the choice_c method for taxa can be either numeric (2038 = Anguilla anguilla) or character.

Usage

## S4 method for signature 'ref_taxa'
choice_c(object, taxa)

Arguments

Value

An S4 object of class ref_taxa-class with data filtered according to the taxa

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
object=new('ref_taxa')
object<-charge(object)
objectreport=new('report_mig_mult')
choice_c(object=object,'Anguilla anguilla')

## End(Not run)

Choice_c method for ref_textbox referential objects

Description

Choice_c method for ref_textbox referential objects

Usage

## S4 method for signature 'ref_textbox'
choice_c(object, value, nomassign = "ref_textbox")

Arguments

Value

An S4 object of class ref_textbox-class label selected

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

choice_c method for class ref_timestep_daily

Description

the choice_c method is intended to have the same behaviour as choice (which creates a widget in the graphical interface) but from the command line.

Usage

## S4 method for signature 'ref_timestep_daily'
choice_c(object, datedebut, datefin)

Arguments

Value

An S4 object of class ref_timestep_daily-class with date selected

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
 object=new('ref_dc')
 object<-charge(object)
 choice_c(object=object,datedebut='2012-01-01',datefin='2013-01-01')

## End(Not run)

choice_c method for ref_year referential from the command line

Description

The choice_c method will issue a warning if the year is not present in the database Allows the selection of year and the assignment in environment envir_stacomi

Usage

## S4 method for signature 'ref_year'
choice_c(
  object,
  annee,
  nomassign = "ref_year",
  funoutlabel = gettext("Year selected\n", domain = "R-stacomiR"),
  silent = FALSE
)

Arguments

Value

object An object of class ref_year-class with year selected

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Examples

## Not run: 
object=new("ref_year")
object<-charge(object)
win=gwindow(title="test ref_year")
group=ggroup(container=win,horizontal=FALSE)
choice(object,nomassign="ref_year",funoutlabel="essai",titleFrame="essai ref_year",preselect=1)
dispose(win)

## End(Not run)

command line interface for report_annual-class

Description

The choice_c method fills in the data slot for classes ref_dc-class, ref_taxa-class, ref_stage-class and two slots of ref_year-class

Usage

## S4 method for signature 'report_annual'
choice_c(object, dc, taxa, stage, start_year, end_year, silent = FALSE)

Arguments

Value

An object of class report_annual-class with data selected

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

command line interface for report_dc class

Description

The choice_c method fills in the data slot for ref_dc, and then uses the choice_c methods of these object to "select" the data.

Usage

## S4 method for signature 'report_dc'
choice_c(object, dc, horodatedebut, horodatefin, silent = FALSE)

Arguments

Value

An object of class ref_dc-class with data selected

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

command line interface for report_df class

Description

The choice_c method fills in the data slot for ref_df, and then uses the choice_c methods of these object to "select" the data.

Usage

## S4 method for signature 'report_df'
choice_c(object, df, horodatedebut, horodatefin, silent = FALSE)

Arguments

Value

An object of class ref_df-class with data selected

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

command line interface for report_env class

Description

The choice_c method fills in the data slot for ref_env-class by runnning the charge method of this object. It then runs the choice method on this object. It also applies the choice method for objects of class ref_horodate-class

Usage

## S4 method for signature 'report_env'
choice_c(object, stationMesure, datedebut, datefin, silent = FALSE)

Arguments

Value

An object of class report_env-class with data selected

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

command line interface for report_ge_weight-class

Description

command line interface for report_ge_weight-class

Usage

## S4 method for signature 'report_ge_weight'
choice_c(object, dc, start_year, end_year, selectedvalue, silent = FALSE)

Arguments

Value

An object of class report_ge_weight-class with data selected The choice_c method fills in the data slot for classes ref_dc-class ref_year-class ref_coe-class ref_list-class

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

command line interface for report_mig class

Description

The choice_c method fills in the data slot for ref_dc, ref_taxa, ref_stage, and refref_timestep_daily and then uses the choice_c methods of these object to select the data.

Usage

## S4 method for signature 'report_mig'
choice_c(object, dc, taxa, stage, datedebut, datefin)

Arguments

Value

An object of class report_mig-class with data selected

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

command line interface for report_mig_char class

Description

command line interface for report_mig_char class

Usage

## S4 method for signature 'report_mig_char'
choice_c(
  object,
  dc,
  taxa,
  stage,
  parquan = NULL,
  parqual = NULL,
  horodatedebut,
  horodatefin,
  echantillon = c("with", "without"),
  silent = FALSE
)

Arguments

Value

An object of class report_sea_age-class The choice_c method fills in the data slot for classes ref_dc-class, ref_taxa-class, ref_stage-class, ref_par-class and two slots of ref_horodate-class and then uses the choice_c methods of these object to select the data.

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

command line interface for report_env class

Description

command line interface for report_env class

Usage

## S4 method for signature 'report_mig_env'
choice_c(
  object,
  dc,
  taxa,
  stage,
  stationMesure,
  datedebut,
  datefin,
  silent = FALSE
)

Arguments

Value

An object of class report_env-class with data selected

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

command line interface for report_mig_interannual class

Description

command line interface for report_mig_interannual class

Usage

## S4 method for signature 'report_mig_interannual'
choice_c(object, dc, taxa, stage, start_year, end_year, silent = FALSE)

Arguments

Value

An object of class report_mig_interannual-class with data selected The choice_c method fills in the data slot for classes ref_dc-class, ref_taxa-class, ref_stage-class and two slots of ref_year-class

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

command line used to build report_mig_mult class

Description

The choice_c method fills in the data slot for ref_dc, ref_taxa, ref_stage and then uses the choice_c methods of these object to 'select' the data.

Usage

## S4 method for signature 'report_mig_mult'
choice_c(object, dc, taxa, stage, datedebut, datefin, silent = FALSE)

Arguments

Value

An object of class report_mig_mult-class with data selected

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

command line interface for report_sample_char class

Description

#' The choice_c method fills in the data slot for classes ref_dc-class, ref_taxa-class, ref_stage-class, ref_par-class and two slots of ref_horodate-class and then uses the choice_c methods of these object to select the data.

Usage

## S4 method for signature 'report_sample_char'
choice_c(
  object,
  dc,
  taxa,
  stage,
  par,
  horodatedebut,
  horodatefin,
  silent = FALSE
)

Arguments

Value

An object of class report_mig-class with data selected

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

command line interface for report_sea_age class

Description

#' The choice_c method fills in the data slot for classes ref_dc-class, ref_taxa-class, ref_stage-class, ref_par-class and two slots of ref_horodate-class and then uses the choice_c methods of these object to select the data.

Usage

## S4 method for signature 'report_sea_age'
choice_c(
  object,
  dc,
  taxa = 2220,
  stage = c("5", "11", "BEC", "BER", "IND"),
  par = c("1786", "1785", "C001", "A124"),
  horodatedebut,
  horodatefin,
  limit1hm,
  limit2hm,
  silent = FALSE
)

Arguments

Value

An object of class report_sea_age-class

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

command line interface for report_silver_eel class

Description

#' The choice_c method fills in the data slot for classes ref_dc-class, ref_taxa-class, ref_stage-class, ref_par-class and two slots of ref_horodate-class and then uses the choice_c methods of these object to select the data.

Usage

## S4 method for signature 'report_silver_eel'
choice_c(
  object,
  dc,
  taxa = 2038,
  stage = "AGG",
  par = c("1786", "CCCC", "BBBB", "CONT", "LINP", "A111", "PECT"),
  horodatedebut,
  horodatefin,
  silent = FALSE
)

Arguments

Value

An object of class report_mig-class

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

command line interface for report_species-class

Description

command line interface for report_species-class

Usage

## S4 method for signature 'report_species'
choice_c(
  object,
  dc,
  taxa = "all",
  split = "none",
  start_year,
  end_year,
  silent = FALSE
)

Arguments

Value

An object of class report_species-class with data selected

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Silvering index coefficients from Caroline Durif (2009) to predict silvering stage from morphological parameters

Description

Classification scores are calculated by multiplying the metrics BL = body length, W = weight, MD = mean eye diameter (Dv+Dh)/2, and FL length of the pectoral fin, with each parameter p as S=Constant+BL*p(bl)+W*p(W)... The stage chosen is the one achieving the highest score

Usage

coef_durif

Format

An object of class matrix (inherits from array) with 5 rows and 6 columns.

References

Durif, C.M., Guibert, A., and Elie, P. 2009. Morphological discrimination of the silvering stages of the European eel. In American Fisheries Society Symposium. pp. 103-111. https://fishlarvae.org/common/SiteMedia/durif%20et%20al%202009b.pdf

Builds a table with colors to merge with a dataframe for later use in ggplot. An initial check will be done on the name of the color vector. A data frame is built. It contains a column color which is a factor. The factor order match the order of the vector (not the alphabetical order of the colors).

Description

Builds a table with colors to merge with a dataframe for later use in ggplot. An initial check will be done on the name of the color vector. A data frame is built. It contains a column color which is a factor. The factor order match the order of the vector (not the alphabetical order of the colors).

Usage

colortable(
  color = NULL,
  vec,
  palette = "Set2",
  color_function = c("brewer.pal", "gray.colors", "random")
)

Arguments

Value

A dataframe with two columns, the vector (name) and the color (color) as a reordered factor

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

connect method for report_annual class this method performs the sum over the year attention this function does not count subsamples.

Description

connect method for report_annual class this method performs the sum over the year attention this function does not count subsamples.

Usage

## S4 method for signature 'report_annual'
connect(object, silent = FALSE)

Arguments

Value

An instantiated object with values filled with user choice

An object of class report_annual-class including a dataframe with column effectif, comprising the sum of report_mig counts

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

connect method for report_dc

Description

loads the working periods and type of arrest or disfunction of the DC

Usage

## S4 method for signature 'report_dc'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_dc-class with slot data filled from the database

Author(s)

cedric.briand

connect method for report_df

Description

connect method for report_df

Usage

## S4 method for signature 'report_df'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_df with slot data filled from the database

Author(s)

cedric.briand

connect method for report_env class

Description

connect method for report_env class

Usage

## S4 method for signature 'report_env'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_env-class with slot data filled from the database

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

connect method for report_Poids_moyen

Description

The connect method adapts queries according to user choices, mean weight w is calculated as car_valeur_quantitatif/lot_effectif. These coefficients are stored in the database, and the connect method loads them from the table using the ref_coe-class

Usage

## S4 method for signature 'report_ge_weight'
connect(object, silent = TRUE)

Arguments

Value

An object of class report_ge_weight-class with slots data and coe filled from the database

Note

dates for the request are from august to august (a glass eel season)

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

connect method for report_mig

Description

uses the report_mig_mult method

Usage

## S4 method for signature 'report_mig'
connect(object, silent = FALSE)

Arguments

Value

report_mig with slot @data filled from the database

connect method for report_mig_char

Description

uses the report_mig_mult method

Usage

## S4 method for signature 'report_mig_char'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_mig_char-class with list in @data$parquan and @data$parqual filled in from the database

connect method for report_mig_env class

Description

connect method for report_mig_env class

Usage

## S4 method for signature 'report_mig_env'
connect(object, silent = FALSE)

Arguments

Value

an object of report_mig_env class

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

connect method for report_mig_interannual

Description

This method will check if the data in the t_reportjournalier_bjo table has no missing data, if missing the program will load missing data. As a second step, the program will check if the numbers in the table t_reportjournalier_bjo differ from those in the database, and propose to re-run the report_mig (which has a write_database methode to write daily reports) for those years.

Usage

## S4 method for signature 'report_mig_interannual'
connect(object, silent = FALSE, check = TRUE)

Arguments

Value

report_mig_interannual an instantiated object with values filled with user choice

Note

We expect different results between daily reports from the t_reportjournalier_bjo table and the annual sums from report_annual for glass eels as those may have been weighted and not only counted. The t_reportjournalier_bjo table used by report_mig_interannual contains the sum of glass eel numbers converted from weights and those directly counted. The report_annual does not.

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

connect method for report_mig_mult

Description

this method loads data from the database for report_mig but also fills the table of conversion coefficient, if the taxa is eel. It also calls connect method for report_df-class, report_dc-class and report_ope-class associated with the report and used by the fungraph and fungraph_glasseel functions. As a side effect it assigns objects report_dc-class, report_df-class and report_ope-class in environment envir_stacomi

Usage

## S4 method for signature 'report_mig_mult'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_mig_mult-class with slot @data filled from the database

connect method for report_ope

Description

connect method for report_ope

Usage

## S4 method for signature 'report_ope'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_ope-class with slot data @data filled

Author(s)

cedric.briand

connect method for report_sample_char

Description

connect method for report_sample_char

Usage

## S4 method for signature 'report_sample_char'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_sample_char-class with slot data @data filled

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

connect method for report_sea_age

Description

connect method for report_sea_age

Usage

## S4 method for signature 'report_sea_age'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_sea_age-class with slot data @data filled

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

connect method for report_silver_eel

Description

connect method for report_silver_eel

Usage

## S4 method for signature 'report_silver_eel'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_silver_eel-class with slot data @data filled

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

connect method for report_species

Description

connect method for report_species

Usage

## S4 method for signature 'report_species'
connect(object, silent = FALSE)

Arguments

Value

An object of class report_species-class with data slot filled with slot data @data filled

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Generic method for getting the final date

Description

Generic method for getting the final date

Usage

end_date(object, ...)

Arguments

Gets the final horodate for an object of class ref_timestep-class

Description

Gets the final horodate for an object of class ref_timestep-class

Usage

## S4 method for signature 'ref_timestep'
end_date(object)

Arguments

Value

end_date, The final date corresponding to nb_step*time duration + initial date

Environment where most objects from the package are stored and then loaded by the charge method

Description

envir_stacomi envir_stacomi <- new.env(parent = baseenv()) is the environment where most object created by the interface are stored

This is where the graphical interface stores its objects try ls(envir=envir_stacomi)

This is where the graphical interface stores its objects try ls(envir=envir_stacomi)

Usage

envir_stacomi

envir_stacomi

envir_stacomi

Format

An object of class environment of length 0.

An object of class environment of length 0.

An object of class environment of length 0.

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Get table content for table t_bilanmigrationjournalier_bjo in report_mig_interannual

Description

Each time a report mig runs, it can write its content in the t_bilanmigrationjournalier_bjo table which stores the results of the report_mig with one value per day

Usage

fn_connect_report_mig_interannual(years, taxa, stage, dc)

Arguments

Value

a data frame with the content of table t_bilanmigrationjournalier_bjo in the database

Calculates a data.frame where all components within the list calcdata are aggregated and formatted for plot

Description

Calculates a data.frame where all components within the list calcdata are aggregated and formatted for plot

Usage

fun_aggreg_for_plot(object)

Arguments

Value

A data.frame

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

function used to remove special non utf8 character which cause the gtk interface to crash

Description

function used to remove special non utf8 character which cause the gtk interface to crash

Usage

fun_char_spe(text)

Arguments

Value

text

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

This function extracts temporal characteristics from a dataframe

Description

This function extracts temporal characteristics from a dataframe

Usage

fun_date_extraction(
  data,
  nom_coldt,
  annee = TRUE,
  mois = TRUE,
  quinzaine = FALSE,
  semaine = TRUE,
  semaine_std = FALSE,
  jour_an = FALSE,
  jour_mois = TRUE,
  heure = FALSE
)

Arguments

Value

The dataframe with date column filled

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

statistics per time period

Description

statistics per time period

Usage

fun_report_mig_interannual(dat, year = NULL, timesplit = NULL)

Arguments

Value

a data frame with mean, max, and min calculated for each timesplit

Calculate daily migration by simple repartition

Description

Function to calculate daily migration from migration monitoring whose length is less than one day, typically video recording whose period are instant events.

Usage

fun_report_mig_mult(time.sequence, datasub, negative = FALSE)

Arguments

Value

A data.frame with number summed over over the time.sequence. The function returns the same output than fun_report_mig_mult_overlaps but is intended to work faster. In the data.frame, the total number is 'Effectif_total' and corresponds to the addition of numbers and numbers converted from weight, the total weight is 'Poids_total'+'poids_depuis_effectifs' and corresponds to weighed glass eel plus glass eel number converted in weights.

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Function to calculate daily migration using overlaps functions

Description

Function to calculate daily migration from migration monitoring whose length is more than one day, this calculation relies on the (false) assumption that migration is evenly spread over time.

Usage

fun_report_mig_mult_overlaps(time.sequence, datasub, negative = FALSE)

Arguments

Value

A data.frame with daily migrations

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

calcule,report_mig_mult-method

Creates a list of available schemas in the db

Description

Creates a list of available schemas in the db

Usage

fun_schema()

Value

A table with of data providers with org_code, the user of each schema, and org_description the description of the schema

Function to calculate the stages from Durif

Description

Function to calculate the stages from Durif

Usage

fun_stage_durif(data)

Arguments

Value

A data.frame with durif stages per individual

Author(s)

Laurent Beaulaton laurent.beaulaton@ofb.fr

functions called in DF and DC

Description

functions called in DF and DC

Usage

fun_table_per_dis(
  typeperiode,
  tempsdebut,
  tempsfin,
  libelle,
  color,
  date = TRUE
)

Arguments

Value

A list

Note

returns either POSIXt or date if date=TRUE

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

returns a table where weights and number are calculated from number and weights respectively performs a query to collect the conversion coefficients

Description

returns a table where weights and number are calculated from number and weights respectively performs a query to collect the conversion coefficients

Usage

fun_weight_conversion(tableau, time.sequence, silent)

Arguments

Value

tableau, the data frame with weight converted to numbers

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

This writes monthly data in t_reportmensuel_mens table

Description

This writes monthly data in t_reportmensuel_mens table

Usage

fun_write_monthly(report_mig, resum, silent)

Arguments

Value

No return value, called for side effects

Note

This function is launched by fun_write_daily, the resum dataset is created by the funstat function

Internal use barchart for report_df class from the graphical interface

Description

Internal use barchart for report_df class from the graphical interface

Usage

funbarchart1DF(...)

Arguments

Value

Nothing, called for its side effect of plotting data

Note

The program cuts periods which overlap between two month

Internal use, function used in the graphical interface to create a barchart for report_df class

Description

Internal use, function used in the graphical interface to create a barchart for report_df class

Usage

funbarchartDF(...)

Arguments

Value

Nothing, called for its side effect of plotting data

Note

The program cuts periods which overlap between two month

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Internal use, rectangles to describe the DF work for report_df class,

Description

Internal use, rectangles to describe the DF work for report_df class,

Usage

funboxDF(...)

Arguments

Value

Nothing, called for its side effect of plotting data

Function to plot calendar like graph, internal use

Description

Function to plot calendar like graph, internal use

Usage

funchartDF(...)

Arguments

Value

Nothing, called for its side effect of plotting data

Function for report_mig graphs including numbers DF DC operations

Description

This graph is for species other than glass eel

Usage

fungraph(
  report_mig,
  tableau,
  time.sequence,
  taxa,
  stage,
  dc = NULL,
  silent,
  color = NULL,
  color_ope = NULL,
  ...
)

Arguments

Value

No return value, called for side effects

Note

this function is intended to be called from the plot method in report_mig_mult and report_mig

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Graph function for glass eel migration. Differs from fungraph as it does not draw the ggplot graph for month

Description

This graph will also plot numbers and bars according to whether the glass eel have been counted through weight or numbers

Usage

fungraph_glasseel(
  report_mig,
  table,
  time.sequence,
  taxa,
  stage,
  dc = null,
  silent,
  color = NULL,
  color_ope = NULL,
  ...
)

Arguments

Value

No return value, called for side effects

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

this function displays text and will be used to convey stacomiR message in shiny

Description

this function displays text and will be used to convey stacomiR message in shiny

Usage

funout(text, arret = FALSE, ...)

Arguments

Value

nblignes Assigned in envir_stacomi

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

funplotreport_silver_eel

Description

assigns an object g in envir_stacomi for eventual modification of the plot

Usage

funplotreport_silver_eel(action, ...)

Arguments

Value

Nothing

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Function to calculate statistics per month

Description

Function to calculate statistics per month

Usage

funstat(tableau, time.sequence, taxa, stage, DC, silent)

Arguments

Value

No return value, called for side effects

Note

this function is intended to be called from within the summary method

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

function to print and save statistics in .csv and .html formats for report_mig and report_mig_mult class

Description

function to print and save statistics in .csv and .html formats for report_mig and report_mig_mult class

Usage

funtable(tableau, time.sequence, taxa, stage, DC, resum, silent)

Arguments

Value

No return value, called for side effects

Note

this function is intended to be called from within the summary method

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Table output for report_df class

Description

Table output for report_df class

Usage

funtableDF(...)

Arguments

Value

Nothing, called for its side effect of running summary

this function gets the name of the stucture as it is set in the database

Description

this function gets the name of the stucture as it is set in the database

Usage

get_org()

Value

The name of the structure (org_code)

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

this function gets the schema from envir stacomi and throws warning

Description

this function gets the schema from envir stacomi and throws warning

Usage

get_schema(default = NULL)

Arguments

Value

The schema in envir_stacomi

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Generic method to get the years

Description

Generic method to get the years

Usage

get_year(object, ...)

Arguments

Gets the year or a vector of years corresponding to the timestep ("ref_timestep") object

Description

Gets the year or a vector of years corresponding to the timestep ("ref_timestep") object

Usage

## S4 method for signature 'ref_timestep'
get_year(object)

Arguments

Value

A numeric with year or vector of years corresponding to the timestep

Generic method getvalue

Description

Generic method getvalue

Usage

getvalue(object, ...)

Arguments

Author(s)

cedric.briand

function used for some lattice graphs with dates

Description

function used for some lattice graphs with dates

Usage

graphdate(vectordate)

Arguments

Value

vectordate (without class)

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Internal function, tests the connection and if it works loads the stacomi interface

Description

Internal function, tests the connection and if it works loads the stacomi interface

Usage

load_stacomi(...)

Arguments

Value

Nothing

Note

base is copied by stacomi into envir_stacomi. Same for database_expected

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Generic for prediction

Description

Generic for prediction

Usage

model(object, ...)

Arguments

Author(s)

cedric.briand

model method for report_ge_weight' this method uses samples collected over the season to model the variation in weight of glass eel or yellow eels.

Description

model method for report_ge_weight' this method uses samples collected over the season to model the variation in weight of glass eel or yellow eels.

Usage

## S4 method for signature 'report_ge_weight'
model(object, model.type = "seasonal", silent = FALSE)

Arguments

Details

Depending on model.type several models are produced

model.type='seasonal'.

The simplest model uses a seasonal variation, it is fitted with a sine wave curve allowing a cyclic variation w ~ a*cos(2*pi*(d'-T)/365)+b with a period T. The modified day d' used is this model is set at 1 the 1st of august doy = d' + d0; d0 = 212, doy=julian days

model.type='seasonal1'.

A time component is introduced in the model, which allows for a long term variation along with the seasonal variation. This long term variation is is fitted with a gam, the time variable is set at zero at the beginning of the first day of observed values. The seasonal variation is modeled on the same modified julian time as model.type='seasonal' but here we use a cyclic cubic spline cc, which allows to return at the value of d0=0 at d=365. This model was considered as the best to model size variations by Diaz & Briand in prep. but using a large set of values over years.

model.type='seasonal2'.

The seasonal trend in the previous model is now modelled with a sine curve similar to the sine curve used in seasonal. The formula for this is sin(\omega vt) + cos(\omega vt), where vt is the time index variable \omega is a constant that describes how the index variable relates to the full period (here, 2\pi/365=0.0172). The model is written as following w~cos(0.0172*doy)+sin(0.0172*doy)+s(time).

model.type='manual'.

The dataset don (the raw data), coe (the coefficients already present in the database, and newcoe the dataset to make the predictions from, are written to the environment envir_stacomi. please see example for further description on how to fit your own model, build the table of coefficients, and write it to the database.

Value

An object of class report_ge_weight-class with @calcdata[["import_coe"]] filled.

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Plot method for report_annual

Description

Plot method for report_annual

Usage

## S4 method for signature 'report_annual,missing'
plot(x, plot.type = "point", silent = FALSE)

Arguments

Value

No return value, called for side effects

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

report_mig_interannual-class for examples

Different plots for report_dc

Description

plot.type=1

A barplot of the operation time per month

plot.type=2

Barchat giving the time per type of operation

plot.type=2

Rectangle plots drawn along a line

plot.type=4

Plots per day drawn over the period to show the operation of a df, days in x, hours in y

Usage

## S4 method for signature 'report_dc,missing'
plot(
  x,
  plot.type = 1,
  silent = FALSE,
  main = NULL,
  color_type_oper = c(`Fonc normal` = "#76BEBE", `Arr ponctuel` = "#FF6700", `Arr maint`
    = "#9E0142", Dysfonc = "#EE1874", `Non connu` = "#999999"),
  color_etat = c(`TRUE` = "#0F313A", `FALSE` = "#CEB99A")
)

Arguments

Value

Nothing but prints the different plots.

Note

The program cuts periods which overlap between two month. The splitting of different periods into month is assigned to the envir_stacomi environment.

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Different plots for report_df

Description

plot.type=1

A barplot of the operation time per month

plot.type=2

Barchat giving the time per type of operation

plot.type=2

Rectangle plots drawn along a line

plot.type=4

Plots per day drawn over the period to show the operation of a df, days in x, hours in y

Usage

## S4 method for signature 'report_df,missing'
plot(
  x,
  plot.type = 1,
  silent = FALSE,
  main = NULL,
  color_type_oper = c(`Fonc normal` = "#1B9E77", `Arr ponctuel` = "#E6AB02", `Arr maint`
    = "#9E0142", Dysfonc = "#E41A1C", `Non connu` = "#999999"),
  color_etat = c(`TRUE` = "chartreuse3", `FALSE` = "orangered3")
)

Arguments

Value

Nothing but prints the different plots.

Note

The program cuts periods which overlap between two month. The splitting of different periods into month is assigned to the envir_stacomi environment.

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Plot method for report_env

Description

Plot method for report_env

Usage

## S4 method for signature 'report_env,missing'
plot(x, silent = FALSE)

Arguments

Value

Nothing, called for its side effect of plotting data

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Plot method for report_ge_weight'

Description

Plot method for report_ge_weight'

Usage

## S4 method for signature 'report_ge_weight,missing'
plot(x, plot.type = 1, silent = FALSE)

Arguments

Value

Nothing, called for its side effect of plotting data

Note

the model method provides plots for the fitted models

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Plots of various type for report_mig.

Description

plot.type="standard"

calls fungraph and fungraph_glasseel functions to plot as many "report_mig" as needed, the function will test for the existence of data for one dc, one taxa, and one stage

plot.type="step"

creates Cumulated graphs for report_mig_mult. Data are summed per day for different dc taxa and stages

plot.type="multiple"

Method to overlay graphs for report_mig_mult (multiple dc/taxa/stage in the same plot)

Usage

## S4 method for signature 'report_mig,ANY'
plot(
  x,
  y,
  plot.type = "standard",
  color = NULL,
  color_ope = NULL,
  silent = FALSE,
  ...
)

Arguments

Value

Nothing, called for its side effect

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

plot method for report_mig_char

Description

plot method for report_mig_char

Usage

## S4 method for signature 'report_mig_char,missing'
plot(x, color_parm = NULL, plot.type = "qual", silent = FALSE, ...)

Arguments

Value

Nothing, called for its side effect of plotting data

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Plot method for report_mig_env

Description

Plot method for report_mig_env

Usage

## S4 method for signature 'report_mig_env,missing'
plot(x, color_station = NULL, color_dc = NULL, silent = FALSE)

Arguments

Value

Nothing, called for its side effect of plotting

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Plot method for report_mig_interannual

Description

Several of these plots are scaled against the same year,i.e.the comparison is based on year 2000, meaning that day 1 would correspond to the first date of 2000, which is also a saturday, the last day of the week.

Usage

## S4 method for signature 'report_mig_interannual,missing'
plot(
  x,
  plot.type = "standard",
  timesplit = "month",
  year_choice = NULL,
  alpha = 1,
  silent = FALSE
)

Arguments

Value

Nothing, called for its side effect of plotting

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Plots of various type for report_mig_mult

Description

plot.type='standard'

calls fungraph and fungraph_glasseel functions to plot as many 'report_mig' as needed, the function will test for the existence of data for one dc, one taxa, and one stage

plot.type='step'

creates Cumulated graphs for report_mig_mult. Data are summed per day for different dc taxa and stages

plot.type='multiple'

Method to overlay graphs for report_mig_mult (multiple dc/taxa/stage in the same plot)

Usage

## S4 method for signature 'report_mig_mult,missing'
plot(
  x,
  plot.type = "standard",
  color = NULL,
  color_ope = NULL,
  silent = FALSE,
  ...
)

Arguments

Value

Nothing, called for its side effect of plotting

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Plots of various type for reportcarlot

Description

Plots of various type for reportcarlot

Usage

## S4 method for signature 'report_sample_char,missing'
plot(x, plot.type = "1", silent = FALSE)

Arguments

Value

Nothing, called for its side effect, plotting

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Plots of various type for report_sea_age

Description

Plots of various type for report_sea_age

Usage

## S4 method for signature 'report_sea_age,missing'
plot(x, plot.type = "1", silent = FALSE)

Arguments

Value

Nothing, called for its side effect of plotting

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Plots of various type for report_silver_eel

Description

Plots of various type for report_silver_eel

Usage

## S4 method for signature 'report_silver_eel,missing'
plot(x, plot.type = c("1", "2", "3", "4"), silent = FALSE)

Arguments

Value

A lattice xy.plot if plot.type =1, a lattice barchart if plot.type=2, nothing but plots a series of graphs in a single plot if plot.type=3, a lattice cloud object if plot.type=4

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Plot method for report_species

Description

Plot method for report_species

Usage

## S4 method for signature 'report_species,missing'
plot(x, plot.type = "pie", color = NULL, silent = FALSE)

Arguments

Value

Nothing, called for producing plots

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Method to print the command line of the object.

Description

Method to print the command line of the object.

Usage

## S4 method for signature 'report_dc'
print(x, ...)

Arguments

Value

Nothing, called for its side effect

Author(s)

cedric.briand

Method to print the command line of the object

Description

Method to print the command line of the object

Usage

## S4 method for signature 'report_df'
print(x, ...)

Arguments

Value

Nothing, called for its side effect of printing data

Author(s)

cedric.briand

Method to print the command line of the object

Description

Method to print the command line of the object

Usage

## S4 method for signature 'report_mig'
print(x, ...)

Arguments

Author(s)

cedric.briand

Method to print the command line of the object

Description

Method to print the command line of the object

Usage

## S4 method for signature 'report_mig_mult'
print(x, ...)

Arguments

Author(s)

cedric.briand

Method to print the command line of the object

Description

Method to print the command line of the object

Usage

## S4 method for signature 'report_sample_char'
print(x, ...)

Arguments

Author(s)

cedric.briand

Method to print the command line of the object

Description

Method to print the command line of the object

Usage

## S4 method for signature 'report_sea_age'
print(x, ...)

Arguments

Author(s)

cedric.briand

Method to print the command line of the object

Description

Method to print the command line of the object

Usage

## S4 method for signature 'report_silver_eel'
print(x, ...)

Arguments

Value

NULL, prints data in the console

Author(s)

cedric.briand

Annual migration of yellow and silver eel for three fishways / counting devices at the Arzal dam (data from 1995 to 2016)

Description

The dataset corresponds to the three fishways located on the Arzal dam, filled with annual data

Usage

r_ann

Format

An object of class report_annual-class with data slot loaded.

Annual migration of salmon in the Adour and tributaries

Description

The dataset corresponds to the fishways DC=33:40 of the Adour for adult migrant salmons from 1996 to 2005 (annual counts). It has been kindly provided as an example set by the Migradour association.

Usage

r_ann_adour

Format

An object of class report_annual-class with data slot loaded.

Counting Device (DC) operation from 2000 to 2015 at the Arzal dam (Vilaine, France)

Description

This data corresponds to the data collected at the vertical slot fishway camera from 2000 to 2015. It represents an object of class report_dc-class with data loaded

Usage

r_dc

Format

An object of class report_dc with 4 slots:

data

A dataframe with 544 obs. of 7 variables

per_dis_identifiant

The number of the DC

per_date_debut

Starting time a POSIXct

per_date_fin

Ending time a POSIXct

ope_dic_identifiant

DC id

per_commentaires

A comment

per_etat_fonctionnement

Integer 1= working, 0 not working

per_tar_code

The type of operation ('1'=normal operation, '2'=Device stopped in normal operation (e.g. the trap is disactivated for the duration of the fish sorting and counting by operators), '3'='Stopped for maintenance or other problem', '4'='Works but not fully operational, i.e. the camera is not working properly because of high turbidity...', '5'='Not known')

libelle

label corresponding to per_tar_code

df

the ref_dc object with 3 slots filled with data corresponding to the iav postgres schema

horodatedebut

the ref_horodate with horodate set for starting date

horodatefin

the ref_horodate with horodate set for ending date

Overview of the fishway operation at Arzal in (Vilaine France).

Description

This dataset corresponds to the data collected at the vertical slot fishway in 2015, the fishway is working daily with a cycle depending on tide. This dataset is used to show an example of detailed output for an object of class report_df-class with data loaded

Usage

r_df

Format

An object of class report_df with 4 slots:

data

A dataframe with 4261 obs. of 7 variables

per_dis_identifiant

The number of the DF

per_date_debut

Starting time a POSIXct

per_date_fin

Ending time a POSIXct

ope_dic_identifiant

DF id

per_commentaires

A comment

per_etat_fonctionnement

Integer 1= working, 0 not working

per_tar_code

The type of operation ('1'=normal operation, '2'=Device stopped in normal operation (ie lift ascending, high tide...), '3'='Stopped for maintenance or other problem', '4'='Works but not fully operational,i.e.flow problem, flood, clogged with debris...', '5'='Not known')

libelle

label corresponding to per_tar_code

df

the ref_df object with 3 slots filled with data corresponding to the iav postgres schema

horodatedebut

the ref_horodate with horodate set for starting date

horodatefin

the ref_horodate with horodate set for ending date

'

An object of class report_env with data loaded

Description

The dataset corresponds to the daily temperatures and moon phases in Arzal (Vilaine estuary, France). This environmental station is used to analyze conditions in which fish migrated at Arzal dam

Usage

r_env

Format

An object of class report_env-class with data slot loaded:

stationMesure

the ref_env object with 5 slots filled with data corresponding to the iav postgres schema

horodatedebut

object of class ref_horodate-class : the start date selected

horodatefin

object of class ref_horodate-class : the end date selected

data

A dataframe with 723 rows and 6 variables

env_date_debut

start date

env_date_fin

end date

env_methode_obtention

method of data collection, measured, calculated...

env_val_identifiant

the value of the parameter if qualitative

env_valeur_quantitatif

the value of the parameter if quantitative

env_stm_identifiant

station id

Wet weight of glass eel from the trapping ladder (Arzal, Vilaine France)

Description

Data correspond to glass eel collected in the Vilaine at the trapping ladder (Arzal, France). The years selected are 2009 to 2012, the query used in the report_ge_weight-class loads from 2008-08-01 to 2012-08-01 Glass eel are too numerous to be counted. They are weighted and in the stacomi database, a table with daily coefficients (in N glass eel/g) to transform weight into number. The weight is called a 'wet weight' as we don't wan't to drain any of the mucus in glass eel when weighting them. Samples of 50 to 200 glass eel are weighted and then counted to provide an idea of the seasonal evolution of wet weight.

Usage

r_gew

Format

An object of class report_ge_weight of length 1.

Video counting of Marine lamprey (Petromyzon marinus) in 2012 in the Vilaine (France)

Description

This dataset corresponds to the data collected at the vertical slot fishway in 2012, video recording marine lamprey migration

Usage

r_mig

Format

An object of class report_mig with 8 slots:

dc

the ref_dc object with 4 slots filled with data corresponding to the iav postgres schema

taxa

the ref_taxa the taxa selected

stage

the ref_stage the stage selected

timestep

the ref_timestep_daily calculated for all 2015

data

A dataframe with 10304 rows and 11 variables

ope_identifiant

operation id

lot_identifiant

sample id

lot_identifiant

sample id

ope_dic_identifiant

dc id

lot_tax_code

species id

lot_std_code

stage id

value

the value

type_de_quantite

either effectif (number) or poids (weights)

lot_dev_code

destination of the fishes

lot_methode_obtention

method of data collection, measured, calculated...

coef_conversion

A data frame with 0 observations : no quantity are reported for video recording of mullets, only numbers

time.sequence

A time sequence generated for the report, used internally

Qualitative and quantitative parameters describing Salmon migration at Decize (Loire)

Description

The dataset corresponds to the characteristics (qualitative and quantitative) of salmo salar migrating at Decize (Loire river) and Vichy (Allier river) counting device in 2012. It has been loaded as an example for the report_mig_char-class and kindly provided by Loire Grands Migrateurs (LOGRAMI).

Usage

r_mig_char

Format

An object of class report_mig_char-class with data slot loaded:

calcdata

slot to be filled with the calcule method

data

A list of 2 elements

parqual

values of all the qualitative parameters

parquan

values of all the quantitative parameters

dc

the ref_dc : the control devices selected

taxa

the ref_taxa : Salmo salar selected

stage

the ref_stage : the stages selected

par

an object of class ref_par-class: the parameters used

horodatedebut

an object of class ref_horodate-class : the start date selected

horodatefin

an object of class ref_horodate-class : the end date selected

Counting device operation for the video recording (Arzal dam, Vilaine, France).

Description

This dataset corresponds to the data collected in the vertical slot fishway for the video recording operation. It is loaded along with r_mig to demonstrate the use of the report_mig-class when the database is not loaded

Usage

r_mig_dc

Format

An object of class report_dc-class

Fishway operation for the vertical slot fishway (Arzal dam, Vilaine, France).

Description

This dataset corresponds to the data collected at in the vertical slot fishway it is loaded along with r_mig and used to demonstrate the report_mig-class when the database is not installed.

Usage

r_mig_df

Format

An object of class report_df-class

An object of class report_mig_env with data loaded

Description

The dataset correspond to data loaded for the Arzal dam (Vilaine) in 2008, two quantitative parameters (temperature and tide coefficient) and a qualitative parameter (moon phase) are loaded.

Usage

r_mig_env

Format

An object of class report_env-class with data slot loaded:

report_mig_mult

An object of class report_mig_mult-class

report_env

An object of class report_env-class

#'

Daily glass eel and elver migration from 1984 to 2016 in the Sevre Niortaise

Description

The first eel trapping ladder in France was built by Antoine Legault and the team from Rennes in the Sevre Niortaise, Marais Poitevin. Also refurbished several times since 1984 it has been operational at the same location and provides one of the longest series of eel migration. For this reason, the dataset has been loaded as an example for the report_mig_interannual-class. It has been kindly provided by the parc du Marais Poitevin. The stage corresponds to small eels (elvers) less than 150 mmm stage name 'PANG'

Usage

r_mig_interannual

Format

An object of class report_mig_interannual-class with data loaded.

Seasonality of salmon migration at the Vichy counting station (Loire)

Description

This data corresponds to the data collected at the Vichy fishway between 1997 and 2012, video recording of the Salmo salar upstream migration. This dataset has been kindly provided by Loire Grands Migrateurs.

Usage

r_mig_interannual_vichy

Format

An object of class report_mig_interannual-class with 7 slots:

dc

the ref_dc object with 4 slots filled with data corresponding to the iav postgres schema

taxa

the ref_taxa the taxa selected

stage

the ref_stage the stage selected

start_year

the ref_timestep_daily calculated for all 2015

end_year

the ref_timestep_daily calculated for all 2015

data

A dataframe with 7138 rows and 10 variables

bjo_identifiant

sample id

bjo_dis_identifiant

dc id

bjo_tax_code

species id

bjo_std_code

stage id

bjo_annee

year

bjo_jour

date

bjo_labelquantite

method of data collection, measured, calculated...

bjo_horodateexport

date with special format for export

bjo_org_code

organisme provided the data

Anguilla migration at the Arzal station (report_mig_mult-class)

Description

This data corresponds to data collected from three fishways and correspond to the migration station at Arzal (Vilaine estuary, France) in 2011 for three continental stages of eel (Anguilla anguilla) : glass eel, yellow eel and silver eel.

Usage

r_mig_mult

Format

An object of class report_mig_mult with slots:

dc

the ref_dc object filled with data

taxa

the ref_taxa object filled in with data corresponding to dc

stage

the ref_stage object filled in with data corresponding to dc, and taxa

timestep

the ref_timestep_daily calculated for all 2011

data

A dataframe with 400 rows and 11 variables

ope_identifiant

operation id

lot_identifiant

sample id

lot_identifiant

sample id

ope_dic_identifiant

dc id

lot_tax_code

species id

lot_std_code

stage id

value

the value

type_de_quantite

either effectif (number) or poids (weights)

lot_dev_code

destination of the fishes

lot_methode_obtention

method of data collection, measured, calculated...

calcdata

slot to be filled with the calcule method

coef_conversion

A data frame with 364 observations with daily coefficients to convert from weight to numbers

time.sequence

A time sequence generated for the report, used internally by the object

Counting device operation for three different counting device in Arzal (Vilaine, France)

Description

This dataset corresponds to data collected at three different control devices. This object is of class report_dc-class with data loaded it is loaded along with r_mig_mult and used in demonstration for the report_mig_mult-class

Usage

r_mig_mult_dc

Format

An object of class report_dc with 4 slots

data

A dataframe with 25 rows and 7 variables

per_dis_identifiant

the df or dc unique id

per_date_debut

the starting date of the counting device operation POSIXct

per_date_fin

the ending date of the counting device operation POSIXct

per_commentaires

comments on the counting device operation

per_etat_fonctionnement

Boolean, is the counting device working ?

lot_std_code

stage id

per_tar_code

The type of operation for the DC, 1 normal operation, 2 device stopped in normal operation (the stop is considered as normal, e.g. you don't monitor video if a cage has been placed to trap fishes), 3 stopped for maintenance or other problem, 4 the DC is working but not well (escapement in a tank, high turbidity preventing video counting...), 5 unknown operation.

libelle

The label for the type or operation

dc

the ref_dc the DC with 4 slots

dc_selected

the selected device

ouvrage

the dam

station

the monitoring station, a section of river

data

A dataset of all dc present in the database with 10 observations

horodatedebut

the beginning date, a ref_horodate-class

horodatefin

the ending date, a ref_horodate-class

Fishway operation at the Arzal Dam (Vilaine France) (3 Fishways in 2011)

Description

This dataset corresponds to the data collected at three different fishways it is loaded along with r_mig_mult and used in demonstration for the report_mig_mult-class

Usage

r_mig_mult_df

Format

An object of class report_df report_df-class

Counting operations for three different counting device in Arzal (Vilaine, France)

Description

This dataset corresponds to the data collected at three different control devices It is an object of class report_ope-class with data loaded. it is loaded along with r_mig_mult

Usage

r_mig_mult_ope

Format

An object of class report_ope

An object of class report_ope-class with data loaded

Description

This dataset corresponds to the data collected at the vertical slot fishway in Arzal (Vilaine river estuary, France). The operation of the fishway is dependent on tide and is recorded every 10 minutes. This dataset has to be loaded along with r_mig to demonstrate the use of the report_mig-class

Usage

r_mig_ope

Format

An object of class report_ope

Size of yellow and glass eel at the Arzal dam (Vilaine, France) in the fishway and main eel trapping ladder.

Description

This dataset corresponds to the data collected at two different control devices at the Arzal control station (see example in report_sample_char-class), all body size parameters (total size, size converted from pixel in video control) are used in example

Usage

r_sample_char

Format

An object of class report_sample_char-class

An object of class report_sea_age with data loaded

Description

This dataset corresponds to the data collected at Vichy (left and right bank fishways) and Decize-Saint Leger des Vignes fishways (respectively on the Allier and Loire river, France) in 2012 on the size structure of Salmo salar. It has been kindly provided by the Loire Grands Migrateurs (LOGRAMI) association.

Usage

r_seaa

Format

An object of class report_sea_age-class with 8 slots:

dc

the ref_dc : the control devices selected

taxa

the ref_taxa : Salmo salar selected

stage

the ref_stage : the stages selected

par

Object of class ref_par-class: the parameters used

horodatedebut

object of class ref_horodate-class : the start date selected

horodatefin

object of class ref_horodate-class : the end date selected

limit1hm

The size limit, in mm between 1 sea winter fishes and 2 sea winter fishes

limit2hm

The size limit, in mm between 2 sea winter fishes and 3 sea winter fishes

data

A dataframe with 898 rows and 20 variables

ope_identifiant

operation id

lot_identifiant

sample id

ope_dic_identifiant

dc id

ope_date_debut

start date

ope_date_fin

end date

lot_effectif

number of fishes

lot_tax_code

species id

lot_std_code

stages id

tax_nom_latin

species latin names

std_libelle

stages names

dev_code

destination of the fishes id

dev_libelle

destination of the fishes names

par_nom

parameter name

car_par_code

parameter id

car_methode_obtention

method of data collection, measured, calculated...

car_valeur_quantitatif

the value of the parameter

Silver eel migration in the Somme

Description

The dataset corresponds to the silver eel traps ('anguilleres) for 2015-2016. This dataset has been kindly provided by the Federation de Peche de la Somme, given the upstream location of the trap, most individuals are female

Usage

r_silver

Format

An object of class report_silver_eel-class with data slot loaded.

Class 'ref_choice'

Description

ref_choice referential class allows to choose within several values with radiobuttons interface

Slots

listechoice

A character vector giving possible choices

label

A character, title of the box giving the possible choices

selected

An Integer the initial selected value (as an index), first=1 used in gradio

Objects from the Class

Objects can be created by calls of the form new('ref_choice', listechoice=character() ,label=character() ,selected=integer()).

Author(s)

cedric.briand@eptb-vilaine.fr

See Also

Other referential objects: charge,ref_choice-method, ref_coe-class, ref_dc-class, ref_df-class, ref_horodate-class, ref_list-class, ref_par-class, ref_parqual-class, ref_parquan-class, ref_stage-class, ref_taxa-class, ref_year-class

Class 'ref_coe'

Description

Enables to load conversion coefficients quantity-number. This class only exists to load the data with its method charge. It is not used directly as component of the graphical interface, as the year is already loaded in the different report objects

Slots

data

A data.frame

datedebut

A 'POSIXlt'

datefin

A 'POSIXlt'

Objects from the Class

Objects can be created by calls of the form new('ref_coe').

Note

Class loading coefficient of conversion between quantity (weights or volumes of glass eel) and numbers between a starting and finishing date

Author(s)

cedric.briand@eptb-vilaine.fr

See Also

Other referential objects: charge,ref_choice-method, ref_choice-class, ref_dc-class, ref_df-class, ref_horodate-class, ref_list-class, ref_par-class, ref_parqual-class, ref_parquan-class, ref_stage-class, ref_taxa-class, ref_year-class

Class 'ref_dc'

Description

Description of a control device.

Slots

dc_selected

Object of class 'integer', The selected device

ouvrage

Object of class 'integer', the attached dam

station

Object of class 'character', the attached migration monitoring station, this is necessary to join the table of escapements calculated at the station level.

data

Object of class 'data.frame' data pertaining to the control device

Objects from the Class

Objects can be created by calls of the form new('ref_dc', dc_selected=integer(), ouvrage=integer(), data=data.frame()).

Author(s)

cedric.briand@eptb-vilaine.fr

See Also

Other referential objects: charge,ref_choice-method, ref_choice-class, ref_coe-class, ref_df-class, ref_horodate-class, ref_list-class, ref_par-class, ref_parqual-class, ref_parquan-class, ref_stage-class, ref_taxa-class, ref_year-class

Class 'ref_df'

Description

Representation of a fishway, contains description data of all fishways from the database along with the selected fishways (df) (integer) Objects from the Class: Objects can be created by calls of the form new('ref_df', df_selected=integer(), ouvrage=integer(), data=data.frame()).

Arguments

Author(s)

cedric.briand@eptb-vilaine.fr

See Also

Other referential objects: charge,ref_choice-method, ref_choice-class, ref_coe-class, ref_dc-class, ref_horodate-class, ref_list-class, ref_par-class, ref_parqual-class, ref_parquan-class, ref_stage-class, ref_taxa-class, ref_year-class

Class 'ref_env'

Description

Enables to load measure stations and to select one of them

Slots

dataframe

Data concerning the measure station

env_selected

The selected measure station

Objects from the Class

Objects can be created by calls of the form new('ref_env', ...).

Author(s)

cedric.briand@eptb-vilaine.fr

Class ref_horodate

Description

choice of date with method to show current and previous year

Slots

horodate

a "POSIXt"

Objects from the Class

Objects can be created by calls of the form new("ref_horodate", ...{}).

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

Other referential objects: charge,ref_choice-method, ref_choice-class, ref_coe-class, ref_dc-class, ref_df-class, ref_list-class, ref_par-class, ref_parqual-class, ref_parquan-class, ref_stage-class, ref_taxa-class, ref_year-class

Class 'ref_list'

Description

Enables to load a 'ref_list' object from a list given by a 'report' object

Arguments

Objects from the Class

Objects can be created by calls of the form new('ref_list', listechoice, label).

list('listechoice')

Object of class 'character'

:

Object of class 'character'

list('label')

Object of class 'character'

:

Object of class 'character'

Author(s)

cedric.briand@eptb-vilaine.fr

See Also

Other referential objects: charge,ref_choice-method, ref_choice-class, ref_coe-class, ref_dc-class, ref_df-class, ref_horodate-class, ref_par-class, ref_parqual-class, ref_parquan-class, ref_stage-class, ref_taxa-class, ref_year-class

Class 'ref_par'

Description

Class enabling to load the list of parameters and select one of them

Slots

data

A data.frame

par_selected

A character vector corresponding to par_code

data='data.frame'

the list of parameters

Objects from the Class

Objects can be created by calls of the form

Author(s)

cedric.briand@eptb-vilaine.fr

See Also

Other referential objects: charge,ref_choice-method, ref_choice-class, ref_coe-class, ref_dc-class, ref_df-class, ref_horodate-class, ref_list-class, ref_parqual-class, ref_parquan-class, ref_stage-class, ref_taxa-class, ref_year-class

Class 'ref_parqual'

Description

Class enabling to load the list of qualitative parameters and to select one of them. It inherits from 'ref_par', uses its 'choice' method

Slots

valqual='data.frame'

the list of qualitative parameters

Author(s)

cedric.briand@eptb-vilaine.fr

See Also

Other referential objects: charge,ref_choice-method, ref_choice-class, ref_coe-class, ref_dc-class, ref_df-class, ref_horodate-class, ref_list-class, ref_par-class, ref_parquan-class, ref_stage-class, ref_taxa-class, ref_year-class

Class 'ref_parquan'

Description

Class enabling to load the list of quantitative parameters and to select one of them. It inherits from 'ref_par', uses its 'choice' method

Author(s)

cedric.briand@eptb-vilaine.fr

See Also

Other referential objects: charge,ref_choice-method, ref_choice-class, ref_coe-class, ref_dc-class, ref_df-class, ref_horodate-class, ref_list-class, ref_par-class, ref_parqual-class, ref_stage-class, ref_taxa-class, ref_year-class

Class 'ref_stage'

Description

Representation of a fish phase

Slots

data

A data frame containing data loaded from the database by either charge or charge_with_filter methods

stage_selected

Contains the code 'tax_code' of the stage selected by choice_c() method

Objects from the Class

Objects can be created by calls of the form new('ref_stage', data='data.frame').

list('data')

Object of class 'data.frame' ~ The phases available in the database

:

Object of class 'data.frame' ~ The phases available in the database

Author(s)

cedric.briand@eptb-vilaine.fr

See Also

Other referential objects: charge,ref_choice-method, ref_choice-class, ref_coe-class, ref_dc-class, ref_df-class, ref_horodate-class, ref_list-class, ref_par-class, ref_parqual-class, ref_parquan-class, ref_taxa-class, ref_year-class

Class 'ref_taxa'

Description

Loading and selection of fish species. This class is a referential class, and it is integrated into refreport objects.

Slots

data

A 'data.frame' of species available in the database

taxa_selected

Contains the code 'tax_code' of the taxa selected by choice_c() method

Objects from the Class

Objects can be created by calls of the form new('ref_taxa', ...).

Author(s)

cedric.briand@eptb-vilaine.fr

See Also

Other referential objects: charge,ref_choice-method, ref_choice-class, ref_coe-class, ref_dc-class, ref_df-class, ref_horodate-class, ref_list-class, ref_par-class, ref_parqual-class, ref_parquan-class, ref_stage-class, ref_year-class

ref_textbox referencial class

Description

allows to a put a value within a glabel

Slots

title='character'

the title of the box giving the possible choices

labels

the logical parameters choice

checked

a vector

Author(s)

cedric.briand@eptb-vilaine.fr

Class "ref_timestep"

Description

Describes a time step

Objects from the Class

Objects can be created by calls of the form new("ref_timestep", dateDebut="POSIXt",step_duration=numeric(),nb_step=numeric(),nocurrent_step=integer()).

list("dateDebut")

Object of class "POSIXt" Starting date

:

Object of class "POSIXt" Starting date

list("step_duration")

Object of class "numeric" Step length

:

Object of class "numeric" Step length

list("nb_step")

Object of class "numeric" Number of steps

:

Object of class "numeric" Number of steps

list("nocurrent_step")

Object of class "integer" Number of the current step

:

Object of class "integer" Number of the current step

Author(s)

cedric.briand@eptb-vilaine.fr

See Also

ref_timestep_daily

Class "ref_timestepChar"

Description

Character to represent a ref_timestep

Objects from the Class

Objects can be created by calls of the form new("ref_timestepChar", ...{})

Author(s)

cedric.briand@eptb-vilaine.fr

See Also

ref_timestep

Examples

showClass("ref_timestepChar")

Class 'ref_timestep_daily'

Description

Representation of a ref_timestep object with a step length equal to one day. It receives an inheritance from ref_timestep

Details

validity_ref_timestep_daily

Objects from the Class

Objects can be created by calls of the form new('ref_timestep_daily', dateDebut='POSIXt',step_duration=numeric(),nb_step=numeric(),nocurrent_step=integer()).

list('dateDebut')

Object of class 'POSIXt' Starting date

:

Object of class 'POSIXt' Starting date

list('step_duration')

Object of class 'numeric' Step length

:

Object of class 'numeric' Step length

list('nb_step')

Object of class 'numeric' Number of steps

:

Object of class 'numeric' Number of steps

list('nocurrent_step')

Object of class 'integer' Number of the current step

:

Object of class 'integer' Number of the current step

Author(s)

cedric.briand@eptb-vilaine.fr

See Also

ref_timestep

Year reference class

Description

Class used to select one or several years

Slots

data

A data.frame with the list of possible years selected as numerics

year_selected

A numeric vector

Objects from the Class

Objects can be created by calls of the form new("ref_year", data=data.frame(), year_selected=numeric()).

Author(s)

cedric.briand@eptb-vilaine.fr

See Also

Other referential objects: charge,ref_choice-method, ref_choice-class, ref_coe-class, ref_dc-class, ref_df-class, ref_horodate-class, ref_list-class, ref_par-class, ref_parqual-class, ref_parquan-class, ref_stage-class, ref_taxa-class

Class "report_annual"

Description

This class displays annual migration counts, for several counting device, taxa or stages.

Slots

dc

Object of class ref_dc-class, the counting device, multiple values allowed

data

Object of class "data.frame" data for report lot

taxa

An object of class ref_taxa-class, multiple values allowed

stage

An object of class ref_stage-class, multiple values allowed

start_year

Object of class ref_year-class. ref_year allows to choose year of beginning

end_year

Object of class ref_year-class ref_year allows to choose last year of the report

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

Other report Objects: report_dc-class, report_df-class, report_env-class, report_ge_weight-class, report_mig-class, report_mig_char-class, report_mig_env-class, report_mig_interannual-class, report_mig_mult-class, report_sample_char-class, report_sea_age-class, report_silver_eel-class, report_species-class

Examples

# launching stacomi without database for demo
stacomi(database_expected=FALSE)
# the following piece of script will load the Arzal dataset and connected to iav postgres schema
# it requires a working database
# prompt for user and password but you can set appropriate options for host, port and dbname
## Not run: 
	stacomi(database_expected=TRUE, sch='iav')
	if (interactive()){
		if (!exists("user")){
			user <- readline(prompt="Enter user: ")
			password <- readline(prompt="Enter password: ")	
		}	
	}
	options(					
			stacomiR.dbname = "bd_contmig_nat",
			stacomiR.host ="localhost",
			stacomiR.port = "5432",
			stacomiR.user = user,
			stacomiR.user = password						
	)	
  r_ann<-new("report_annual")
  r_ann<-choice_c(r_ann,
	  dc=c(5,6,12),
	  taxa=c("Anguilla anguilla"),
	  stage=c("AGJ","AGG"),
	  start_year="1996",
	  end_year="2015",
	  silent=FALSE)
  r_ann<-connect(r_ann)	

## End(Not run)
# the following dataset has been generated by the previous code
data(r_ann)
xtr_ann<-stacomiR::xtable(r_ann,
	dc_name=c("Passe bassins","Piege anguille RG","Piege anguille RD"),
	tax_name="Anguille",
	std_name=c("Arg.","Jaun."))
# below not run but one can create a file as following
## Not run: 
  path=file.path(path.expand(get("datawd",envir=envir_stacomi)),
	  paste(paste(r_ann@dc@dc_selected,collapse="+"),"_",
		  paste(r_ann@taxa@taxa_selected,collapse="+"),"_",
		  paste(r_ann@stage@stage_selected,collapse="+"),"_",
		  r_ann@start_year@year_selected,":",
		  r_ann@end_year@year_selected,".html",sep=""),fsep ="/")
# here you can add an argument file=path
  print(xtr_ann,type="html")
  
# the following uses the "addtorow" argument which creates nice column headings,
# format.args creates a thousand separator
# again this will need to be saved in a file using the file argument
  print(xtr_ann,
	  add.to.row=get("addtorow",envir_stacomi),
	  include.rownames = TRUE,
	  include.colnames = FALSE,
	  format.args = list(big.mark = " ", decimal.mark = ",")
  )
# barplot transforms the data, further arguments can be passed as to barplot
  barplot(r_ann)
  barplot(r_ann,
	  args.legend=list(x="topleft",bty = "n"),
	  col=c("#CA003E","#1A9266","#E10168","#005327","#FF9194"))
  
# An example with custom arguments for legend.text (overriding plot defauts)
  data(r_ann_adour)
  if (requireNamespace("RColorBrewer", quietly = TRUE)){
	lesdc<-r_ann_adour@dc@data$dc_code[r_ann_adour@dc@data$dc%in%r_ann_adour@dc@dc_selected]
    barplot(r_ann_adour,
		legend.text=lesdc,
		args.legend=list(x="topleft",bty = "n"),
		col=RColorBrewer::brewer.pal(9,"Spectral"),
		beside=TRUE)
  }
  plot(r_ann_adour)

## End(Not run)

Class "report_dc" report du fonctionnement du dispositif de comptage

Description

The counting device is not always working. It may me stopped either following a monitoring protocol, or due to malfunction of the device, this class allows to draw graphics allowing an overview of the device operation

Slots

data

A data frame

dc

An object of class ref_dc-class

horodatedebut

An object of class ref_horodate-class

horodatefin

An object of class ref_horodate-class

Objects from the Class

Objects can be created by calls of the form new("report_dc", ...).

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

Other report Objects: report_annual-class, report_df-class, report_env-class, report_ge_weight-class, report_mig-class, report_mig_char-class, report_mig_env-class, report_mig_interannual-class, report_mig_mult-class, report_sample_char-class, report_sea_age-class, report_silver_eel-class, report_species-class

Examples

# An example that will work only if the database is present 
# and the program installed and comprises the schema iav
# prompt for user and password but you can set appropriate options for host, port and dbname
## Not run: 
	if (interactive()){
		if (!exists("user")){
			user <- readline(prompt="Enter user: ")
			password <- readline(prompt="Enter password: ")	
		}	

	options(					
			stacomiR.dbname = "bd_contmig_nat",
			stacomiR.host ="localhost",
			stacomiR.port = "5432",
			stacomiR.user = user,
			stacomiR.password = password						
	)	
}
 stacomi(TRUE,sch="iav")
  r_dc=new("report_dc")
  r_dc<-choice_c(r_dc,
	  5,
	  horodatedebut="2000-01-01",
	  horodatefin="2015-12-31",
	  silent=TRUE)
  r_dc<-connect(r_dc)

##
	
  # this dataset has been loaded by the previous lines
  ###########################################################	
# Without connexion to the database (use dataset r_dc)
  ##########################################################
	# this option allows to launch the program without the interface to display 
# some of the program features.
	stacomi(database_expected=FALSE)
  data("r_dc")
  plot(r_dc,plot.type="1")
  plot(r_dc,plot.type="2")
  plot(r_dc,plot.type="3",main="trial title")
  plot(r_dc,plot.type="4",main="trial title")
# the following will write in the datawd folder
   summary(r_dc)

## End(Not run)

Report on fishway operation

Description

Fishways (DF) are of various nature, from very simple eel ladders fed by water discharged from the river, to more complex fishways with levels adjusted by the opening of various gates and regulators. The objective of this class is to provide an assessment of the working status of a fishway throughout the year. A number of fishes ascending a fishway has meaning only if we know that the fishway is operational, and that the counting operated on the fishway has remained operational. In the database the operation of the fishway (DF) and counting device (DC) is agregated in one table (t_periodefonctdispositif_per). The column per_etat_fonctionnement indicates whether the fishway is operational (with a boolean) and the column per_tar_code indicates the status of either the fishway or DC. In the database four types of operation are set, "1"=normal operation, "2"=Device stopped in normal operation (ie lift ascending, high tide...), "3"="Stopped for maintenance or other problem", "4"="Works but not fully operational,i.e.flow problem, flood, clogged with debris...", "5"="Not known")

Slots

data

A data frame

df

An object of class ref_df-class

horodatedebut

An object of class ref_horodate-class

horodatefin

An object of class ref_horodate-class

Objects from the Class

Objects can be created by calls of the form new("report_df").

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

Other report Objects: report_annual-class, report_dc-class, report_env-class, report_ge_weight-class, report_mig-class, report_mig_char-class, report_mig_env-class, report_mig_interannual-class, report_mig_mult-class, report_sample_char-class, report_sea_age-class, report_silver_eel-class, report_species-class

Examples

stacomi(
	database_expected=FALSE)
# An example that will work with the database installed only and schema iav in the database
# prompt for user and password but you can set appropriate options for host, port and dbname

## Not run: 
	stacomi(
			database_expected=TRUE, sch='iav')	
	if (interactive()){
		if (!exists("user")){
			user <- readline(prompt="Enter user: ")
			password <- readline(prompt="Enter password: ")	
		}	
	}
	options(					
			stacomiR.dbname = "bd_contmig_nat",
			stacomiR.host ="localhost",
			stacomiR.port = "5432",
			stacomiR.user = user,
			stacomiR.user = password						
	)	
  r_df=new("report_df")
  r_df<-choice_c(r_df,
	  1,
	  horodatedebut="2015-01-01",
	  horodatefin="2015-12-31",
	  silent=TRUE)
  Sys.setenv(TZ='GMT')
  # the times at Arzal are recorded continuously
  # they are converted to date when a time appears while the hour is changing
  # hence the following
  r_df<-connect(r_df)

## End(Not run)

data("r_df")
plot(r_df,plot.type="4")
# the following examples work but take a while to compute
## Not run: 
  plot(r_df,plot.type="1")
  plot(r_df,plot.type="2",main="A nice title")
  plot(r_df,plot.type="3",main="A nice title")	

## End(Not run)

class report_env simple output of one or several environmental conditions...

Description

Annual overview of environmental conditions. This class enables to draw some plot, but will mostly used to build joined graphs crossing the information from report_mig_mult-class and report_mig_env-class

Slots

horodatedebut

ref_horodate-class

horodatefin

ref_horodate-class

stationMesure

ref_env-class

data

data.frame

Author(s)

cedric.briand@eptb-vilaine.fr

See Also

Other report Objects: report_annual-class, report_dc-class, report_df-class, report_ge_weight-class, report_mig-class, report_mig_char-class, report_mig_env-class, report_mig_interannual-class, report_mig_mult-class, report_sample_char-class, report_sea_age-class, report_silver_eel-class, report_species-class

Examples

stacomi(
	database_expected=FALSE)
## Not run: 
	if (interactive()){
		if (!exists("user")){
			user <- readline(prompt="Enter user: ")
			password <- readline(prompt="Enter password: ")	
		}	
	}
	options(					
			stacomiR.dbname = "bd_contmig_nat",
			stacomiR.host ="localhost",
			stacomiR.port = "5432",
			stacomiR.user = user,
			stacomiR.user = password						
	)	
  r_env<-new("report_env")
  r_env<-choice_c(r_env,
	  stationMesure=c("temp_gabion","coef_maree"),
	  datedebut="2008-01-01",
	  datefin="2008-12-31",
	  silent=FALSE)	
  r_env<-connect(r_env)
  

## End(Not run)	

data("r_env")
plot(r_env,silent=TRUE)

Trend of wet weight in glass eel

Description

In trapping ladders, glass eel are seldom counted, as they are too tiny to handle and too numerous to count. The usual operation is to weight them, or to use a bucket to measure their volume. These weights or volumes will later need to be converted to numbers. The glass eel weight may follow a seasonal pattern. It's the case for Anguilla anguilla glass eel in the Bay of Biscay. Weights can be modelled using sine wave curves, or more complex gam models. This class has a model method to try those models, which can also be used to extact coefficients manually to manually test more complex models. Some plots are provided to display the coefficients stored in the database, and the model results. A parameter provided in the graphical interface or in the command line (slot liste) takes values '1', '>1', 'tous' which mean respectively use only individual sample of glass eels, or use 'group weights' which can be more close to the real weight of glass eel during counts as glass eel are not completely drained from their water during handling to preserve their mucus. The list choice 'tous' means that both individual and group weights are selected.

Slots

data

A 'data.frame' data for report lot

calcdata

A list containing two processed data frames, data and coe

dc

Object of class ref_dc-class, the counting device

start_year

Object of class ref_year-class. ref_year allows to choose the year of beginning

end_year

Object of class ref_year-class ref_year allows to choose last year of the report

coe

Object of class ref_coe-class class loading coefficient of conversion between quantity (weights or volumes of glass eel) and numbers

liste

Object of class ref_list-class ref_list referential class choose within a list, here the choice is whether subsamples or not. Subsamples in the stacomi database are samples with a non null value for parent sample. Migration counts are never made on subsamples but those can be integrated to calculate mean weights.

Note

In this class some tools are available to import glass eel measurement from experimental fishing in the estuary. For the charge method dates for the request are from august to august (a glass eel season)

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

Other report Objects: report_annual-class, report_dc-class, report_df-class, report_env-class, report_mig-class, report_mig_char-class, report_mig_env-class, report_mig_interannual-class, report_mig_mult-class, report_sample_char-class, report_sea_age-class, report_silver_eel-class, report_species-class

Examples

require(stacomiR)
# launching stacomi without selecting the scheme or interface
stacomi(
	database_expected=FALSE, sch='iav')
# this requires a working database with the schema iav
# prompt for user and password but you can set appropriate options for host, port and dbname
## Not run: 
	stacomi(
			database_expected=TRUE, sch='iav')	
	if (interactive()){
		if (!exists("user")){
			user <- readline(prompt="Enter user: ")
			password <- readline(prompt="Enter password: ")	
		}	
	}
	options(					
			stacomiR.dbname = "bd_contmig_nat",
			stacomiR.host ="localhost",
			stacomiR.port = "5432",
			stacomiR.user = user,
			stacomiR.user = password						
	)	
  #create an instance of the class
  r_gew<-new("report_ge_weight")
  r_gew@liste<-charge(object=r_gew@liste,listechoice=c("=1",">1","tous"),label="")
  # here I'm using weights when number are larger than 1i.e.wet weight
  # always choose a date from one year to the next eg 2010 to 2011
  # as the dates are from august to august
  r_gew<-choice_c(r_gew,
	  dc=c(6),			
	  start_year="2009",
	  end_year="2015",
	  selectedvalue=">1",
	  silent=FALSE)
  r_gew<-connect(r_gew)	
  r_gew<-calcule(r_gew)

## End(Not run)	
# load the dataset generated by previous lines
data("r_gew")
# the calculation will fill the slot calcdata

# A ggplot showing the trend in weight
plot(r_gew, plot.type=1)
# A plot showing both the data and the trend as recorded in the database
plot(r_gew, plot.type=2)
# Same as plot.type=1 but with size according to size of the sample,
# usefull for wet weights where weight are recorded on a number of glass eel
plot(r_gew, plot.type=3)
## Not run: 
# First model with nls, see Guerault and Desaunay (1993) 
  model(r_gew,model.type="seasonal")
  model(r_gew,model.type="seasonal1")

## End(Not run)

Migration report for one DC, one species and one stage

Description

This class performs a migration summary. A migration monitoring operation can correspond to a single horodate (in the case of some video monitoring operation) or comprise a period which does not necessarily span a full day. The daily migration is calculated by splitting the operation between days, and the migration is either grouped or split according to the lenth of the different time spans.

Slots

dc

Object of class ref_dc-class: the control device

taxa

Object of class ref_taxa-class: the species

stage

Object of class ref_stage-class : the stage of the fish

timestep

Object of class ref_timestep_daily-class : the time step constrained to daily value and 365 days

data

Object of class data.frame with data filled in from the connect method

calcdata

A "list" of calculated daily data, one per dc, filled in by the calcule method

coef_conversion

A data.frame of daily weight to number conversion coefficients, filled in by the connect method if any weight are found in the data slot.

time.sequence

Object of class POSIXct : a time sequence of days generated by the calcule method

Note

In practise, the report_mig class uses methods (calcule, connect...) from the more elaborate report_mig_mult-class

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

Other report Objects: report_annual-class, report_dc-class, report_df-class, report_env-class, report_ge_weight-class, report_mig_char-class, report_mig_env-class, report_mig_interannual-class, report_mig_mult-class, report_sample_char-class, report_sea_age-class, report_silver_eel-class, report_species-class

Examples

stacomi(database_expected=FALSE) 
# If you have a working database
# the following line of code will create the r_mig dataset from the iav (default) 
# schema in the database
## Not run: 	
	stacomi(database_expected=TRUE)	
	if (interactive()){
		if (!exists("user")){
			user <- readline(prompt="Enter user: ")
			password <- readline(prompt="Enter password: ")	
		}	
	}
	options(					
			stacomiR.dbname = "bd_contmig_nat",
			stacomiR.host ="localhost",
			stacomiR.port = "5432",
			stacomiR.user = user,
			stacomiR.user = password						
	)	
  stacomi(
	  database_expected=TRUE)	
  r_mig=new("report_mig")
  r_mig=choice_c(r_mig,
	  dc=5,
	  taxa=c("Chelon ramada"),
	  stage=c("IND"),
	  datedebut="2015-01-01",
	  datefin="2015-12-31")
  r_mig<-charge(r_mig)
  # launching charge will also load classes associated with the report
  # e.g. report_ope, report_df, report_dc
  r_mig<-connect(r_mig)
  ########################
# calculations
  ########################
  r_mig<-calcule(r_mig,silent=TRUE)

## End(Not run)
########################
# loading data
## use the following to get the raw data loaded by the connect method
# not shown there as the database and program might not be installed
# All three classes report... were created by the charge and connect method 
# of report_mig_mult
# in the previous example
################################
data("r_mig")
data("r_mig_ope")
assign("report_ope",r_mig_ope,envir=envir_stacomi)
data("r_mig_df")
assign("report_df",r_mig_df,envir=envir_stacomi)
data("r_mig_dc")
assign("report_dc",r_mig_dc,envir=envir_stacomi)


#Individual plot for all DC (standard), taxa and stage where data present
#silent argument to stop all messages
plot(r_mig,plot.type="standard",silent=TRUE)
#cumulated migration at the station (all stages and DC grouped)
plot(r_mig,plot.type="step")

# data will be written in the data directory specified in datawd argument to stacomi default "~"
#file

## Not run: 
  summary(r_mig,silent=TRUE)

## End(Not run)
# this will write the daily report for later in in the reportnMigrationInterannuelle-class
## Not run: 
  write_database(r_mig,silent=TRUE,dbname="bd_contmig_nat",host="localhost",port=5432)

## End(Not run)

Migration report along with quantitative and qualitative characteristics

Description

Migration along with qualitative or quantitative characteristics or both (e.g.) weight of eels according to the size class per period of time, weight of fish according to gender, number of fish per age class. This class does not split migration evenly over time period. So, unlike calculations made in class report_mig and report_mig_mult the whole time span of the migration operation is not considered, only the date of beginning of the operation is used to perform calculations.

Slots

calcdata

A 'list' of calculated data, filled in by the calcule method

data

A data.frame inherited from report_sample_char-class

dc

An object of class ref_dc-class inherited from report_sample_char-class

taxa

An object of class ref_taxa-class inherited from report_sample_char-class

stage

An object of class ref_stage-class inherited from report_sample_char-class

horodatedebut

An object of class ref_horodate-class inherited from report_sample_char-class

horodatefin

An object of class ref_horodate-class inherited from report_sample_char-class

par

An object of class ref_par-class inherited from report_sample_char-class

echantillon

An object of class ref_choice-class, vector of choice

parquan

An object of class ref_parquan-class, quantitative parameter

parqual

An object of class ref_parqual-class, qualitative parameter

Objects from the Class

Objects can be created by calls of the form new('report_mig_char', ...). they are loaded by the interface using interface_report_mig_char function.

Note

The main difference between this class and report_sample_char-class is that this class allows to select (or not) the samples, and that it handles quantitative and qualitative parameters separately.

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

Other report Objects: report_annual-class, report_dc-class, report_df-class, report_env-class, report_ge_weight-class, report_mig-class, report_mig_env-class, report_mig_interannual-class, report_mig_mult-class, report_sample_char-class, report_sea_age-class, report_silver_eel-class, report_species-class

Examples

require(stacomiR)

stacomi(
	database_expected=FALSE, sch='logrami')
# this requires a database with the schema logrami
# prompt for user and password but you can set appropriate options for host, port and dbname
## Not run: 
	stacomi(database_expected=TRUE, sch='logrami')	
	if (interactive()){
		if (!exists("user")){
			user <- readline(prompt="Enter user: ")
			password <- readline(prompt="Enter password: ")	
		}	
	}
	options(					
			stacomiR.dbname = "bd_contmig_nat",
			stacomiR.host ="localhost",
			stacomiR.port = "5432",
			stacomiR.user = user,
			stacomiR.user = password						
	)	
  r_mig_char <- new("report_mig_char")
  # here parqual is not in the list
  # so this is equivalent to parqual=NULL
  # default for echantillon is "with"
  r_mig_char <- choice_c(r_mig_char,
	  dc=c(107,108,101),
	  taxa=c("Salmo salar"),
	  stage=c('5','11','BEC','BER','IND'),
	  parquan=c('C001','1786','1785'),
	  horodatedebut="2012-01-01",
	  horodatefin="2012-12-31",
	  silent=FALSE)
  # r_mig_char<-charge(r_mig_char) not necessary there
  r_mig_char <- connect(r_mig_char)
  

## End(Not run)	
# load the dataset generated by previous lines
data("r_mig_char")

r_mig_char<-calcule(r_mig_char, silent=TRUE)
plot(r_mig_char,plot.type="quant", silent=TRUE)
# one quantitative parameter found, manual choice of color
plot(r_mig_char,plot.type="quant",color_parm=c("C001"="red"), silent=TRUE)
# age will be plotted as a qualitative variable
# here we split size data accoding to the limit known between different ages from
# scale reading in the Loire
r_mig_char <- setasqualitative(r_mig_char,par='C001',
		breaks=c(0,675,850,2000),
		labels=c("age 1","age 2","age 3"))
r_mig_char<-calcule(r_mig_char, silent=TRUE)
plot(r_mig_char, plot.type="qual", silent=TRUE)
plot(r_mig_char, plot.type="crossed")
plot(r_mig_char, plot.type="crossed",
    color_parm=c("age 1"="#379ec6","age 2"="#173957","age 3"="#b09953"))
xt<-xtable(r_mig_char)
# use method print.xtable to get the output

Class "report_mig_env"

Description

Enables to compute an annual overview of fish migration and environmental conditions in the same chart. Environmental conditions may trigger migration events, variation in flow or temperatures can be plotted along migration to check graphically for a possible relation. To enable this, environmental conditions are loaded from an "environmental monitoring station", which records environmental parameters and is attached to a migratory station in the database. This class enables both continuous output (temperature -flow) as well as discrete parameters (qualitative = moon phase, type of operation of a gate, opening of a gate...) which will be displayed on the graph. Values are scaled so that single plot can display migration numbers and environmental parameters. Environmental parameters when stored at a time scale lower that a day are averaged per day, unless they are qualitative parameters, in which case only the first event of the day is displayed on the annual plot.

Slots

report_mig_mult

report_mig_mult-class

report_env

report_env-class

Author(s)

cedric.briand@eptb-vilaine.fr marion.legrand@logrami.fr

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

Other report Objects: report_annual-class, report_dc-class, report_df-class, report_env-class, report_ge_weight-class, report_mig-class, report_mig_char-class, report_mig_interannual-class, report_mig_mult-class, report_sample_char-class, report_sea_age-class, report_silver_eel-class, report_species-class

Other report Objects: report_annual-class, report_dc-class, report_df-class, report_env-class, report_ge_weight-class, report_mig-class, report_mig_char-class, report_mig_interannual-class, report_mig_mult-class, report_sample_char-class, report_sea_age-class, report_silver_eel-class, report_species-class

Examples

require(stacomiR)
stacomi(
	database_expected=FALSE)
# the following will load the data provided the user has access to the database
# with data in the iav example scheme.
# prompt for user and password but you can set appropriate options for host, port and dbname
## Not run: 
	stacomi(
			database_expected=TRUE)	
	if (interactive()){
		if (!exists("user")){
			user <- readline(prompt="Enter user: ")
			password <- readline(prompt="Enter password: ")	
		}	
	}
	options(					
			stacomiR.dbname = "bd_contmig_nat",
			stacomiR.host ="localhost",
			stacomiR.port = "5432",
			stacomiR.user = user,
			stacomiR.user = password						
	)	
  r_mig_env<-new("report_mig_env")
  r_mig_env<-choice_c(r_mig_env,
	  dc=c(5,6,12),
	  taxa=c("Anguilla anguilla"),
	  stage=c("AGJ","AGG","CIV"),
	  stationMesure=c("temp_gabion","coef_maree","phases_lune"),
	  datedebut="2008-01-01",
	  datefin="2008-12-31",
	  silent=FALSE)	
  r_mig_env<-charge(r_mig_env) # this is necessary to load operations, DF and DC
  r_mig_env<-connect(r_mig_env)
  r_mig_env<-calcule(r_mig_env,silent=TRUE)

## End(Not run)	

data("r_mig_env")
# An example of plot with custom colors.
plot(r_mig_env,
	color_station=c("temp_gabion"="red","coef_maree"="blue","phases_lune"="pink"),
 	color_dc=c("5"="yellow","6"="orange","12"="purple")
)

Class "report_mig_interannual"

Description

When daily report are written in the t_reportjournalier_bjo table by the report_mig-class they can be used by this class to display interannual comparisons of migration. When running its connect method, this class will run the report_mig-class for each year where data are missing, or where the annual sum in the t_reportjournalier_bjo table differs from the counts generated by the report_annual-class : rows have been changed in the database. Different charts are produced with different period grouping. See write_database,report_mig-method for details about how this method inserts data in the t_reportjournalier_bjo table.

Slots

dc

An object of class ref_dc-class, the counting device

data

A data.frame data loaded from the daily migration table t_bilanmigrationjournalier_bjo

taxa

An object of class ref_taxa-class, there can only be one taxa

stage

An object of class ref_stage-class, there can only be one stage

start_year

An object of class ref_year-class. ref_year allows to choose year of beginning

end_year

An object of class ref_year-class ref_year allows to choose last year of the report

calcdata

A list of calculated data, filled in by the calcule method

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

Other report Objects: report_annual-class, report_dc-class, report_df-class, report_env-class, report_ge_weight-class, report_mig-class, report_mig_char-class, report_mig_env-class, report_mig_mult-class, report_sample_char-class, report_sea_age-class, report_silver_eel-class, report_species-class

Examples

require(stacomiR)
# launching stacomi without selecting the scheme or interface
stacomi(
	database_expected=FALSE, sch='pmp')
# If you have connection to the database with the pmp scheme 
# prompt for user and password but you can set appropriate options for host, port and dbname
## Not run: 
	stacomi(database_expected=TRUE, sch="pmp")	
	if (interactive()){
		if (!exists("user")){
			user <- readline(prompt="Enter user: ")
			password <- readline(prompt="Enter password: ")	
		}	
	}
	options(					
			stacomiR.dbname = "bd_contmig_nat",
			stacomiR.host ="localhost",
			stacomiR.port = "5432",
			stacomiR.user = user,
			stacomiR.user = password						
	)	

  # (longest historical dataset available
  # in France for eel ...) this suppose you have access to the pmp schema...
  # a glimpse of the dataset is still available in the r_mig_interannual dataset 
  # loaded in the package...
  r_mig_interannual <- new("report_mig_interannual")
  r_mig_interannual <- choice_c(r_mig_interannual,
	  dc=c(16),
	  taxa=c("Anguilla anguilla"),
	  stage=c("PANG"),
	  start_year="1990",
	  end_year="2015",
    year_choice=NULL,
	  silent=TRUE)
  r_mig_interannual <- charge(r_mig_interannual)
  r_mig_interannual <- connect(r_mig_interannual, check=TRUE)	
  r_mig_interannual <- calcule(r_mig_interannual, silent=TRUE)	

## End(Not run)	
#############otherwise use this ######################
# load the dataset generated by previous lines
data("r_mig_interannual")

#######################################################
# the first plot is of little interest, it allows to see what data 
# are available... simple lines
# For irregular operations like those reported at the enfrenaux eel ladder....
plot(r_mig_interannual,plot.type="line", year_choice=2015, silent=TRUE)

# a plot to show the seasonality, this graph may be misleading if the
# migration is not monitored all year round. Note the y unit is not very informative
# you need to have the viridis package loaded to run this example
plot(r_mig_interannual,plot.type="density",year_choice=2015, silent=TRUE)
## Not run: 
  if (requireNamespace("ggplot2", quietly = TRUE)&
	  requireNamespace("viridis", quietly = TRUE)){
	g<-get("g",envir=envir_stacomi)	
	g+
		ggplot2::scale_fill_manual(values=viridis::viridis(22))+
		ggplot2::ggtitle("Saisonnalite de la migration aux Enfrenaux")
  }
  #############################################
# the standard plot is showing daily values
  ###########################################
  plot(r_mig_interannual,plot.type="standard",year_choice=2015,silent=TRUE)
# Manual edition of the graph produced
  if (requireNamespace("ggplot2", quietly = TRUE)){
    g1<-get("g1",envir=envir_stacomi)
    g1<-g1+ggplot2::ggtitle("Les Enfrenaux")+
		ggplot2::scale_fill_manual(name="Source", 
			values=c("purple","#0A0C01"),
			labels = c("historical set","2015 values"))+
		ggplot2::scale_colour_manual(name="Source", values="#B8EA00",
			labels = c("historical mean"))	+
		ggplot2::ylab("Nombre d'anguilles")
    print(g1)
  }
  #########################################################
# Another graph to show a "manual" processing of the data
# and their extraction from the data slot
  #########################################################	
  if (requireNamespace("ggplot2", quietly = TRUE)&
	      requireNamespace("viridis", quietly = TRUE)){
    dat<-fun_date_extraction(r_mig_interannual@data, # data to import
		"bjo_jour", # name of the column where dates are found
		annee=FALSE,
		mois=TRUE,
		semaine =TRUE,
		jour_mois=FALSE)
# sum per month
    res<-dplyr::select(dat,bjo_valeur,bjo_annee,semaine)
    res<-dplyr::group_by(res,bjo_annee,semaine)
    res<-dplyr::summarize(res,effectif=sum(bjo_valeur))
    ggplot2::ggplot(res, ggplot2::aes(x = semaine, y = bjo_annee,fill=effectif)) +
	        ggplot2::geom_tile(colour="black") + ggplot2::coord_fixed() +
	        viridis::scale_fill_viridis(begin=0,option="D") + ggplot2::theme_bw()+
	        ggplot2::theme(panel.background= ggplot2::element_rect(fill = "#9360A9"),
			panel.grid.major=ggplot2::element_line(colour="#C1DB39"),
			panel.grid.minor=ggplot2::element_line(colour="#7DD632"))+
	        ggplot2::ylab("year")+ggplot2::xlab("week")+
	        ggplot2::ggtitle("Historical trend at Les Enfrenaux Eel trap")
	
  }
  ###############################################
# barchart with different splitting periods
# the migration is displayed against seasonal data
# extacted from all other years loaded in the report
  ################################################
# available arguments for timesplit are "quinzaine" and "mois" and "semaine"
# with the silent=TRUE argument, it's always the latest year that is selected,
# otherwise the user is prompted with a choice, to select the year he wants
# to compare will all others...
  plot(r_mig_interannual,plot.type="barchart",timesplit="quinzaine",year_choice=2015,silent=TRUE)
# Comparison with historical values. Each year and 2 weeks values 
# is a point on the graph...
  plot(r_mig_interannual,plot.type="pointrange",timesplit="mois",year_choice=2015,silent=TRUE)
  ###############################################
# Step plot
# different years shown in the graph
# the current year (or the selected year if silent=FALSE)
# is displayed with a dotted line
  ################################################
  plot(r_mig_interannual,plot.type="step",year_choice=2015,silent=TRUE)
  if (requireNamespace("ggplot2", quietly = TRUE)&
	  requireNamespace("viridis", quietly = TRUE)){
	g<-get("g",envir=envir_stacomi)	+ ggplot2::theme_minimal()
	g+viridis::scale_color_viridis(discrete=TRUE)+
		ggplot2::ggtitle("Cumulated migration step plot 
				at les Enfrenaux eel trap")
	
  }
  ###############################################
# Plots for seasonality of the salmon migration
# using a Loire river dataset (Vichy fishway)
  ################################################
  data("r_mig_interannual_vichy")
# the following show how data are processed to get
# statistics for seaonal migration, daily values
  r_mig_interannual_vichy<-calcule(r_mig_interannual_vichy,
      timesplit="jour",year_choice=2012,silent=TRUE)
#r_mig_interannual_vichy@calcdata #check this to see the results
# statistics for seaonal migration, weekly values
  r_mig_interannual_vichy<-calcule(r_mig_interannual_vichy,timesplit="semaine"
                                   ,year_choice=2012,silent=TRUE)
#r_mig_interannual_vichy@calcdata 
  
# the plot method also runs the calcule method
  plot(r_mig_interannual_vichy,plot.type="seasonal",
      timesplit="semaine", year_choice=2012, silent=TRUE)
  plot(r_mig_interannual_vichy,plot.type="seasonal",
      timesplit="mois", year_choice=2012, silent=TRUE)
  plot(r_mig_interannual_vichy,plot.type="seasonal",
      timesplit="jour",year_choice=2012, silent=TRUE)
  
  
  ###############################################
# Plots for seasonality using another Loire river dataset
# with the migration of Lampreys (Petromyzon marinus) 
# recorded at the the Descarte DF (Vienne)
  ################################################
# run this only if you are connected to the logrami dataset
stacomi(database_expected = TRUE, sch = 'logrami')
  bmi_des<-new("report_mig_interannual")
  bmi_des<-choice_c(bmi_des,
	  dc=c(23),
	  taxa=c("Petromyzon marinus"),
	  stage=c("5"),
	  start_year="2007",
	  end_year="2014",
	  silent=TRUE)
  bmi_des<-connect(bmi_des)	
  bmi_des<-calcule(bmi_des,timesplit="semaine")
  plot(bmi_des,plot.type="seasonal",timesplit="semaine",year_choice=2014)
  plot(bmi_des,plot.type="seasonal",timesplit="jour",year_choice=2014)
  plot(bmi_des,plot.type="seasonal",timesplit="mois",year_choice=2014)

## End(Not run)	

Migration reports for multiple DC / species / stages

Description

Migration counts for several Fish counting devices (DC), several taxa and several stages. This migration count can be built either by the graphical interface or from the command line (see examples).

Slots

dc

An object of class ref_dc-class

taxa

An object of class ref_taxa-class

stage

An object of class ref_stage-class

timestep

An object of class ref_timestep_daily-class

data

A data.frame containing raw data filled by the connect method

calcdata

A 'list' of calculated daily data, one per dc, filled in by the calcule method

coef_conversion

A data frame of daily weight to number conversion coefficients, filled in by the connect method if any weight are found in the data slot.

time.sequence

A POSIXt time sequence

Note

A Migration report comes from a migration monitoring : the fishes are monitored in a section of river, this section is called a control station (station). Most often, there is a dam, one or several fishways (DF) which comprise one or several counting devices (DC). On each counting device, the migration is recorded. It can be either an instant recording (video control) or the use of traps, Operations are monitoring operations during a period. For each operation, several species of fishes can be recorded (samples). In the case of migratory fishes the stage of development is important as it may indicate generic migrations, to and fro, between the river and the sea.

Hence a Multiple Migration report is built from several one or several counting devices (DC), one or several Taxa (Taxon), one or several stages (stage). The migration can be also recorded not as numbers, but in the case of glass eels, as weight, which will be later transformed to number, from daily conversion coefficients. The methods in this class test whether the counts are numbers or another type of quantity. This class makes different calculations than report_mig, it does not handle escapement coefficients, it uses quantities other than numbers if necessary (only used for glass eel in the connect method).

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

Other report Objects: report_annual-class, report_dc-class, report_df-class, report_env-class, report_ge_weight-class, report_mig-class, report_mig_char-class, report_mig_env-class, report_mig_interannual-class, report_sample_char-class, report_sea_age-class, report_silver_eel-class, report_species-class

Examples

library(stacomiR)

stacomi(database_expected=FALSE) 
## launches the application in the command line
## here an example of loading
## the following lines will only run if you have the program installed
## and the iav scheme available in the database
## this example generates the r_mig_mult dataset
# prompt for user and password but you can set appropriate options for host, port and dbname
## Not run: 
  stacomi(
	  database_expected=TRUE)	
if (interactive()){
	if (!exists("user")){
		user <- readline(prompt="Enter user: ")
		password <- readline(prompt="Enter password: ")	
	}	
}
options(					
		stacomiR.dbname = "bd_contmig_nat",
		stacomiR.host ="localhost",
		stacomiR.port = "5432",
		stacomiR.user = user,
		stacomiR.password = password						
)	
  r_mig_mult <- new("report_mig_mult")
  r_mig_mult <- choice_c(r_mig_mult,
	  dc=c(5,6,12),
	  taxa=c("Anguilla anguilla"),
	  stage=c("AGG","AGJ","CIV"),
    datedebut="2011-01-01",
    datefin="2011-12-31")
  r_mig_mult <- charge(r_mig_mult)
  # launching charge will also load classes associated with the report
  # e.g. report_ope, report_df, report_dc
  r_mig_mult <- connect(r_mig_mult)
  # calculations 
  r_mig_mult <- calcule(r_mig_mult,silent=TRUE)

## End(Not run)

# Use this as example if you don't have a connexion to the database
data("r_mig_mult")
# The following re-create the object at the time of loading
# All three classes were created by the charge and connect 
# method of report_mig_mult in the previous example
data("r_mig_mult_ope")
assign("report_ope",r_mig_mult_ope,envir=envir_stacomi)
data("r_mig_mult_df")
assign("report_df",r_mig_mult_df,envir=envir_stacomi)
data("r_mig_mult_dc")
assign("report_dc",r_mig_mult_dc,envir=envir_stacomi)
# use the following to get the raw data loaded by the connect method
# not shown there as the database and program might not be installed

#Individual plot for all DC, taxa and stage where data present



## Not run: 	
plot(r_mig_mult,plot.type="standard",silent=TRUE)
# colors in the following order (glass eel)
# working, stopped, 1...5 types of operation,numbers, weight, 2 unused colors
# for yellow eel and other taxa
# stopped, 1...5 types of operation, ponctuel, expert, calcule,mesure,working,
  plot(r_mig_mult,plot.type="standard",
	  color=c("#DEF76B","#B950B5","#9ABDDA","#781A74","#BF9D6E","#FFC26E",
		  "#A66F24","#012746","#6C3E00","#DC7ED8","#8AA123"),
	  color_ope=c("#5589B5","#FFDB6E","#FF996E","#1C4D76"),
	  silent=TRUE)
#For the following plot, beware, all stages and DC are grouped. This can make sense
# for instance if you want to display the cumulated migration for one species
# in several counting devices located on the same dam...
  plot(r_mig_mult,plot.type="step",silent=TRUE)
  
  
# Combined plot for ggplot2
  plot(r_mig_mult,plot.type="multiple",silent=TRUE)
# Data will be written in the data directory specified in 
# the datawd argument to stacomi, default "~"
  summary(r_mig_mult,silent=FALSE)

## End(Not run)

Report on operations

Description

Operations are monitoring operations generated between two dates. In the case of video monitoring or similar, they can be instantaneous

Objects from the Class

Objects can be created by calls of the form new("report_ope").

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Class 'report_sample_char'

Description

The report_sample_char class is used to load and display sample characteristics, which can be either continuous or discrete variable, for instance, it can be used to analyze size or sex structure during a given period.

Slots

data

A data frame

dc

An object of class ref_dc-class: the control devices

taxa

An object of class ref_taxa-class: the species

stage

An object of class ref_stage-class : the stages of the fish

par

An object of class ref_par-class: the parameters used

horodatedebut

An object of class ref_horodate-class

horodatefin

An object of class ref_horodate-class

Objects from the Class

Objects can be created by calls of the form new('report_sample_char', ...)

Note

This class is displayed by interface_report_sample_char, in the database, the class calls the content of the view vue_lot_ope_car

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

Other report Objects: report_annual-class, report_dc-class, report_df-class, report_env-class, report_ge_weight-class, report_mig-class, report_mig_char-class, report_mig_env-class, report_mig_interannual-class, report_mig_mult-class, report_sea_age-class, report_silver_eel-class, report_species-class

Examples

# launching stacomi without connection to the database
stacomi(	database_expected=FALSE)
# If you have a working database
# the following line of code will create the r_sample_char 
# dataset from the iav (default) schema in the database
## Not run: 
	stacomi(database_expected=TRUE)	# uses default option sch = 'iav'
	# prompt for user and password, you can set these in the options, 
	# including dbname and host
	if (interactive()){
		if (!exists("user")){
			user <- readline(prompt="Enter user: ")
			password <- readline(prompt="Enter password: ")	
		}	
	}
	options(					
			stacomiR.dbname = "bd_contmig_nat",
			stacomiR.host ="localhost",
			stacomiR.port = "5432",
			stacomiR.user = user,
			stacomiR.user = password						
	)	
  #create an instance of the class
  r_sample_char <- new("report_sample_char")
  # the following will load data for size, 
  # parameters 1786 (total size) C001 (size at video control)
  # dc 5 and 6 are fishways located on the Arzal dam
  # two stages are selected
  r_sample_char <- choice_c(r_sample_char,
	  dc=c(5,6),
	  taxa=c("Anguilla anguilla"),
	  stage=c("AGJ","CIV"),
	  par=c(1785,1786,1787,"C001"),
	  horodatedebut="2013-01-01",
	  horodatefin="2013-12-31",
	  silent=FALSE)
  # two warning produced, ignored if silent=TRUE
  r_sample_char <- connect(r_sample_char)
  r_sample_char <- calcule(r_sample_char,silent=TRUE)
  

## End(Not run)	
# load the dataset generated by previous lines
data("r_sample_char")

# A "violin" plot
plot(r_sample_char,plot.type="1",silent=TRUE)
# get the plot from envir_stacomi to change labels for name
# if you use require(ggplot2) the :: argument is not needed
# e.g. write require(ggplot2);g<-get("g",envir=envir_stacomi)
# g+xlab("size")+ylab("year")
if (requireNamespace("ggplot2", quietly = TRUE)){
  g<-get("g",envir=envir_stacomi)
  g+ggplot2::xlab("size")+ggplot2::ylab("year")
}
# A boxplot per month
plot(r_sample_char,plot.type="2",silent=TRUE)
# A xyplot
plot(r_sample_char,plot.type="3",silent=TRUE)

## Not run: 
  
  #####################################
# an example graph created manually from data
  #####################################
# two variables one on DC, one on stage
# passing dc information to the stage variable
  r_sample_char@data$std_libelle[r_sample_char@data$ope_dic_identifiant==5]<-
      "Yellow eel (vert. slot fishway)"
  r_sample_char@data$std_libelle[r_sample_char@data$std_libelle=="Anguille jaune"]<-
      "Yellow eel (ramp)"
  r_sample_char@data$std_libelle[r_sample_char@data$std_libelle=="civelle"]<-
      "Glass eel (ramp)"
# creating a boxplot with custom output : an example
# again if you use require(ggplot2) the :: argument is not needed
  
  if (requireNamespace("ggplot2", quietly = TRUE)){
	g<-ggplot2::ggplot(r_sample_char@data)+
		ggplot2::geom_boxplot(ggplot2::aes(x=annee,
				y =car_valeur_quantitatif,
				fill = std_libelle))+		
		ggplot2::xlab("size")+ggplot2::ylab("year")+
		ggplot2::scale_fill_manual("stage & fishway",
			values=c("Yellow eel (vert. slot fishway)"="blue",
				"Yellow eel (ramp)"="turquoise3",
				"Glass eel (ramp)"="Cyan"))+
		ggplot2::theme_bw()
	print(g)
  }
  
# get a simple summary using Hmisc::describe
  
  summary(r_sample_char)
# get the command line to create the object using choice_c 
# when the graphical interface has been used
  print(r_sample_char)

## End(Not run)

Class "report_sea_age"

Description

the report_sea_age class is used to dispatch adult salmons to age class according to their size and to basin dependent limits set by the user. Once checked with graphs and summary statistics, the results are to be written to the database.

Slots

data

A data frame with data generated from the database

calcdata

A list of dc with processed data. This lists consists of two elements

• (1) data A dataset with age set to be used by the plot and summary methods

• (2) tj_caracteristitiquelot_car A dataset to import into the database

dc

Object of class ref_dc-class: the control devices

taxa

Object of class ref_taxa-class: the species

stage

Object of class ref_stage-class : the stages of the fish

par

Object of class ref_par-class: the parameters used

horodatedebut

An object of class ref_horodate-class

horodatefin

An object of class ref_horodate-class

limit1hm

The size limit, in mm between 1 sea winter fishes and 2 sea winter fishes

limit2hm

The size limit, in mm between 2 sea winter fishes and 3 sea winter fishes

Objects from the Class

Objects can be created by calls of the form new("report_sea_age", ...)

Note

This class is displayed by interface_report_sea_age

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

Other report Objects: report_annual-class, report_dc-class, report_df-class, report_env-class, report_ge_weight-class, report_mig-class, report_mig_char-class, report_mig_env-class, report_mig_interannual-class, report_mig_mult-class, report_sample_char-class, report_silver_eel-class, report_species-class

Examples

require(stacomiR)
stacomi(
	database_expected=FALSE)
# If you have a working database
# the following line of code will create the r_seaa dataset 
# from the logrami schema in the database
## Not run: 
		stacomi(database_expected=TRUE, sch='logrami')	
		# overrides the default option sch = 'iav'
		# prompt for user and password, you can set these in the options,
	  # including dbname and host
		if (interactive()){
			if (!exists("user")){
				user <- readline(prompt="Enter user: ")
				password <- readline(prompt="Enter password: ")	
			}	
		}
		options(					
				stacomiR.dbname = "bd_contmig_nat",
				stacomiR.host ="localhost",
				stacomiR.port = "5432",
				stacomiR.user = user,
				stacomiR.user = password						
		)	
  #create an instance of the class
  r_seaa<-new("report_sea_age")
  r_seaa<-choice_c(r_seaa,
	  dc=c(107,108,101),			
	  horodatedebut="2012-01-01",
	  horodatefin="2012-12-31",
	  limit1hm=675,
	  limit2hm=875,
	  silent=FALSE
  )
  r_seaa<-connect(r_seaa)
  r_seaa<-calcule(r_seaa)
  

## End(Not run)	
# load the dataset generated by previous lines
# Salmons from the loire on two dams
data("r_seaa")
# the calculation will fill the slot calcdata

# stages are in r_seaa@calcdata[["6"]][,"stage"] 
#look at data structure using str(r_seaa@calcdata[["6"]])

# plot data to confirm the split by limits is correct
plot(r_seaa, plot.type=1)

# if there are several dc, data it split by dc
plot(r_seaa, plot.type=2)
## Not run: 
# print a summary statistic, and save the output in a list for later use
  stats<-summary(r_seaa)
  
  
  write_database(r_seaa)

## End(Not run)

Class "report_silver_eel"

Description

the report_silver_eel class is used to calculate various statistics about the silver eel run. It comprises calculation of various maturation index such as Durif's stages and Pankhurst eye index. The objective is to provide standardized output to the stations monitoring the silver eel run.

Slots

data

A data frame with data generated from the database

calcdata

A list of dc with processed data. Each dc contains a data frame with

• (1) qualitative data on body contrast (CONT), presence of punctuation on the lateral line (LINP)

• (2) quantitative data "BL" Body length,"W" weight,"Dv" vertical eye diameter,"Dh" horizontal eye diameter,"FL" pectoral fin length

• (3) calculated durif stages, Pankhurst's index, Fulton's body weight coefficient K_ful

• (4) other columns containing data pertaining to the sample and the control operation: lot_identifiant,ope_identifiant, ope_dic_identifiant,ope_date_debut,ope_date_fin,dev_code (destination code of fish), dev_libelle (text for destination of fish)

dc

Object of class ref_dc-class: the control devices

taxa

An object of class ref_taxa-class: the species

stage

An object of class ref_stage-class : the stages of the fish

par

An object of class ref_par-class: the parameters used

horodatedebut

An object of class ref_horodate-class

horodatefin

An object of class ref_horodate-class

Objects from the Class

Objects can be created by calls of the form new("report_silver_eel", ...)

Note

This class is displayed by interface_report_silver_eel

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

Other report Objects: report_annual-class, report_dc-class, report_df-class, report_env-class, report_ge_weight-class, report_mig-class, report_mig_char-class, report_mig_env-class, report_mig_interannual-class, report_mig_mult-class, report_sample_char-class, report_sea_age-class, report_species-class

Examples

# launching stacomi without selecting the scheme or interface
stacomi(	database_expected=FALSE)
# the following script will load data from the two Anguillere monitored in the Somme

# If you have a working database
# the following line of code will create the r_silver dataset 
# from the "fd80." schema in the database
## Not run: 
	stacomi(database_expected=TRUE, sch="fd80.")	# overrides the default option sch = 'iav'
	# prompt for user and password, you can set these in the options, 
	# including dbname and host
	if (interactive()){
		if (!exists("user")){
			user <- readline(prompt="Enter user: ")
			password <- readline(prompt="Enter password: ")	
		}	
	}
	options(					
			stacomiR.dbname = "bd_contmig_nat",
			stacomiR.host ="localhost",
			stacomiR.port = "5432",
			stacomiR.user = user,
			stacomiR.user = password						
	)	
	
  #create an instance of the class
  r_silver<-new("report_silver_eel")
  r_silver<-choice_c(r_silver,
	  dc=c(2,6),			
	  horodatedebut="2010-09-01",
	  horodatefin="2016-10-04",
	  silent=FALSE)
  r_silver<-connect(r_silver)	

## End(Not run)	
# load the dataset generated by previous lines
data("r_silver")
# the calculation will fill the slot calcdata
r_silver<-calcule(r_silver)
# stages are in r_silver@calcdata[["6"]][,"stage"] 
#look at data structure using str(r_silver@calcdata[["6"]])

# standard plot as drawn by Laurent Beaulaton (Analyse des donnees d'argenture acquises en France)
# showing Durif's stage according to size and eye diameter
plot(r_silver, plot.type=1)

# number per month or year and Durif's stage (year if number of dc >1)
plot(r_silver, plot.type="2")

# plot showing fulton's coefficient, and size weight graphs
# inspired from Acou et al., 2009 
# Differential Production and Condition Indices of Premigrant
# Eels in Two Small Atlantic Coastal Catchments
# of France
plot(r_silver, plot.type="3")
# get a list of summary data and print output to screen

plot(r_silver, plot.type="4")
# print a summary statistic, and save the output in a list for later use
stats<-summary(r_silver)

Counts of number per taxa/stages

Description

This class is used to make the assessment of all species, and their number. It is intended as a simple way to check what fishes are present (taxa + development stage). It was altered to include ref_taxa, to allow excluding some of the most numerous taxa from reports. The taxa is reported unless a taxa has several stages, in which case the different stages for the taxa will be reported Using the split arguments the calc method of the class will count numbers, subsamples are not accounted for in the Overview. The split argument currently takes values year or month. The class is intended to be used over long periods e.g years. The plot method writes either an histogram or a pie chart of number per year/week/month.

Slots

dc

an object of class ref_dc-class

taxa

Object of class ref_taxa-class: the species

start_year

Object of class ref_year-class

end_year

Object of class ref_year-class

data

data.frame

calcdata

data.frame with data processed by the calc method

split

Object of class ref_list-class ref_list referential class choose within a list

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

See Also

Other report Objects: report_annual-class, report_dc-class, report_df-class, report_env-class, report_ge_weight-class, report_mig-class, report_mig_char-class, report_mig_env-class, report_mig_interannual-class, report_mig_mult-class, report_sample_char-class, report_sea_age-class, report_silver_eel-class

Examples

# launching stacomi without selecting the scheme or interface
stacomi(	database_expected=FALSE)
# the following script will load data 
# from the two Anguillere monitored in the Somme
# If you have a working database
# the following line of code will create the bilesp dataset from the "iav." 
# schema in the database

## Not run: 
  bilesp<-new("report_species")
  # split is one of "none", "year", "week", "month
  bilesp<-choice_c(bilesp,
	  dc=c(5,6,12),
	  split="year", 
	  start_year="2008",
	  end_year="2012",
	  silent=FALSE)	
  bilesp <- connect(bilesp)
  bilesp <- calcule(bilesp)
  plot(bilesp, plot.type="pie", silent=FALSE)
  plot(bilesp, plot.type="barplot", silent=FALSE)
  bilesp <- choice_c(bilesp,
	  dc=c(5,6,12),
	  split="month",
	  start_year="2015",
	  end_year="2016",
	  silent=FALSE)
  bilesp <- charge(bilesp)
  bilesp <- connect(bilesp)
  plot(bilesp, plot.type="pie", silent=FALSE)
  plot(bilesp, plot.type="barplot", silent=FALSE)
  #length(unique(bilesp@calcdata$taxa_stage)) # 15
  # here creating a vector of length 15 with nice blending colours
	if (requireNamespace("grDevices", quietly = TRUE)) {
	mycolorrampblue <-
			grDevices::colorRampPalette(c("#395B74", "#010F19"))
	mycolorrampyellow <-
			grDevices::colorRampPalette(c("#B59C53", "#271D00"))
	mycolorrampred <-
			grDevices::colorRampPalette(c("#B56F53", "#270B00"))
  color<-c(mycolorrampblue(5),
	  mycolorrampyellow(5),
	  mycolorrampred(5))
  plot(bilesp,plot.type="barplot",color=color,silent=TRUE)
	}
  summary(bilesp)

## End(Not run)	

Generic method to transform quantitative par into a qualitative one

Description

Generic method to transform quantitative par into a qualitative one

Usage

setasqualitative(object, ...)

Arguments

Author(s)

cedric.briand

Turns a continuous parameter into discrete values

Description

The parm name becomes "parm_discrete". New values are created in the 'data[["parqual"]]' slot of the report and the parqual slot is updated

Usage

## S4 method for signature 'report_mig_char'
setasqualitative(object, par, silent = FALSE, ...)

Arguments

Value

An object of class ref_parquan-class with lines removed from r@data[["parquan"]] and added (after transformation to qualitative values) in r@data[["parqal"]]

Author(s)

Cedric Briand cedric.briand@eptb-vilaine.fr

Create a dataframe suitable for charts per 24h and day

Description

This functions takes a data frame with a column with starting time and another with ending time If the period extends over midnight, it will be split into new lines, starting and ending at midnight

Usage

split_per_day(data, horodatedebut, horodatefin)

Arguments

Value

A data frame with four new columns, Hmin (hour min), Hmax (hmax), xmin (day) and xmax (next day), and new rows

Author(s)

cedric.briand

Examples

datatemp<-structure(list(per_dis_identifiant = c(1L, 1L, 1L), 
per_date_debut = structure(c(1420056600, 
1420071000, 1420081200), class = c("POSIXct", "POSIXt"), tzone = ""), 
per_date_fin = structure(c(1420071000, 1420081200, 1421000000
), class = c("POSIXct", "POSIXt"), tzone = ""), per_commentaires = c("fonct calcul", 
"fonct calcul", "fonct calcul"), per_etat_fonctionnement = c(1L, 
0L, 0L), per_tar_code = 1:3, libelle = c("Fonc normal", "Arr ponctuel", 
"Arr maint")), .Names = c("per_dis_identifiant", "per_date_debut", 
"per_date_fin", "per_commentaires", "per_etat_fonctionnement", 
"per_tar_code", "libelle"), row.names = c(NA, 3L), class = "data.frame")
 newdf<-split_per_day(data=datatemp,horodatedebut="per_date_debut",
horodatefin="per_date_fin")

stacomi Main launcher for program stacomi

Description

When database_expected=FALSE a connection to the database is not expected. Therefore test are run by calling examples object stored in Rdata. To change the language use Sys.setenv(LANG = 'fr') or Sys.setenv(LANG = 'en')

Usage