relationship matrix

breeding values

sex indicator

target gain in inbreeding

If FALSE multiple individuals can be removed at the same type (this is faster but potentially inaccurate!)

Set to FALSE to not display any prints

maximum number of male with positive contributions

maximum number of females with positive contributions

population list

Vector with number of SNP entries coding if each marker is on the array (TRUE/FALSE)

Name of the added array

population list

trait nr. for which to implement a combination of other traits

Weights (only linear combinations of other traits are allowed!)

Name of the trait generated

Matrix

Vector to add to the diagonal of the matrix

Population list

Number of individuals to generate (default: 100)

Proportion of individuals to select in each breeding cycle (default: 0.5)

Generations of individuals to consider as founder pool to start from (default: NULL)

Groups of individuals to consider as founder pool to start from (default: NULL)

Cohorts of individuals to consider as founder pool to start from (default: NULL)

Generations of individuals to consider to calculate target genomic value to get to (default: NULL)

Groups of individuals to consider to calculate target genomic value to get to (default: NULL)

Cohorts of individuals to consider to calculate target genomic value to get to (default: NULL)

Target genomic value to get (default: NULL - calculated based on target.gen/database/cohorts)

Traits that already exceed the target are bred against. Weighting is scaled by this factor.

Name of the newly added cohort

Share of newly added female individuals (default: 0.5)

Generation you want to add the new individuals to (default: 1)

Manual select with traits are supposed to increase / decrease (1 target high, -1 target low)

Set to FALSE to not display any prints

If TRUE store computation times in $info$comp.times.general (default: TRUE)

Set to TRUE to use recalculate.manual to calculate genomic values (all individuals and traits jointly, default: FALSE)

Population to start with as founder pool (default: NULL - generation from pool.gen/database/cohorts)

Default: FALSE. Exporting this is helpful if add.diversity is used frequently to avoid initializing this multiple times

population list

Matrix containing fixed effects (p x k -matrix with p being the number of traits and k being number of fixed effects; default: not fixed effects (NULL))

Set to TRUE to delete previously added fixed effects

population list

Default is to use vanRaden relationship. Alternative is to enter a pedigree-matrix (order of individuals is first male then female)

Generation for which to enter the pedigree-matrix

alpha

kinship-matrix

genomic information matrix

Population list

Quick-insert for database (vector of all generations to export)

Groups of individuals to consider for the export

Quick-insert for database (vector of names of cohorts to export)

Which traits to display

Set to TRUE to also look at offspring pheno

Set to TRUE to extract phenotyping

Population list

Number of the chromosome of the relevant SNP

Number of the relevant SNP

Name of the SNP to analyze

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

bitwise stored SNP sequence

Number of usable bits (default: 30)

Population list

Bit to start on

SNP sequence

Number of usable bits (default: 30)

Population list

Number of selected individuals as parents (default: all individuals in selection.m/f.gen/database/gen - alt: positive numbers)

What to use in the selection process (default: "bve", alt: "bv", "pheno", "random", "offpheno")

Generations/cohorts/groups available for selection of first/paternal parent

Generations available for selection of maternal parent

Maximum number of individual to select from the same family (same sire & dam)

Maximum number of individual to select from the same family (same sire or same dam)

For selection only individuals from this class (included in selection.m/f.gen/database/cohorts) will be considered for selection (default: 0 - which is all individuals if never used class elsewhere)

Initial classes of cohorts used in selection.m/f.cohorts are automatically added to class.m/f (default: TRUE)

Way to handle multiple traits in selection (default: "add" - use values directly in an index, alt: "ranking" - ignore values but only use ranking per trait)

Weighting between traits (default: 1)

Default: "bv_sd"; Set to "pheno_sd" when using gains per phenotypic SD, "unit" when using gains per unit, "bve" when using estimated breeding values

Include avg. kinship to a reference population (selection.index.gen/database/cohorts) as part of the selection index (Default: 0)

Generation/cohorts/groups to use as a reference of the kinship value in the selection index

If FALSE to select individuals with lowest value for the selection criterium (default c(TRUE,TRUE) - (m,w))

Not consider the top individuals of the selected individuals (e.g. to use 2-10 best individuals)

Ratio of the frequency of the selection of the best best individual and the worst best individual (default=1)

Criteria to calculate this ratio (default: "bv", alt: "bve", "pheno")

vector containing probability to draw from for every individual (e.g. c(0.1,0.2,0.7))

Set to FALSE to not use the order from best to worst selected individual but plain order based on database-order

Use this parameter to control the probability of each individual to be selected when doing random selection

Use only a subset of individuals of the potential selected ones ("Split in user-interface")

Selection index on which to access (matrix which one index per row)

Minimum value in the selection index selected individuals have to have

Pick all individuals above (">") the threshold. Alt: ("<", "=", "<=", ">=")

Criterium on which to evaluate the index (default: "bve", alt: "bv", "pheno")

Minimum value in the selection index selected individuals have to have

Pick all individuals above (">") the threshold. Alt: ("<", "=", "<=", ">=")

Set to FALSE to select the same individual multiple times when the gen/database/cohorts for selection contains it multiple times

Use Weighted selection index according to Miesenberger 1997 for paternal/maternal selection

If available reliability estimated are used. If not use default: "derived" (cor(BVE,BV)^2) , alt: "heritability", "estimated" (SD BVE / SD Pheno) as replacement

Ignore all eigenvalues below this threshold and apply dimension reduction (default: 0 - use all)

Set to TRUE to arrange selected individuals according to position in the database (not by breeding value)

If TRUE use optimal genetic contribution theory to perform selection ( This requires the use of the R-package optiSel)

Method to calculate relationship matrix for OGC (Default: "pedigree", alt: "vanRaden", "CE", "non_stand", "CE2", "CM")

Depth of the pedigree in generations (default: 7)

Target of OGC (default: "min.sKin" - minimize inbreeding; alt: "max.BV" / "min.BV" - maximize genetic gain; both under constrains selected below)

This corresponds to the uniform constrain in optiSel

This corresponds to the ub constrain in optiSel

This corresponds to the lb constrain in optiSel

This corresponds to the ub.sKin constrain in optiSel

This corresponds to the lb.BV constrain in optiSel

This corresponds to the ub.BV constrain in optiSel

This corresponds to the eq.BV constrain in optiSel

This corresponds to the upper bound (current sKin + ogc.ub.sKin.increase) as ub.sKin in optiSel

This corresponds to the lower bound (current BV + ogc.lb.BV.increase) as lb.BV in optiSel

Only applicable when TN-version of OGC is available

Only applicable when TN-version of OGC is available

Only applicable when TN-version of OGC is available

Only applicable when B4F-version of OGC is available

Only applicable when B4F-version of OGC is available

Set to FALSE in case no selection of individuals should be performed (just skips some unneccessary computations)

Number of individuals to generate (default: 0, use vector with two entries to control offspring per sex)

Number of litters to generate (default: NULL - use breeding.size; only single positive number input allowed)

Name of the newly added cohort

Share of female individuals (if single value is used for breeding size; default: 0.5)

If TRUE randomly chose sex of new individuals (default: FALSE - use expected values)

Specify which newly added individuals are male (1) or female (2)

Generation you want to add the new individuals to (default: New generation)

Share of individuals newly generated individuals that are genotyped (Default: 0). Also applies if individuals are copied with copy.individual

Starting phenotypes of newly generated individuals (default: "zero", alt: "mean" of both parents, "obs" - regular observation)

Parametrization for the fixed effects (default: c(0,0..,0), if multiple different parametrizations are possible use a matrix with one parametrization per row)

Frequency of each different parametrization of the fixed effects

Migration level of newly generated individuals (default: 0 / use vector for different classes for different sexes)

Maximum number of offspring per individual (default: c(Inf,Inf) - (m,w))

Vector with maximum number of offspring for first/second parent (default: NULL). Order in the vector by order of selection

matrix with first column generation with limited number offspring, second column number of allowed offspring

matrix with first four columns database with limited number offspring, fifth column number of allowed offspring

matrix with first column cohort with limited number offspring, second column number of allowed offspring

Maximum number of litters per individual (default: c(Inf,Inf) - (m,w))

Maximum number of matings between two specific individuals (default: Inf)

Set to TRUE to not generate offspring of full siblings

Set to TRUE to not generate offspring from half or full siblings

Set to TRUE to not generate offspring from parent / sibling matings

Maximum allowed expected inbreeding to allow a mating combination (based on kinships)

Use this to not perform mating between more related potential parents (quantile of all expected inbreeding levels)

Share of mating to at minimum perform for each individual (default: 0)

Maximum allowed expected kinship of an offspring to a reference group of individuals

Maximum allowed expected kinship of an offspring to a reference group of individuals

Gen/database/cohorts of individuals to consider as a reference pool in avoid.mating.kinship

Set to TRUE to use median kinship instead of mean kinship in avoid.mating.kinship (default: FALSE)

Depth of the pedigree to calculate expected inbreeding levels / kinships

Set to TRUE to automatically exclude any selected individuals from the sample of parents

Set to value higher 0 for avoid.mating.inb/kinship restrictions to not always be applied

Number of sampling attempts to avoid unwanted matings (( last couple of individuals otherwise can have unwanted relatedness, default = 1000))

Set of targeted matings to perform (matrix with 7 columns: database position first parent (gen, sex, nr), database position second parent (gen,sex,nr), likelihood to be female (optional))

Perform targeted matings in the group of selected individuals (matrix with 5 columns: position first parent (male/female pool of selected individuals, ranking in selected animals), position second parent (male/female pool of selected individuals, ranking in selected animals), likelihood to be female (optional))

Set of target matings to perform (matrix with 3 columns: id first parent, id second parent, likelihood to be female (optional))

Set to "bestbest" / TRUE for targeted mating of best-best individual till worst-worst (of selected). set to "bestworst" for best-worst mating

Set to TRUE to automatically perform each mating combination possible exactly ones.

Generate multiple mating from the same dam/sire combination (first column: number of offspring; second column: probability)

Generate multiple copies from a copy action (combine / copy.individual.m/f) (first column: number of offspring; second column: probability)

Vector containing number of times each mating is repeated. This will overwrite sampling from repeat.mating / repeat.mating.copy (default: NULL)

Set to FALSE to not use the current repeat.mating / repeat.mating.copy input as the new standard values (default: TRUE)

Trait that should be linked to the litter size

Maximum number of individuals in a litter

Use this parameter to manually provide the size of each litter generated

If TRUE allow matings of individuals of same sex (Sex here is a general term with the first sex referring to the first parent, second sex second parent)

Probability to use female individuals as parents (default: 0.5)

Set to TRUE to allow for selfing when using same.sex matings (default: FALSE)

If TRUE generate new individuals via selfing

Share of female individuals used for selfing (default: 0.5)

If TRUE generate a DH-line in mating process

Share of DH-lines generated from selected female individuals

Copy existing individuals (e.g. to merge individuals from different groups in a joined cohort). Individuals to use are used as the first parent

Set TRUE to generate a copy of an already existing individual. If only one of the sexes has individuals to select from it will automatically detect with sex to chose. Otherwise the first/male parent will be copied

If TRUE generate exactly one copy of all selected male/female in a new cohort (or more by setting breeding.size)

Set to FALSE to not keep estimated breeding value in case of use of copying individuals instead of regular meiosis

Set to FALSE to not keep phenotypes in case of use of copying individuals instead of regular meiosis

(OLD! use share.genotyped) Share of individuals that is additionally genotyped (only for copy.individual, default: 0)

Vector of traits to ignore in the calculation of the genomic value (default: NULL; Only recommended for high number of traits and experienced users!)

Number of cores used for the generation of new individuals (This will only be active when generating more than 500 individuals)

Set to TRUE to delete not necessary individuals during parallelization

Share of errors in the pedigree (default: 0; vector with two entries for errors on male/female side)

Share of individuals with unknown parents (default: 0; vector with two entries for differences in unknown-share between male/female side)

Generations/cohorts/groups to generate genotype data (that can be used in a BVE)

Share of individuals in genotyped.gen/database/cohort to generate genotype data from (default: 1)

Genotyping array used

Generations/cohorts/groups from which to remove genotyping information (this will affect all copies of an individual unless genotyped.remove.all.copy is set to FALSE)

Set to FALSE to only change the genotyping state of this particular copy of an individual (default: TRUE)

Set to TRUE to genotype all selected individuals

Quick access to phenotyping for (all: "all", non-phenotyped: "non_obs", non-phenotyped male: "non_obs_m", non-phenotyped female: "non_obs_f")

Generations/cohorts/groups from which to generate additional phenotypes

Number of phenotypic observations generated per trait and per individuals (use repeatability to control correlation between observations)

Classes of individuals for which to generate phenotypes (default: NULL –> all classes)

Use sigma.e to obtain a certain heritability (default: NULL)

Set this to control the share of the residual variance (sigma.e) that is permanent (there for each observation)

If an already phenotyped trait is phenotyped again this will on NOT lead to an additional phenotyped observation unless this is set to TRUE

Set to TRUE to phenotype all selected individuals

Share of the individuals to phenotype (use vector for different probabilities for different traits)

Generations/groups/cohorts to consider to derive phenotype from offspring phenotypes

Active generations/cohorts/groups for import of offspring phenotypes

Enviromental standard deviation (default: use sigma.e from last run / usually fit by use of heritability; if never provided: 10; used in BVE for variance components if manually set)

Generations/cohorts/groups to consider when estimating sigma.e when using heritability

Correlation of the simulated residual variance

Correlation of the simulated genetic variance (only impacts non-QTL based traits. Needs to be fit in creating.diploid/trait for QTL-based traits)

Additional input parameter for phenotypic transformation function

If TRUE perform a breeding value estimation (default: FALSE)

Generations/Groups/Cohorts of individuals to consider in breeding value estimation (default: NULL)

Method to calculate relationship matrix for the breeding value estimation. This will automatically chosen between GBLUP, ssGBLUP, pBLUP based on if genotyped individuals are available (Default: "GBLUP", alt: "pedigree", "CE", "non_stand", "CE2", "CM")

Depth of the pedigree in generations (default: 7)

Set FALSE remove all individuals without genomic data from the breeding value estimation

Vector of traits to ignore in the breeding value estimation (default: NULL, use: "zero" to not consider traits with 0 index weight in selection.index.weights.m/.w)

Array to use in the breeding value estimation (default: NULL; chose largest possible based on used individuals in BVE)

Set to FALSE to not perform imputation up to the highest marker density of genotyping data that is available

Share of errors in the imputation procedure (default: 0)

Set to TRUE to act as if every individual in the breeding value estimation has been genotyped

Generations/Groups/Cohorts of individuals to compute breeding values for (default: all groups in bve.database)

Correct for "parental.mean" or "generation.mean" in the estimation of sigma.g for BVE / sigma.e estimation (default: "none")

Consider only individuals of those class classes in breeding value estimation (default: NULL - use all)

Genetic standard deviation (default: calculated based on individuals in BVE ; used in BVE for variance components if manually set; mostly recommended to be used for non-QTL based traits)

Generations/cohorts/groups to consider when estimating sigma.g

Set FALSE to not estimate sigma.g (Default: TRUE // in case sigma.g is set this is automatically set to FALSE)

If TRUE remove real QTLs in breeding value estimation

If TRUE estimate additive genetic variance and heritability based on parent model

If TRUE estimate total variance in breeding value estimation

If set to FALSE multiple generations of the same individual can be used in the bve (only possible by using copy.individual to generate individuals)

Set TRUE to calculate a reliability when performing Direct-Mixed-Model BVE

Set TRUE to estimate the reliability in the BVE by calculating the correlation between estimated and real breeding values

Select what to use in BVE (default: own phenotype ("own"), offspring phenotype ("off"), their average ("mean") or a weighted average ("weighted"))

If TRUE use marker assisted selection in the breeding value estimation

Vector containing markers to be used in marker assisted selection

If no markers are provided this nr of markers is selected (if single marker QTL are present highest effect markers are prioritized)

Effects assigned to the MAS markers (Default: estimated via lm())

Genotype dataset used in MAS (default: NULL, automatic internal calculation)

Set to TRUE to use the average parental performance as the breeding value estimate

Set to TRUE to use the average grandparental performance as the breeding value estimate

Select if you want to use the "bve", "bv", "pheno" or "bvepheno" to form the mean (default: "bvepheno" - if available bve, else pheno)

Vector of fixed effects to ignore in the BVE (default: NULL)

Set to FALSE to use the true underlying value for beta_hat for the fixed effect in the direct BVE model. rrBLUP, BGLR, sommer will always estimate beta_hat.

Set to FALSE to deactivate the use of a heritability based on the number of observations generated per sample

Vector of allele frequencies to be used when calculating the genomic relationship matrix (default: calculate them based on Z)

Generations/cohorts/groups to use when manually calculating allele frequencies for genomic relationship matrix

Set to TRUE to exclude non-genotyped individuals when calculating allele frequencies for genomic relationship matrix standardization

Set to TRUE to use phenotypes and genotyped status from all copies of an individual instead of just the provided ones in the bve.gen/database/cohorts (default: FALSE)

Set to FALSE to ignore/correct for any pedigree errors

If TRUE predict BVEs in direct estimation with assumed known heritability (default: TRUE; activating use of any other BVE method to TRUE will overwrite this)

Set to TRUE to activate breeding value estimation via MiXBLUP (requires MiXBLUP license!)

Set to TRUE to activate breeding value estimation via BLUPF90 (requires blupf90 software!)

Set to TRUE to activate breeding value estimation via MiXBLUP (requires MiXBLUP license!)

If TRUE use REML estimator from R-package EMMREML in breeding value estimation

If TRUE use REML estimator from R-package rrBLUP in breeding value estimation

If TRUE use REML estimator from R-package sommer in breeding value estimation

Set TRUE to use a multi-trait model in the R-package sommer for BVE

If TRUE use BGLR to perform breeding value estimation

If set to TRUE the breeding value estimation will be simulated with resulting accuracy pseudo.bve.accuracy (default: 1)

The accuracy to be obtained in the "pseudo" - breeding value estimation

Provide solver to be used in BVE (default: "exact" solution via inversion, alt: "pcg", function with inputs A, b and output y_hat)

Set to TRUE to use Jeremies suggested MiXBLUP settings

Set to TRUE to use hpblup in MiXBLUP (default: FALSE)

Set to FALSE to manually generate your MiXBLUP pedfile

Set to FALSE to manually generate your MiXBLUP parfile

Set to FALSE to manually write your MiXBLUP datafile

Set to FALSE to manually write your MiXBLUP inputfile

Set to FALSE to manually write the MiXBLUP genotypefile

Provide path to MiXBLUP.exe (default is your working directory: Windows: MixBLUP; Linux ./MixBLUP.exe)

Path from where to import the MiXBLUP pedfile

Path from where to import the MiXBLUP parfile

Path from where to import the MiXBLUP datafile

Path from where to import the MiXBLUP inputfile

Path from where to import the MiXBLUP genofile

Path from where to import the MiXBLUP genofile

Directory to generate all files generated when using MiXBLUP (default: MiXBLUP_files/ )

Set to TRUE to display MiXBLUP prints

Set to TRUE to display blupf90 prints

Provide genetic covariance matrix to be used in MiXBLUP (lower-triangle is sufficent) (default: underlying true values)

Provide residual covariance matrix to be used in MiXBLUP (lower-triangle is sufficent) (default: underlying true values)

Lambda parameter in MiXBLUP (default: 1)

Alpha parameter in MiXBLUP (default: 0.95, with alpha + beta = 1 , warning: MiXBLUP software this is 1)

Beta parameter in MiXBLUP (default: 0.05, with alpha + beta = 1 , warning: MiXBLUP software this is 0)

Omega parameter in MiXBLUP (default: mixblup.lambda)

!Maxit qualifier in MiXBLUP (default: 5.000)

!STOPCRIT qualifier in MiXBLUP (default: not used, suggested value 1.E-4 for ssGBLUP) // will overwrite maxit

!MAF qualifier in MiXBLUP (default: 0.005)

Numproc parameter in MiXBLUP (default: not set // 1)

Set to TRUE to use APY inverse in MiXBLUP (default: FALSE)

Number of core individuals in the APY algorithm (default: 5000)

Set to TRUE to use the !Ta flag in MixBLUP

Set to TRUE to use the !TAC flag in MixBLUP

Set to TRUE to skip the actually system call to MiXBLUP and only write the MiXBLUP files

Set to TRUE to skip the actually system calls of blupf90 and only write the blupf90 input files

Set to TRUE to set the !RESTART flag in MiXBLUP (requires a "Solunf" file in the working directory)

Set to TRUE to set the !NOPEEK flag in MiXBLUP

Set to TRUE to set the !CalcInbr flag to S

Set to TRUE to write multiple phenotypic records for an individual

Set TRUE to just extent the existing genotype file instead of writting it completely new

Set TRUE to set debugging flags for mixblup call (-Dmst > mixblup_debug.log) (default: FALSE)

Set TRUE to write genotype files in PLINK format (requires R-package genio, default: FALSE)

Delete all mixblup output files above the indicated size after MiXBLUP run completes (default: Inf)

Set to FALSE to manually generate your MiXBLUP pedfile

Set to FALSE to manually generate your MiXBLUP parfile

Set to FALSE to manually generate your blupf90 datafile

Set to FALSE to manually write your MiXBLUP inputfile

Set to FALSE to manually write the blupf90 genotypefile

Set TRUE to use DGV-PBLUP (Only applicable with TAC-BLUP)

Path of allele frequency file for DGV-PBLUP

Path of SNP effect file for DGV-PBLUP

Provide path to blupf90 (default is your working directory: Windows: ./blupf90+.exe ; Linux ./blupf90+.exe)

Provide path to blupf90 (default is your working directory: Windows: ./renumf90.exe ; Linux ./renumf90.exe)

Path from where to import the blupf90 pedfile

Path from where to import the blupf90 parfile

Path from where to import the blupf90 data file

Path from where to import the blupf90 inputfile

Path from where to import the blupf90 genotype file

Directory to generate all files generated when using blupf90 (default: blupf90_files/ )

blupf90 parameter blksize (Default: number of traits)

blupf90 setting OPTION no_quality_control (Default: FALSE)

blupf90 parameter conv_crit (Default: blupf90 default)

Select which BGLR model to use (default: "RKHS", alt: "BRR", "BL", "BayesA", "BayesB", "BayesC")

Number of burn-in steps in BGLR (default: 1000)

Number of iterations in BGLR (default: 5000)

If TRUE set verbose to TRUE in BGLR

Method to use in BGLR (default: "RKHS" - alt: NON currently)

Add random number to store location of internal BGLR computations (only needed when simulating a lot in parallel!)

If TRUE use miraculix to perform computations (ideally already generate population in creating.diploid with this; default: automatic detection from population list)

Number of cores used in miraculix applications (default: 1)

If TRUE use miraculix for matrix multiplications even if miraculix is not used for storage

Set to FALSE to deactive miraculix based Cholesky-decomposition (default: TRUE)

If FALSE A will not be destroyed in the process of inversion (less computing / more memory)

If TRUE estimate u in breeding value estimation (Y = Xb + Zu + e)

Set to FALSE to derive inverse of A in rrBLUP (only required when this becomes numerical unstable otherwise)

If TRUE estimate u via GWAS (relevant for gene editing)

If FALSE calculate the variance for each marker separatly instead of using a set variance (does not change order - only p-values)

Generations/cohorts/groups to consider in GWAS analysis

If TRUE standardize phenotypes by group mean

What y value to use in GWAS study (Default: "pheno", alt: "bv", "bve")

If TRUE perform gene editing on newly generated individuals

If TRUE perform gene editing on selected individuals

Which sex to perform editing on (Default c(TRUE,TRUE), mw)

Which sex to perform editing on (Default c(TRUE,TRUE), mw)

Number of edits to perform per individual

Set TRUE to cull all non-selected individuals (default: FALSE)

Generations/cohorst/groups to consider to culling

Default: 0, can be set to code different type of culling reasons (e.g. 0 - aging, 1 - selection, 2 - health)

Age of the individuals at culling // use time.point if the age of individuals is variable and culling is executed on individuals of different ages culled at the same time

Name of the culling action (user-interface stuff)

Reference Breeding value

Probability of death for individuals with bv1

Alternative breeding value (linear extended for other bvs)

Probability of death for individuals with bv2

Genomic index (default:0 - no genomic impact, use: "lastindex" to use the last selection index applied in selection)

Set to FALSE to not apply the culling module on all individuals of the cohort

Set to FALSE to not kill copies of the same individual in the culling module

Mutation rate in each marker (default: 10^-8)

Remutation rate in each marker (default: 10^-8)

Average number of recombination per 1 length unit (default: 1M)

Select a trait which BV will be used as a scalar for the expected number of recombination (default: 0)

Function used to calculate position of recombination events (default: MoBPS::recombination.function.haldane())

Minimum distance between two points of recombination (default: 0)

Reduced probability for recombination events closer than this value - linear penalty (default: 0)

Reduced probability for recombination events closer than this value - quadratic penalty (default: 0)

Use step function for recombination map (transform snp.positions if possible instead)

Function to calculate recombination point into adjacent/following SNP

Share of recombination points with a duplication (default: 0 - DEACTIVATED)

Average length of a duplication (Exponentially distributed)

Average number of recombinations per 1 length uit of duplication (default: 1)

Genetic architecture for male/female individuals (default: 0 - no transformation)

List with two vectors containing (A: length of chromosomes, B: position in cM of SNPs)

Chose which function will be used for simulation of meiosis (default: 0, alt: 1,2) - can be faster for specific cases

Generations for with haplotypes of founders can be deleted from population list for memory reduction (default: NULL)

Generations for which recombination points can be deleted from the population list for memory reduction (default: NULL)

Set TRUE to only remove points of recombination for non-genotyped individuals

Set TRUE to only remove points of recombination for individuals from a specific class

Generations for with individuals are completely deleted from population list for memory reduction (default: NULL)

Generations to entirely deleted fro population list for memory reduction (default: NULL)

Remove all individuals from these sex from generation delete.individuals (default: 1:2 ; note:delete individuals=NULL)

If TRUE delete recombination points when genetic origin of adjacent segments is the same

If TRUE store the time point of each recombination event

Set to TRUE to store the pedigree relationship matrix as a sparse matrix

Lower numbers will lead to less memory but slightly higher computing time for calculation of the pedigree relationship matrix (default: 1.5, min: 1)

Set to FALSE to not display any prints

Report the accuracy of the breeding value estimation

If TRUE store information on selected individuals in $info$breeding.totals (default: FALSE)

If TRUE store information of bve in $info$bve.data

If TRUE store computation times in $info$comp.times.general (default: TRUE)

If TRUE store computation times of breeding value estimation in $info$comp.times.bve (default: TRUE)

If TRUE store computation times of mating simulations in $info$comp.times.generation (default: TRUE)

If TRUE store the allele frequency of effect markers per generation

Store computation times of each function

Set random seed of the process

Set FALSE to not display progress bars. Setting verbose to FALSE will automatically deactive progress bars

Time point at which the new individuals are generated

Time point at which the new individuals are born (default: time.point - mostly useful in the founder generation)

Technique to generate new individuals (use mostly intended for web-based application)

Input the wanted relationship matrix with this parameter (default: NULL - relationship matrix will be calculated from other sources)

Set to TRUE to export the list of selected individuals

Set to TRUE to export a database of the selected individuals

Export the relationship matrix used in the breeding value estimation

This is a placeholder to deactivate this module for now

Pen size. When different types of pen are used: use a matrix with two columns coding Number of individuals per pen, Probability for each pen size

Only individuals of the same sex are put in the same pen (default: TRUE)

Only individuals of the same litter are put in the same pen (default: FALSE)

Set to FALSE to not use the input for pen.size for down-stream use of breeding.diploid (default: TRUE)

(OLD! use selection criteria) Selection criteria for male/female individuals (Set to "random" to randomly select individuals - default: "function" based on selection.criteria ((usually breeding values)))

(OLD! use phenotyping.gen/cohorts/database) Vector of generation from which to generate additional phenotypes

(OLD!- use selection.m.database/cohorts) Groups of individuals to consider as First Parent / Father (also female individuals are possible)

(OLD!- use selection.f.database/cohorts) Groups of individuals to consider as Second Parent / Mother (also male individuals are possible)

(OLD! - use phenotyping) Quick access to phenotyping for (all: "all", non-phenotyped: "non_obs", non-phenotyped male: "non_obs_m", non-phenotyped female: "non_obs_f")

(OLD! - use culling modules) Groups of individuals for reduce to a new size (by changing class to -1)

(OLD! - use culling modules) Selection criteria for reduction of groups (cf. selection.m / selection.f - default: "random")

(OLD! - use phenotyping.child) Starting phenotypes of newly generated individuals (default: "zero", alt: "mean" of both parents, "obs" - regular observation)

(OLD! - use relationship.matrix) Method to calculate relationship matrix for the breeding value estimation (Default: "vanRaden", alt: "pedigree", "CE", "non_stand", "CE2", "CM")

(OLD! use relationship.matrix.ogc) Method to calculate pedigree matrix in OGC (Default: "pedigree", alt: "vanRaden", "CE", "non_stand", "CE2", "CM")

(OLD! - use new.residual.correlation!) Correlation of the simulated enviromental variance

(OLD! use offpheno.parents.gen/database/cohorts) Generations/cohorts/groups to consider to derive phenotype from offspring phenotypes

(OLD! use offpheno.offspring.gen/database/cohorts) Active generations/cohorts/groups for import of offspring phenotypes

(OLD! use bve.input.phenotype) Select what to use in BVE (default: own phenotype ("own"), offspring phenotype ("off"), their average ("mean") or a weighted average ("weighted"))

(OLD! use selection.index.weights.m/f) Weighting between traits (default: 1)

(OLD! use selection.index.scale.m/f) Default: "bv_sd"; Set to "pheno_sd" when using gains per phenotypic SD, "unit" when using gains per unit, "bve" when using estimated breeding values

Set to TRUE to use recalculate.manual to calculate genomic values (all individuals and traits jointly, default: FALSE)

Maximum number of individuals to process at the same time (( genotypes are in memory ))

compute share of genome inherited from each grandparent based on recombination points (default: FALSE)

Set to value to scale all input for breeding.size / selection.size (This will not work for all breeding programs / less general than json.simulation)

Internal parameter for the parallelization

Experimental parameter for Tobias Niehoff (do not touch!)

Set to FALSE to not compute genetic gains compared to previous generation (selection)

Id to assign to first next individual generated

Use this to skip copying some entries from the internal storage ((minor speed up))

position of the parent in the dataset

list of information regarding the parent

Population list

Mutation rate in each marker (default: 10^-5)

Remutation rate in each marker (default: 10^-5)

Average number of recombination per 1 length unit (default: 1M)

Use step function for recombination map (transform snp.positions if possible instead)

Share of recombination points with a duplication (default: 0 - DEACTIVATED)

Average length of a duplication (Exponentially distributed)

Average number of recombinations per 1 length uit of duplication (default: 1)

If TRUE delete recombination points when genetic origin of adjacent segments is the same

If TRUE perform gene editing on newly generated individual

Number of edits to perform per individual

Used underlying genetic architecture (genome length in M)

Used function for the decoding of genetic origins [[5]]/[[6]]

Function used to calculate position of recombination events (default: MoBPS::recombination.function.haldane())

Internal parameter to check if duplications have to be simulated

Internal parameter to check if RTs have to be simulated

Internal parameter to check if grandsibling contributions have to be calculated

position of the parent in the dataset

list of information regarding the parent

Population list

Mutation rate in each marker (default: 10^-5)

Remutation rate in each marker (default: 10^-5)

Average number of recombination per 1 length unit (default: 1M)

Use step function for recombination map (transform snp.positions if possible instead)

Share of recombination points with a duplication (default: 0 - DEACTIVATED)

Average length of a duplication (Exponentially distributed)

Average number of recombinations per 1 length uit of duplication (default: 1)

If TRUE delete recombination points when genetic origin of adjacent segments is the same

If TRUE perform gene editing on newly generated individual

Number of edits to perform per individual

Used underlying genetic architecture (genome length in M)

Used function for the decoding of genetic origins [[5]]/[[6]]

Function used to calculate position of recombination events (default: MoBPS::recombination.function.haldane())

Internal parameter to check if duplications have to be simulated

Internal parameter to check if RTs have to be simulated

Internal parameter to check if grandsibling contributions have to be calculated

position of the parent in the dataset

list of information regarding the parent

Population list

Mutation rate in each marker (default: 10^-5)

Remutation rate in each marker (default: 10^-5)

Average number of recombination per 1 length unit (default: 1M)

Use step function for recombination map (transform snp.positions if possible instead)

Share of recombination points with a duplication (default: 0 - DEACTIVATED)

Average length of a duplication (Exponentially distributed)

Average number of recombinations per 1 length uit of duplication (default: 1)

If TRUE delete recombination points when genetic origin of adjacent segments is the same

If TRUE perform gene editing on newly generated individual

Number of edits to perform per individual

Used underlying genetic architecture (genome length in M)

Used function for the decoding of genetic origins [[5]]/[[6]]

Function used to calculate position of recombination events (default: MoBPS::recombination.function.haldane())

Internal parameter to check if duplications have to be simulated

Internal parameter to check if RTs have to be simulated

Internal parameter to check if grandsibling contributions have to be calculated

position of the parent in the dataset

list of information regarding the parent

Population list

Mutation rate in each marker (default: 10^-5)

Remutation rate in each marker (default: 10^-5)

Average number of recombination per 1 length unit (default: 1M)

Use step function for recombination map (transform snp.positions if possible instead)

Share of recombination points with a duplication (default: 0 - DEACTIVATED)

Average length of a duplication (Exponentially distributed)

Average number of recombinations per 1 length uit of duplication (default: 1)

If TRUE delete recombination points when genetic origin of adjacent segments is the same

If TRUE perform gene editing on newly generated individual

Number of edits to perform per individual

Used underlying genetic architecture (genome length in M)

Used function for the decoding of genetic origins [[5]]/[[6]]

Function used to calculate position of recombination events (default: MoBPS::recombination.function.haldane())

Internal parameter to check if duplications have to be simulated

Internal parameter to check if RTs have to be simulated

Internal parameter to check if grandsibling contributions have to be calculated

position of the parent in the dataset

list of information regarding the parent

Population list

Mutation rate in each marker (default: 10^-5)

Remutation rate in each marker (default: 10^-5)

Average number of recombination per 1 length unit (default: 1M)

Use step function for recombination map (transform snp.positions if possible instead)

Share of recombination points with a duplication (default: 0 - DEACTIVATED)

Average length of a duplication (Exponentially distributed)

Average number of recombinations per 1 length uit of duplication (default: 1)

If TRUE delete recombination points when genetic origin of adjacent segments is the same

If TRUE perform gene editing on newly generated individual

Number of edits to perform per individual

Used underlying genetic architecture (genome length in M)

Used function for the decoding of genetic origins [[5]]/[[6]]

Function used to calculate position of recombination events (default: MoBPS::recombination.function.haldane())

Internal parameter to check if duplications have to be simulated

Internal parameter to check if RTs have to be simulated

Internal parameter to check if grandsibling contributions have to be calculated

position of the parent in the dataset

list of information regarding the parent

Population list

Mutation rate in each marker (default: 10^-5)

Remutation rate in each marker (default: 10^-5)

Average number of recombination per 1 length unit (default: 1M)

Use step function for recombination map (transform snp.positions if possible instead)

Share of recombination points with a duplication (default: 0 - DEACTIVATED)

Average length of a duplication (Exponentially distributed)

Average number of recombinations per 1 length uit of duplication (default: 1)

If TRUE delete recombination points when genetic origin of adjacent segments is the same

If TRUE perform gene editing on newly generated individual

Number of edits to perform per individual

Used underlying genetic architecture (genome length in M)

Used function for the decoding of genetic origins [[5]]/[[6]]

Function used to calculate position of recombination events (default: MoBPS::recombination.function.haldane())

Internal parameter to check if duplications have to be simulated

Internal parameter to check if RTs have to be simulated

Internal parameter to check if grandsibling contributions have to be calculated

position of the parent in the dataset

list of information regarding the parent

Population list

Mutation rate in each marker (default: 10^-5)

Remutation rate in each marker (default: 10^-5)

Average number of recombination per 1 length unit (default: 1M)

Use step function for recombination map (transform snp.positions if possible instead)

Share of recombination points with a duplication (default: 0 - DEACTIVATED)

Average length of a duplication (Exponentially distributed)

Average number of recombinations per 1 length uit of duplication (default: 1)

If TRUE delete recombination points when genetic origin of adjacent segments is the same

If TRUE perform gene editing on newly generated individual

Number of edits to perform per individual

Used underlying genetic architecture (genome length in M)

Used function for the decoding of genetic origins [[5]]/[[6]]

Function used to calculate position of recombination events (default: MoBPS::recombination.function.haldane())

Internal parameter to check if duplications have to be simulated

Internal parameter to check if RTs have to be simulated

Internal parameter to check if grandsibling contributions have to be calculated

position of the parent in the dataset

list of information regarding the parent

Population list

Mutation rate in each marker (default: 10^-5)

Remutation rate in each marker (default: 10^-5)

Average number of recombination per 1 length unit (default: 1M)

Use step function for recombination map (transform snp.positions if possible instead)

Share of recombination points with a duplication (default: 0 - DEACTIVATED)

Average length of a duplication (Exponentially distributed)

Average number of recombinations per 1 length uit of duplication (default: 1)

If TRUE delete recombination points when genetic origin of adjacent segments is the same

If TRUE perform gene editing on newly generated individual

Number of edits to perform per individual

Used underlying genetic architecture (genome length in M)

Used function for the decoding of genetic origins [[5]]/[[6]]

Function used to calculate position of recombination events (default: MoBPS::recombination.function.haldane())

Internal parameter to check if duplications have to be simulated

Internal parameter to check if RTs have to be simulated

Internal parameter to check if grandsibling contributions have to be calculated

position of the parent in the dataset

list of information regarding the parent

Population list

Mutation rate in each marker (default: 10^-5)

Remutation rate in each marker (default: 10^-5)

Average number of recombination per 1 length unit (default: 1M)

Use step function for recombination map (transform snp.positions if possible instead)

Share of recombination points with a duplication (default: 0 - DEACTIVATED)

Average length of a duplication (Exponentially distributed)

Average number of recombinations per 1 length uit of duplication (default: 1)

If TRUE delete recombination points when genetic origin of adjacent segments is the same

If TRUE perform gene editing on newly generated individual

Number of edits to perform per individual

Used underlying genetic architecture (genome length in M)

Used function for the decoding of genetic origins [[5]]/[[6]]

Function used to calculate position of recombination events (default: MoBPS::recombination.function.haldane())

Internal parameter to check if duplications have to be simulated

Internal parameter to check if RTs have to be simulated

Internal parameter to check if grandsibling contributions have to be calculated

population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Draw confidence intervals for (1- bv, 2- bve, 3- pheno; default: c(1,2,3))

Include development of (1- bv, 2- bve, 3- pheno; default: c(1,2,3))

Quantile of the confidence interval to draw (default: 0.05)

Which traits to display (for multiple traits separate plots (par(mfrow)))

Cohorts with only 0 individuals are not displayed (default: TRUE)

If TRUE extract which cohorts to plot according to the json-file used in json.simulation

Set TRUE to use time point of generated to sort groups

Set TRUE to show Breedingtype used in generation (web-interface)

Set TRUE to display the name of the cohort in the x-axis

Set TRUE to display the creating.type (Shape of Points - web-based-application)

Equal distance between groups (independent of time.point)

Set TRUE to order cohorts according to the time point of generation

Set FALSE to not display the line connecting cohorts

Set this to fix the y-axis of the plot

Set TRUE to not use mfrow - use for custom plots

population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Which traits to display (for multiple traits separate plots (par(mfrow)))

If TRUE extract which cohorts to plot according to the json-file used in json.simulation

Choose between "bv", "pheno", "bve" (default: "bv")

Display lines between generated cohorts via selection (webinterface)

Display lines between generated cohorts via reproduction (webinterface)

Set this to fix the y-axis of the plot

Set TRUE to not use mfrow - use for custom plots

Population list

Target mean

Target variance

Quick-insert for database (vector of all generations to export)

Groups of individuals to consider for the export

Quick-insert for database (vector of names of cohorts to export)

Modify previous breeding value estimations by scaling (default: TRUE)

Modify previous phenotypes by scaling (default: TRUE)

Set to TRUE to display prints

Set to TRUE to have no effect on the 0 genotype (or 00 for QTLs with 2 underlying SNPs)

Set to TRUE to scale sigma.e values used based on scaling

Use this parameter to only perform scaling of these traits (alternatively set values in mean/var.target to NA, default: all traits)

Population list

Generation of the individual of interest

Sex of the individual of interest

Number of the individual of interest

traits to consider

Function to calculate recombination point into adjacent/following SNP

Used function for the decoding of genetic origins [[5]]/[[6]]

If TRUE store the allele frequency of effect markers per generation

Set to TRUE if the MoBPS (not-miraculix! bit-storing is used)

Bits available in MoBPS-bit-storing

Set to TRUE to get a miraculix-compressed genotype/haplotype

Vector of traits to ignore in the calculation of the genomic value (default: NULL; Only recommended for high number of traits and experienced users!)

Population list

position of the first parent in the dataset

position of the second parent in the dataset

maximal allowed relationship (default: 2, alt: 1 no full-sibs, 0 no half-sibs)

Set to TRUE to avoid matings of an individual to its parents

Internal parameter (avoid.mating.parent check)

Population list

Generations to clean up (default: "current")

Groups of individuals to consider

Quick-insert for database (vector of names of cohorts to export)

Origins matrix

Population list

Vector containing the traits (numbers) to combine into a joined trait

Name of the combined trait

Remove a selected previously generated combined trait

Set TRUE to remove all previously generated combined traits

population-list

Costs for the generation of a phenotype

Costs for the generation of a genotype

one time occurring fixed costs

annually occurring fixed costs

profit generated by bv per animal

Groups of individuals to consider

Quick-insert for database (vector of all generations to consider)

Quick-insert for database (vector of names of cohorts to consider)

Applied yearly interest rate

Base generation (application of interest rate)

population-list

Quick-insert for database (vector of all generations to consider)

Groups of individuals to consider

Quick-insert for database (vector of names of cohorts to consider)

If TRUE extract which cohorts to plot according to the json-file used in json.simulation

Costs for the generation of a phenotype

Costs for the generation of a genotype

Costs for housing

one time occurring fixed costs

annually occurring fixed costs

profit generated by bv per animal

Applied yearly interest rate

Set to FALSE to not display any prints

Population list

Generation of the individual to compute

Gender of the individual to compute

Number of the individual to compute

If FALSE use slower version to compute markers between recombination points

Function to calculate recombination point into adjacent/following SNP

First SNP to consider

Last SNP to consider

Used function for the decoding of genetic origins [[5]]/[[6]]

Set to TRUE if the MoBPS (not-miraculix! bit-storing is used)

Bits available in MoBPS-bit-storing

Set to TRUE to get a miraculix-compressed genotype/haplotype

Population list

vector of currently activ recombination points

vector of currently activ mutations

vector of currently activ origins

If FALSE use slower version to compute markers between recombination points

Function to calculate recombination point into adjacent/following SNP

Used function for the decoding of genetic origins [[5]]/[[6]]

Population list

Number of markers to generate (Split equally across chromosomes (chr.nr) unless vector is used)

Number of individuals to generate (you can also provide number males / females in a vector)

Number of QTLs to generate (this will be a subset of the generated SNPs; default: NULL; all SNPs are potential QTLs)

Name of the newly added cohort

Generation to which newly individuals are added (default: 1)

Founder pool an individual is assign to (default: 1)

Activating this will ignore all sex specific parameters and handle each individual as part of the first sex (default: FALSE)

Set TRUE to automatically remove females in selection.m and remove males in selection.f

Specify which newly added individuals are male (1) or female (2)

Share of newly added female individuals (deterministic if sex.s="fixed", alt: sex.s="random")

Migration level of the newly added individuals (default: 0)

Set to FALSE to not display any prints

map-file that contains up to 5 colums (chromosome, SNP-id, M-position, Bp-position, allele freq - Everything not provides it set to NA). A map can be imported via MoBPSmaps::ensembl.map()

Number of chromosomes (SNPs are equally split) or vector containing the associated chromosome for each marker

Length of the newly added chromosome in Morgan; can be a vector when generating multiple chromosomes (default: 5)

Vector containing the physical position (bp) for each marker (default: 1,2,3...)

Use equidistant markers (computationally faster! ; default: TRUE)

Import genetic map and chip from a species ("cattle", "chicken", "pig")

Location of each marker on the genetic map

Markers are automatically sorted according to their snp.position unless this is set to FALSE (default: TRUE)

If TRUE add an additional chromosome to the population

Convert physical position (bp) into a cM position (default: 0 - not done)

Vector containing the name of each marker (default ChrXSNPY - XY chosen accordingly)

Vector containing the first allelic variant in each marker (default: 0)

Vector containing the second allelic variant in each marker (default: 1)

SNP dataset, use "random", "allhetero" "all0" when generating a dataset via nsnp,nindi

frequency of allele 1 when randomly generating a dataset (default: "beta" with parameters beta.shape1, beta.shape2; Use "same" when generating additional individuals and using the same allele frequencies)

First parameter of the beta distribution for simulating allele frequencies

Second parameter of the beta distribution for simulating allele frequencies

Share of individuals genotyped in the founders

Specify with newly added individuals are genotyped (1) or not (0)

Path to a vcf-file used as input genotypes (correct haplotype phase is assumed!)

Maximum number of SNPs to include in the genotype file (default: Inf)

Maximum number of individuals to include in the genotype file (default: Inf)

Vector of chromosomes to import from vcf. Use on bgziped and tabixed vcf only. (default: NULL - all chromosomes)

Use the VariantAnnotation package to load in a vcf file when available (default: TRUE)

Name of the traits generated

Target mean for each trait

Target variance for each trait

Set to TRUE to put QTL effects on the same markers for different traits

Target correlation between QTL-based traits (underlying true genomic values)

Vector of traits to be included in the modelling of correlated traits (default: all - needs to match with trait.cor)

Number of additive QTL with effect size drawn from a gaussian distribution

Number of additive QTL with equal effect size (effect.size)

Number of dominant QTL with effect size drawn from a gaussian distribution

Number of dominant QTL with equal effect size

Number of overdominant QTL with effect size drawn from absolute value of a gaussian distribution

Number of overdominant QTL with equal effect size

Number of qualitative epistatic QTL

Number of quantitative epistatic QTL

Set to "gamma" for gamma distribution effects with gamma.shape1, gamma.shape2 instead of gaussian (default: "gauss")

Default: 1

Default: 1

Single Marker effects (list for each trait with columns for: SNP Nr, Chr Nr, Effect 00, Effect 01, Effect 11, Position (optional), Founder pool genotype (optional), Founder pool origin (optional))

Two Marker effects

Multi-marker effects

Correlation of the simulated enviromental variance

Correlation of the simulated genetic variance (child share! heritage is not influenced!

Covariance matrix of the litter effect (default: no effects)

Covariance matrix of the pen effect (default: no effects)

Vector coding if a trait is caused by a maternal effect (Default: FALSE)

Vector coding if a trait is caused by a paternal effect (Default: FALSE)

Matrix containing fixed effects (p x k -matrix with p being the number of traits and k being number of fixed effects; default: not fixed effects (NULL))

Vector providing information for which pools QTLs of which trait are activ (default: 0 - all pools)

Correlation matrix between locations / environments (default: only one location, sampled from gxe.max / gxe.min)

Number of locations / environments to consider for the GxE model

Maximum correlation between locations / environments when generating correlation matrix via sampling (default: 0.85)

Minimum correlation between locations / environments when generating correlation matrix via sampling (default: 0.70)

Same of the different locations / environments used

Set to FALSE to not view the same trait from different locations / environments as the sample trait in the prediction model (default: TRUE)

Number of traits (If more than traits via real.bv.X use traits with no directly underlying QTL)

Intercept of underlying true genomic values (excluding all QTL effects, default: 100)

Set to TRUE to always assign the heterozygous variant with the higher of the two homozygous effects (e.g. hybrid breeding); default: FALSE

Vector contain markers on which no QTL effects are placed

Variance of additive QTL

Variance of dominante QTL

Variance of overdominante QTL

Variance of qualitative epistatic QTL

Variance of quantitative epistatic QTL

Effect size of the QTLs in n.equal.additive

Effect size of the QTLs in n.equal.dominant

Effect size of the QTLs in n.equal.overdominant

Genetic variance of traits with no underlying QTL

Multiplicate trait value times this

Potency trait value over this

Set to TRUE to have no effect on the 0 genotype (or 00 for QTLs with 2 underlying SNPs)

Set TRUE to standardize trait mean and variance via bv.standardization() - automatically set to TRUE when mean/var.target are used

If TRUE delete the simulated traits added before

Vector of traits to ignore in the calculation of the genomic value (default: NULL; Only recommended for high number of traits and experienced users!)

Set to FALSE to deactive the automatic removal of QTLs on markers that do not exist

Set random seed of the process

Add genetic architecture (marker positions)

Time point at which the new individuals are generated

Technique to generate new individuals (usage in web-based application)

Set to value to scale all input for breeding.size / selection.size (This will not work for all breeding programs / less general than json.simulation)

Set to FALSE to not use progress bars in any application of breeding.diploid() downstream (Keep log-files lean!)

If TRUE use miraculix package for data storage, computations and dataset generation

Set FALSE to deactivate miraculix package for dataset generation

Add chromosome ends as recombination points

Set to TRUE to use recalculate.manual to calculate genomic values (all individuals and traits jointly, default: FALSE)

Set to FALSE to not store computing times needed to execute creating.diploid in $info$comp.times.creating

Internal variable needed when adding multiple chromosomes jointly

Internal parameter

Do not touch!

Do not touch!

Do not touch!

Bits available in MoBPS-bit-storing

Set to TRUE if the MoBPS (not-miraculix! bit-storing is used)

(OLD! - use new.residual.correlation) Correlation of the simulated enviromental variance

Length before the first SNP of the dataset (default: 5)

Length after the last SNP of the dataset (default: 5)

Manual scaling of snp.position

OLD! Use trait.cor - Target Correlation between traits

OLD! Use trait.cor.include - Vector of traits to be included for modelling of correlated traits (default: all - needs to match with shuffle.cor)

OLD! Use n.traits instead. Number of traits (If more than traits via real.bv.X use traits with no directly underlying QTL)

Population list

Phenotypic transformation to apply

Trait for which a transformation is to be applied

Set to FALSE to not perform heritability check

Quick-insert for database (vector of all generations to export)

Groups of individuals to consider for the export

Quick-insert for database (vector of names of cohorts to export)

Vector of heritability input to test (before introducing noise from trafo; default: seq(0.05,0.5, by = 0.05))

Set TRUE to export matrix of heritability before/after transformation

Sample size to use in test.h2 (default: 1000)

Population list

Name of the trait generated

Target mean

Target variance

Set to TRUE to put QTL effects on the same markers for different traits

Target correlation between QTL-based traits (underlying true genomic values)

Vector of traits to be included in the modelling of correlated traits (default: all - needs to match with trait.cor)

Number of additive QTL with effect size drawn from a gaussian distribution

Number of additive QTL with equal effect size (effect.size)

Number of dominant QTL with effect size drawn from a gaussian distribution

Number of dominant QTL with equal effect size

Number of overdominant QTL with effect size drawn from absolute value of a gaussian distribution

Number of overdominant QTL with equal effect size

Number of qualitative epistatic QTL

Number of quantitative epistatic QTL

Set to "gamma" for gamma distribution effects with gamma.shape1, gamma.shape2 instead of gaussian (default: "gauss")

Default: 1

Default: 1

Single Marker effects

Two Marker effects

Multi-marker effects

Number of traits (If more than traits via real.bv.X use traits with no directly underlying QTL)

Average genetic value of a trait

Correlation of the simulated enviromental variance

Correlation of the simulated genetic variance (child share! heritage is not influenced!

Vector coding if a trait is caused by a maternal effect (Default: all FALSE)

Vector coding if a trait is caused by a paternal effect (Default: all FALSE)

Matrix containing fixed effects (p x k -matrix with p being the number of traits and k being number of fixed effects; default: p x 1 matrix with 0s (additional intercept))

Vector providing information for which pools QTLs of this trait are activ (default: 0 - all pools)

Correlation matrix between locations / environments (default: only one location, sampled from gxe.max / gxe.min)

Number of locations / environments to consider for the GxE model

Maximum correlation between locations / environments when generating correlation matrix via sampling (default: 0.85)

Minimum correlation between locations / environments when generating correlation matrix via sampling (default: 0.70)

Same of the different locations / environments used

Set to FALSE to not view the same trait from different locations / environments as the sample trait in the prediction model (default: TRUE)

Set to TRUE to always assign the heterozygous variant with the higher of the two homozygous effects (e.g. hybrid breeding); default: FALSE

Marker were no QTL are simulated on

Variance of additive QTL

Variance of dominante QTL

Variance of overdominante QTL

Variance of qualitative epistatic QTL

Variance of quantitative epistatic QTL

Effect size of the QTLs in n.equal.additive

Effect size of the QTLs in n.equal.dominant

Effect size of the QTLs in n.equal.overdominant

Genetic variance of traits with no underlying QTL

Multiplicate trait value times this

Potency trait value over this

Set to TRUE to have no effect on the 0 genotype (or 00 for QTLs with 2 underlying SNPs)

Set TRUE to standardize trait mean and variance via bv.standardization()

If TRUE delete the simulated traits added before

Set to FALSE to deactive the automatic removal of QTLs on markers that do not exist

Set random seed of the process

Set to FALSE to not display any prints

Set to TRUE to use recalculate.manual to calculate genomic values (all individuals and traits jointly, default: FALSE)

(OLD! - use new.residual.correlation) Correlation of the simulated enviromental variance

OLD! Use trait.cor.include - Vector of traits to be included for modelling of correlated traits (default: all - needs to match with shuffle.cor)

OLD! Use trait.cor - Target Correlation between traits

OLD! Use n.traits instead. Number of traits (If more than traits via real.bv.X use traits with no directly underlying QTL)

coded origins vector

row to decode

Population list

Population list

Groups of individuals to consider in breeding value estimation

Consider only animals of those class classes in breeding value estimation (default: NULL - use all)

If set to FALSE multiple generatations of the same individual can be used in the bve (only possible by using copy.individual to generate individuals)

Internal parameter to derive number of added individuals per database entry (only relevant internally for GWAS)

Internal parameter to derive which individuals are copy entries

Internal parameter to derive further information on the copies individuals

vector with entries to put on the diagonal of a matrix

Edges of the json-file generated via the web-interface

Population list

Generation of the individual to edit

Gender of the individual to edit

Number of the individual to edit

Number of edits to perform

Used function for the decoding of genetic origins [[5]]/[[6]]

Set to TRUE if the MoBPS (not-miraculix! bit-storing is used)

Bits available in MoBPS-bit-storing

genotype dataset (marker x individuals)

phenotype dataset (each phenotype in a row)

genomic map

Set FALSE to not perform variance scaling

ld between markers

distance between markers in Morgan

Population size

y

genomic information matrix

kinship matrix

Population list

Cohort to check if it is contained in the population list

position in the genome

Length of each chromosome

Position on the genome

Position of the SNPs on the genome

number of individuals to generate in a random dataset

Share of newly added female individuals (deterministic if sex.s="fixed", alt: sex.s="random")

number of markers to generate in a random dataset

Number of generations to simulate (default: 100)

Number of final individuals to include (default: nindi)

Share of female individuals in the final generation

Set to TRUE to export map, population list and pedigree relationship

Set to FALSE to not generate LD-decay plot and allele frequency spectrum

Set FALSE to not display progress bars. Setting verbose to FALSE will automatically deactive progress bars

Depth of the pedigree in generations (default: 7)

SNP dataset, use "random", "allhetero" "all0" when generating a dataset via nsnp,nindi

Path to a vcf-file used as input genotypes (correct haplotype phase is assumed!)

Vector containing the associated chromosome for each marker (default: all on the same)

Vector containing the physical position (bp) for each marker (default: 1,2,3...)

Vector containing the name of each marker (default ChrXSNPY - XY chosen accordingly)

Vector containing the first allelic variant in each marker (default: 0)

Vector containing the second allelic variant in each marker (default: 1)

Convert physical position (bp) into a cM position (default: 0 - not done)

frequency of allele 1 when randomly generating a dataset

Specify which newly added individuals are male (1) or female (2)

Length of the newly added chromosome (default: 5)

Length before the first SNP of the dataset (default: 5)

Length after the last SNP of the dataset (default: 5)

Use equidistant markers (computationally faster! ; default: TRUE)

Location of each marker on the genetic map

Manual scaling of snp.position

Set to TRUE if the MoBPS (not-miraculix! bit-storing is used)

Bits available in MoBPS-bit-storing

Set random seed of the process

If TRUE use miraculix package for data storage, computations and dataset generation

Set FALSE to deactive miraculix package for dataset generation

Import genetic map and chip from a species ("cattle", "chicken", "pig")

First parameter of the beta distribution for simulating allele frequencies

Second parameter of the beta distribution for simulating allele frequencies

map-file that contains up to 5 colums (Chromsome, SNP-id, M-position, Bp-position, allele freq - Everything not provides it set to NA). A map can be imported via MoBPSmaps::ensembl.map()

Set to FALSE to not display any prints

Maximum number of SNPs to include in the genotype file (default: Inf)

Set FALSE to not generate the LD plot (default; TRUE)

Set FALSE to not generate the allele frequency spectrum plot (default: TRUE)

Axis limits for the x-axis in the LD plot (default: NULL)

Axis limits for the y-axis in the LD plot (default: NULL)

Number of classes to consider in the allele frequency spectrum plot (default: 20)

Axis limits for the allele frequency spectrum plot (default: NULL)

Mutation rate in each marker (default: 10^-8)

Remutation rate in each marker (default: 10^-8)

Set to FALSE to not estimate the effective population size (default: TRUE)

Set to FALSE to not estimate the ld decay (default: TRUE)

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

windows parallel internal test

Population list

Manually provided genotype dataset to use instead of gen/database/cohorts

Quick-insert for database (vector of all generations to consider)

Groups of individuals to consider

Quick-insert for database (vector of names of cohorts to consider)

Individual IDs to search/collect in the database

dimensions to consider in admixture plot (default: automatically estimate a reasonable number)

Set to FALSE to not display any prints

Set to FALSE to not generate an admixture plot

Set to TRUE to sort individuals according to contributes from the first dimension

Skip individuals with contributions under this threshold (and use next dimension instead) data(ex_pop) get.admixture(ex_pop, gen=4:6, d=2, sort=TRUE)

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

Population list

extended cohorts

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names

To not change order of individuals when ids are provided (default: TRUE)

Population list

Set to FALSE to not display any prints

Set to TRUE to return computing times with detailled overview on generation and BVE (default: FALSE)

Set to TRUE to return computing times per call of breeding.diploid / creating.diploid() (default: FALSE)

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

Set to TRUE to extract phenotyping

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: FALSE)

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: FALSE)

Population list

Quick-insert for database (vector of all generations to export)

Groups of individuals to consider for the export

Quick-insert for database (vector of names of cohorts to export)

Set to TRUE to avoid different cohorts to be merged in a joint group when possible

Set TRUE to obtain a database with one row per individual instead of concatenating (default: FALSE)

Individual IDs to search/collect in the database

MoPBS internal names (SexNr_Generation)

Set to TRUE to show all copies of an individual in the database (default: FALSE)

Set to TRUE to use the last copy of an individual for the database (default: FALSE - pick first copy)

To not change order of individuals when ids are provided (default: FALSE)

Only include individuals of the following classes in the database (can also be vector with multiple classes; default: ALL)

Only include individuals that are genotyped (TRUE) or not-genotyped (FALSE); default: NULL (all individuals)

Only include individuals with the certain number of phenotypes generated (default: NULL (all individuals))

Set to FALSE to not display any prints

Set to 1 to only include males and set 2 to only include females in database (default: 0)

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

Population list

provide a path if the dendrogram would be saved as a png-file

Groups of individuals to consider

Quick-insert for database (vector of all generations to consider)

Quick-insert for database (vector of names of cohorts to consider)

Individual IDs to search/collect in the database

Method used to calculate genetic distances (default: "Nei", alt: "Rogers", "Prevosti", "Modified Rogers"

Names of the individuals in the database ((default are MoBPS internal names based on position))

Population list

provide a path if the dendrogram would be saved as a png-file

Groups of individuals to consider

Quick-insert for database (vector of all generations to consider)

Quick-insert for database (vector of names of cohorts to consider)

Individual IDs to search/collect in the database

Method used to calculate genetic distances (default: "Nei", alt: "Rogers", "Prevosti", "Modified Rogers"

Names of the individuals in the database ((default are MoBPS internal names based on position))

Traits to include in the dendrogram (default: all traits)

Which traits values to consider (default: "pheno", alt: "bv", "bve")

Population list

provide a path if the dendrogram would be saved as a png-file

Groups of individuals to consider

Quick-insert for database (vector of all generations to consider)

Quick-insert for database (vector of names of cohorts to consider)

Individual IDs to search/collect in the database

Traits to include in the dendrogram (default: all traits)

Which traits values to consider (default: "pheno", alt: "bv", "bve")

population list

Chose type of distance to compute (default: Neis standard genetic distance "nei"). Alt: Reynolds distance ("reynold"), Cavalli-Sforza ("cavalli"), Neis distance ("nei_distance"), Neis minimum distance ("nei_minimum")

Vector with SNPs to consider (Default: "all" - use of all markers)

Set to TRUE to return per marker statistics on genetic distances

Quick-insert for database (vector of all generations to consider)

First Groups of individuals to consider

Quick-insert for database (vector of names of cohorts to consider)

Individual IDs to search/collect in the database

Quick-insert for database (vector of all generations to consider)

Second Groups of individuals to consider

Quick-insert for database (vector of names of cohorts to consider)

Individual IDs to search/collect in the database

List of databases to consider (use when working with more than 2 populations)

Quick-insert for database (vector of all generations to consider)

Quick-insert for database (vector of names of cohorts to consider)

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to FALSE to not sort markers according to position on the genome

Population list

Quick-insert for database (vector of all generations to export)

Groups of individuals to consider for the export

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: FALSE)

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Limit the genotype output to a selected chromosome (default: "all")

If TRUE export underlying alleles instead of just 012

Set to TRUE to replace non-genotyped markers with NA

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

Use only markers available on the array

Remove markers not genotyped in any individual from the export

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

Set to TRUE to extract phenotyping

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

Set to TRUE to extract phenotyping

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

If TRUE export underlying alleles instead of just 012

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

Use only markers available on the array

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Limit the genotype output to a selected chromosome (default: "all")

If TRUE export underlying alleles instead of just 012

Set to TRUE to replace non-genotyped markers with NA

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

Use only markers available on the array

Remove markers not genotyped in any individual from the export

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

To not change order of individuals when ids are provided (default: FALSE)

Population list

Which traits to include in the index (all weight with factor 1)

Which locations to include in the index (all weight weight factor 1)

Vector with a weight per trait

Vector weight a weight per location

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

To not change order of individuals when ids are provided (default: FALSE)

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

To not change order of individuals when ids are provided (default: FALSE)

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Population list

Set to TRUE to display SNP number and not SNP name

Set to FALSE to Morgan position continuously over the genome

Population list

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to export information on number of phenotyped, genotyped, and both pheno&genotyped individuals

Set to TRUE to double count individuals if multiple copies of an individual are included in gen/database/cohorts

Population list

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)

Quick-insert for database (vector of names of cohorts to export)

Individual IDs to search/collect in the database

Set to TRUE to extract phenotyping

Set to TRUE to use MoBPS ids instead of Sex_Nr_Gen based names (default: TRUE)

Population list

Population list

Location were to save the PCA-plot

Groups of individuals to consider for the export

Quick-insert for database (vector of all generations to export)