Help for package SoyURT

Title:

USDA Northern Region Uniform Soybean Tests Dataset

Version:

1.0.0

Author:

Matheus Dalsente Krause

[aut, cre], William Dale Beavis

[aut]

Maintainer:

Matheus Dalsente Krause <krause.d.matheus@gmail.com>

Description:

Data sets used by 'Krause et al. (2022)' <doi:10.1101/2022.04.11.487885>. It comprises phenotypic records obtained from the USDA Northern Region Uniform Soybean Tests from 1989 to 2019 for maturity groups II and III. In addition, soil and weather variables are provided for the 591 observed environments (combination of locations and years).

URL:

https://github.com/mdkrause/soyurt

NeedsCompilation:

Language:

en-US

License:

CC BY 4.0

Encoding:

UTF-8

Depends:

R (≥ 3.5.0)

LazyData:

true

LazyDataCompression:

RoxygenNote:

7.2.0

Suggests:

spelling

Packaged:

2022-06-10 14:41:03 UTC; mdkrause

Repository:

CRAN

Date/Publication:

2022-06-13 06:30:03 UTC

Phenotype

Description

Modeled data set by Krause et al. (2022) from the USDA Northern Region Uniform Soybean Tests. The data contains 4,257 experimental genotypes evaluated at 63 locations and 31 years resulting in 591 location-year combinations (environments) with 39,006 yield values belonging to matirity groups II and III from 1989 to 2019. Annual PDF reports from the Northern Region of the USDA Uniform Soybean Tests were obtained from https://ars.usda.gov/mwa/lafayette/cppcru/ust. The data retrieved from the published PDF files represent averages for seed yield for each genotype evaluated at each trial in location-year combinations. Seed yield was adjusted to 13% moisture and results were reported in bushels per acre (bu/ac). For more information about the trial field plot design and agronomic practices, please refer to the PDF files. The raw data can also be downloaded from Soybase: https://soybase.org/ncsrp/queryportal/.

Usage

pheno

Format

A data frame in tidy format with 39,006 observations on the following 13 variables:

year: years, 31 levels (1989 - 2019)
location: locations, 63 levels (observed locations in the historical series)
latitude: latitude
longitude: longitude
altitude: altitude
trial: name of the trial that originated the phenotypic record
check: indicator variable for variety checks, 2 levels (yes or no)
maturity_group: genotype's maturity group, 2 levels (II or III)
G: genotype, 4,257 levels
eBLUE: empirical best linear unbiased estimate of genotype means
SE: standard error of genotype means on a location level
average_planting_date: average planting date on a location level (MM/DD/YY)
average_maturity_date: average maturity date on a location level in days after planting

Source

Krause, M. D., Dias, K. O. G., Singh, A. K., and Beavis. W. D. (2022). Using large soybean historical data to study genotype by environment variation and identify mega-environments with the integration of genetic and non-genetic factors. bioRxiv, doi: 10.1101/2022.04.11.487885

Soil variables

Description

Soil variables in a depth interval of 5 to 15 cm were obtained from Soilgrids (https://soilgrids.org/) for the 63 observed locations in the historical series analyzed by Krause et al. (2022). The R code used to download and process the soil data can be retrieved at https://github.com/mdkrause/VarComp-ME/blob/main/soil_data.R.

Usage

soil

Format

A data frame in tidy format with 504 observations on the following 5 variables:

Feature: soil variables, 8 levels
location: locations, 63 levels (observed locations in the historical series)
Soil_Grid: mean values of the soil variables (Feature)
LAT: location latitude
LON: location longitude

Details

Levels of Feature:

bdod_5-15cm_mean:: Bulk density of the fine earth fraction (cg/m^3)
cec_5-15cm_mean:: Cation Exchange Capacity of the soil (mmol(c)/kg)
clay_5-15cm_mean:: Proportion of clay particles (< 0.002 mm) in the fine earth fraction (g/kg)
nitrogen_5-15cm_mean:: Total nitrogen (cg/kg)
phh2o_5-15cm_mean:: Soil pH (pH\times10)
sand_5-15cm_mean:: Proportion of sand particles (> 0.05 mm) in the fine earth fraction (g/kg)
silt_5-15cm_mean:: Proportion of silt particles (\ge 0.002 mm and \leq 0.05 mm) in the fine earth fraction (g/kg)
soc_5-15cm_mean:: Soil organic carbon content in the fine earth fraction (dg/kg)

Source

Weather variables

Description

Weather variables obtained from NASA's Prediction of Worldwide Energy Resource (https://power.larc.nasa.gov/) for the 591 environments in the historical series analyzed by Krause et al. (2022).

Usage

weather

Format

A data frame in messy format with 504 observations on the following 5 variables:

location: locations, 63 levels (observed locations in the historical series)
LON: longitude
LAT: latitude
DOY: day of the year
YYYYMMDD: calendar date in the format YYYY/MM/DD
daysFromStart: days from average planting date
T2M: daily average temperature at 2 meters
T2M_MAX: daily maximum temperature at 2 meters
T2M_MIN: daily minimum average temperature at 2 meters
PRECTOT: rainfall precipitation
WS2M: wind speed at 2 meters
RH2M: relative humidity at 2 meters
T2MDEW: dew point at 2 meters
ALLSKY_SFC_LW_DWN: downward thermal infrared (longwave) radiative flux
ALLSKY_SFC_SW_DWN: insolation incident on a horizontal surface
n: duration of sunshine in hours
VPD: the deficit of vapor pressure
SPV: the slope of saturation vapor pressure curve
ETP: evapotranspiration
PETP: deficit of evapotranspiration
GDD: growing degree-days
FRUE: effect of temperature on radiation use efficiency
T2M_RANGE: daily temperature range at 2 meters
PTT: photothermal time (GDD \times daylight in hours)
PTR: photothermal ratio (GDD / daylight in hours)

Note

Comprehensive R Archive Network (CRAN) policy limits R package size to 5 Mb. In order to give the users new opportunities of data analysis, we provide weather data for all combinations of locations (63) and years (31), resulting in information for 1,953 environments. If an environment was not observed in a given year, weather data was retrieved with the average planting and maturity data based on the empirical data for that location. This data set can be downloaded here.