Package 'SoyURT'

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

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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$\times$10)

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

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

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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.

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

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