In khaled-alshamaa/QBMS: Query the Breeding Management System(s)

QBMS

This R package assists breeders in linking data systems with their analytic pipelines, a crucial step in digitizing breeding processes. It supports querying and retrieving phenotypic and genotypic data from systems like EBS, BMS, BreedBase, and GIGWA (using BrAPI calls). Extra helper functions support environmental data sources, including TerraClimate and FAO HWSDv2 soil database.

FAO HWSD v2 Soil Database

The Harmonized World Soil Database version 2.0 (HWSD v2.0) is a unique global soil inventory providing information on the morphological, chemical and physical properties of soils at approximately 1 km resolution. Its main objective is to serve as a basis for prospective studies on agro-ecological zoning, food security and climate change.

For more details, you can get the HWSD v2.0 technical report and instructions https://doi.org/10.4060/cc3823en.

Install

install.packages("remotes")
remotes::install_github("icarda-git/QBMS")

Example

# load the QBMS library
library(QBMS)

# create a simple data.frame for a list of locations and their coordinates
Location  <- c('Tel-Hadya', 'Terbol', 'Marchouch')
Latitude  <- c(36.016, 33.808, 33.616)
Longitude <- c(36.943, 35.991, -6.716)

sites <- data.frame(Location, Latitude, Longitude)

# initiate, download, and setup the HWSD v2 in a given local directory
hwsd2 <- ini_hwsd2()

# query soil attributes for given sites using the HWSD v2 connection object
#  
# sequence parameter, range between 1 and 12 (max), 1 is the dominant soil. 
# returned df has SHARE column refers to share% 
# 
# layer parameter refers to depth layer (D1 to D7). 
# returned df has TOPDEP/BOTDEP columns represent top/bottom layer depth in cm.
sites <- get_hwsd2(df = sites, 
                   con = hwsd2, 
                   x = 'Longitude', 
                   y = 'Latitude', 
                   sequence = 1, 
                   layer = 'D1')

Advanced Users

# check the HWSD v2 raster 
print(hwsd2$raster)

# display the metadata for the layers table
DBI::dbGetQuery(hwsd2$sqlite, 'select * from HWSD2_LAYERS_METADATA')

# the lookup tables are shown for the coded fields
# for example, the USDA Texture Class codes (the column TEXTURE_USDA value)
# are linked to their names in table D_TEXTURE_USDA
DBI::dbGetQuery(hwsd2$sqlite, 'select * from D_TEXTURE_USDA')

# disconnect (close) the SQLite connection
DBI::dbDisconnect(hwsd2$sqlite)