A set of R functions for calling the PopGen web service and for extracting data from the response.
Use devtools::install_github() to download the package from version control and install it:
install.packages("devtools")
library(devtools)
install_github("HSL/Rpgcli")You will require R version 3.1 or later.
If you are behind a firewall and internet access is via a proxy, configure access with:
store_proxy_settings("name_of_proxy_server", 8080)If on a corporate network, you will need to supply credentials too:
store_proxy_settings("name_of_corporate_proxy_server", 8080, "kevin", "pass123!")If you are not already a PopGen user, go to PopGen, enter your email address, and follow the instructions.
Use the email address to initialize the service inputs:
parameters <- list(PopGenUserName = "kevin.soandso@some.sci.org")Add other required inputs with typical values:
parameters <- apply_defaults(parameters)Call the PopGen web service:
pop_gen_out <- generate_population(parameters)Check for success:
summary(pop_gen_out)Extract population data as data frame:
individuals <- extract_individuals(pop_gen_out)The following code samples from PopGen's four datasets. As PopGen throttles access to the service, this may take a minute or two to run to completion:
datasets <- c("P3M", "ICRP", "HSE", "NDNS")
n_datasets <- length(datasets)
data <- lapply(1:n_datasets, function(i) {
dataset <- datasets[i]
parameters <- list(
Dataset = dataset,
PopGenUserName = "kevin.soandso@some.sci.org",
PopulationSize = 100
)
if (dataset == "NDNS") {
# Must override defaults for this dataset.
# See https://discover.ukdataservice.ac.uk/series/?sn=2000033#abstract
parameters$AgeLower <- 2
parameters$AgeUpper <- 4
parameters$BodyMassIndexLower <- 10
parameters$HeightLower <- 80
parameters$HeightUpper <- 120
}
parameters <- apply_defaults(parameters)
cat(paste("Sampling ", dataset, "\n", sep = ""))
# call service with no activity feedback
pop_gen_out <- generate_population(parameters, silent = T)
if (generate_failed(pop_gen_out)) {
# show error messages now
print(summary(pop_gen_out))
stop()
}
if (i < n_datasets) {
# service is throttled - must pause here
cat("Waiting for service to resume...\n")
Sys.sleep(pop_gen_out$wait_for)
}
individuals <- extract_individuals(pop_gen_out)
return(individuals)
})
names(data) <- datasets
Refer to the service's inputs schema for concise coverage of the input requirements.
Once installed, review the complete package API with:
help(package="Rpgcli")Licensed under the MIT license. (More information here.)