Rpgcli

R Client for PopGen Web Service

A set of R functions for calling the PopGen web service and for extracting data from the response.

Installation

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.

Usage

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)

A more complete example

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#abstractparameters$AgeLower<-2parameters$AgeUpper<-4parameters$BodyMassIndexLower<-10parameters$HeightLower<-80parameters$HeightUpper<-120
}
parameters<- apply_defaults(parameters)
cat(paste("Sampling ", dataset, "\n", sep=""))
# call service with no activity feedbackpop_gen_out<- generate_population(parameters, silent=T)
if (generate_failed(pop_gen_out)) {
# show error messages now
print(summary(pop_gen_out))
stop()
}
if (i<n_datasets) {
# service is throttled - must pause here
cat("Waiting for service to resume...\n")
Sys.sleep(pop_gen_out$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")

License

Licensed under the MIT license. (More information here.)