TODO section on BioSys.
If the data consumer however wishes to analyse data in a statistical package like R, the data need to be transformed from a nested list of lists (JSON) into a two-dimensional tablular structure.
The main purpose of biosystR is to facilitate reading, parsing and using BioSys data by providing helpers to access the API and flatten the API outputs into a tidy dplyr::tibble.
Install biosystR from GitHub:
# install.packages("devtools")
devtools::install_github("parksandwildlife/biosystR")While the WAStD API is only accessible to a selected audience, and wastdr is under active development, it is not feasible to release wastdr on CRAN yet. Therefore, wastdr will be distributed via GitHub for the time being.
Obtain a Biosys username and password and add to your ~/.Rprofile:
Sys.setenv(BIOSYS_API_USERNAME = "USERNAME")
Sys.setenv(BIOSYS_API_PASSWORD = "PASSWORD")Restart your R session to load the new environment variables. ## Usage example
TODO
See the vignette for in-depth examples of transforming, analysing and visualising data.
vignette("biosystR")Every contribution, constructive feedback, or suggestion is welcome!
Send us your ideas and requests as issues or submit a pull request.
Pull requests should eventually pass tests and checks (not introducing new ERRORs, WARNINGs or NOTEs apart from the "New CRAN package" NOTE):
devtools::document(roclets=c('rd', 'collate', 'namespace', 'vignette'))
devtools::test()
devtools::check(check_version = T, force_suggests = T, cran = T)
covr::codecov()To enable local testing of the API as well as checking and upload of test coverage, add these two lines with the respective tokens to your .Rprofile:
Sys.setenv(CODECOV_TOKEN = "my-codecov-token")
Sys.setenv(MY_API_TOKEN = "my-api-token")