diff --git a/README.md b/README.md index 8759c71..9e541fc 100644 --- a/README.md +++ b/README.md @@ -26,14 +26,14 @@ remotes::install_github("pharmaverse/pharmaversesdtm", ref = "devel") # Data Sources -Some of the test datasets has been sourced from the [CDISC pilot project](https://github.com/cdisc-org/sdtm-adam-pilot-project), while other datasets have been constructed ad-hoc by the admiral team. Please check the [Github repository](https://github.com/pharmaverse/pharmaversesdtm/blob/main/data) for detailed information regarding the source of specific datasets. +Some of the test datasets has been sourced from the [CDISC pilot project](https://github.com/cdisc-org/sdtm-adam-pilot-project), while other datasets have been constructed ad-hoc by the admiral team. Please check the [Reference page](https://pharmaverse.github.io/pharmaversesdtm/cran-release/reference/index.html) for detailed information regarding the source of specific datasets. # Naming Conventions {#naming} * Datasets that are TA-agnostic: same as SDTM domain name (e.g., `dm`, `rs`). * Datasets that are TA-specific: domain_TA_others, others go from broader categories to more specific ones (e.g., `oe_ophtha`, `rs_onco`, `rs_onco_irecist`). -**Note**: *If an SDTM domain is used by multiple TAs, `{pharmaversesdtm}` may provide multiple versions of the corresponding test dataset. For instance, the package contains `ex` and `ophtha_ex` as the latter contains ophthalmology-specific variables such as `EXLAT` and `EXLOC`, and `EXROUTE` is exchanged for a plausible ophthalmology value.* +**Note**: *If an SDTM domain is used by multiple TAs, `{pharmaversesdtm}` may provide multiple versions of the corresponding test dataset. For instance, the package contains `ex` and `ex_ophtha` as the latter contains ophthalmology-specific variables such as `EXLAT` and `EXLOC`, and `EXROUTE` is exchanged for a plausible ophthalmology value.* # How To Update @@ -44,9 +44,7 @@ Then there are two main ways to extend the test data: either by adding new datas * Each of these programs is written as a standalone R script: if any packages need to be loaded for a given program, then call `library()` at the start of the program (but please do **not** call `library(pharmaversesdtm)`). * Most of the packages that you are likely to need will already be specified in the `renv.lock` file, so they will already be installed if you have been keeping in sync--you can check this by entering `renv::status()` in the Console. However, you may also wish to install `{metatools}` and `{ggplot2}`, which are currently not specified in the `renv.lock` file. If you feel that you need to install any other packages in addition to those just mentioned, then please tag `@pharmaverse/admiral` to discuss with the development core team. * When you have created a program in the `data-raw/` folder, you need to run it as a standalone R script, in order to generate a test dataset that will become part of the `{pharmaversesdtm}` package, but you do not need to build the package. -* Following [best practice](https://r-pkgs.org/data.html#sec-data-data), each dataset is stored as a `.rda` file whose name is consistent with the name of the dataset, e.g., dataset `xx` is stored as `xx.rda` - * `save(xx, file = "data/xx.rda", compress = "bzip2")` - * or an easier way to achieve this is to use `usethis::use_data()` +* Following [best practice](https://r-pkgs.org/data.html#sec-data-data), each dataset is stored as a `.rda` file whose name is consistent with the name of the dataset, e.g., dataset `xx` is stored as `xx.rda`. The easiest way to achieve this is to use `usethis::use_data(xx)` * The programs in `data-raw/` are stored within the `{pharmaversesdtm}` GitHub repository, but they are **not** part of the `{pharmaversesdtm}` package--the `data-raw/` folder is specified in `.Rbuildignore`. * When you run a program that is in the `data-raw/` folder, you generate a dataset that is written to the `data/` folder, which will become part of the `{pharmaversesdtm}` package. * The names and sources of test datasets are specified in `R/data.R`, for the purpose of generating documentation in the `man/` folder. @@ -60,6 +58,7 @@ Then there are two main ways to extend the test data: either by adding new datas * Reflect this update, by specifying `` in `R/data.R`. * Run `devtools::document()` in order to update `NAMESPACE` and update the `.Rd` files in `man/`. * Add your GitHub handle to `.github/CODEOWNERS` +* Update `NEWS.md` ## Updating Existing SDTM Datasets @@ -67,3 +66,5 @@ Then there are two main ways to extend the test data: either by adding new datas * Run the program, and output updated `.rda` to the `data/` folder. * Run `devtools::document()` in order to update `NAMESPACE` and update the `.Rd` files in `man/`. * Add your GitHub handle to `.github/CODEOWNERS` +* Update `NEWS.md` +