diff --git a/R/build.R b/R/build.R index df5b91d..845b741 100644 --- a/R/build.R +++ b/R/build.R @@ -7,7 +7,7 @@ #' that is optional to specify. #' @param metacore Metacore object that contains the specifications for the #' dataset of interest. -#' @param ds_list Named list of datsets that are needed to build the from +#' @param ds_list Named list of datasets that are needed to build the from #' @param dataset_name Optional string to specify the dataset. This is only #' needed if the metacore object provided hasn't already been subsetted. #' @param predecessor_only By default `FALSE`, but if `TRUE` will only use diff --git a/README.Rmd b/README.Rmd index 2e705da..68623a8 100644 --- a/README.Rmd +++ b/README.Rmd @@ -16,6 +16,7 @@ knitr::opts_chunk$set( # metatools +[](https://pharmaverse.org) [![R-CMD-check](https://github.com/pharmaverse/metatools/workflows/R-CMD-check/badge.svg)](https://github.com/pharmaverse/metatools/actions) [![codecov](https://codecov.io/gh/pharmaverse/metatools/branch/main/graph/badge.svg?token=55N5APFLPA)](https://codecov.io/gh/pharmaverse/metatools) [](https://github.com/pharmaverse/metatools/blob/main/LICENSE) @@ -54,7 +55,6 @@ ds_list <- list(DM = read_xpt(metatools_example("dm.xpt"))) build_from_derived(metacore, ds_list) %>% # To pull in columns from DM to be in ADSL create_cat_var(metacore, AGE, AGEGR1, AGEGR1N) %>% #Add an AGEGR1 and AGEGR1N column convert_var_to_fct(metacore, ETHNIC) # Change ETHNIC to as factor - ``` Metatools can also be used to run checks diff --git a/README.md b/README.md index 65e93db..8a2e014 100644 --- a/README.md +++ b/README.md @@ -5,6 +5,7 @@ +[](https://pharmaverse.org) [![R-CMD-check](https://github.com/pharmaverse/metatools/workflows/R-CMD-check/badge.svg)](https://github.com/pharmaverse/metatools/actions) [![codecov](https://codecov.io/gh/pharmaverse/metatools/branch/main/graph/badge.svg?token=55N5APFLPA)](https://codecov.io/gh/pharmaverse/metatools) [](https://github.com/pharmaverse/metatools/blob/main/LICENSE) diff --git a/_pkgdown-BREWL19H13393.yml b/_pkgdown-BREWL19H13393.yml deleted file mode 100644 index f002eba..0000000 --- a/_pkgdown-BREWL19H13393.yml +++ /dev/null @@ -1,3 +0,0 @@ -template: - bootstrap: 5 - bootswatch: materia diff --git a/_pkgdown.yml b/_pkgdown.yml index a1759eb..7d3afb1 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1 +1,4 @@ url: https://pharmaverse.github.io/metatools +template: + bootstrap: 5 + bootswatch: sandstone diff --git a/man/build_from_derived.Rd b/man/build_from_derived.Rd index 8f69161..05037ee 100644 --- a/man/build_from_derived.Rd +++ b/man/build_from_derived.Rd @@ -15,7 +15,7 @@ build_from_derived( \item{metacore}{Metacore object that contains the specifications for the dataset of interest.} -\item{ds_list}{Named list of datsets that are needed to build the from} +\item{ds_list}{Named list of datasets that are needed to build the from} \item{dataset_name}{Optional string to specify the dataset. This is only needed if the metacore object provided hasn't already been subsetted.} diff --git a/tests/testthat/test-sort.R b/tests/testthat/test-sort.R index d44f6cd..974f5a0 100644 --- a/tests/testthat/test-sort.R +++ b/tests/testthat/test-sort.R @@ -1,18 +1,18 @@ library(haven) spec <- define_to_metacore(metacore_example("ADaM_define.xml"), quiet = TRUE) %>% - select_dataset("ADSL") + select_dataset("ADSL") data <- read_xpt(metatools_example("adsl.xpt")) test_that("sort_order", { - data %>% - select(AGE, SITEID, everything()) %>% - sort_order(spec) %>% - expect_equal(data) + data %>% + select(AGE, SITEID, everything()) %>% + order_cols(spec) %>% + expect_equal(data) }) test_that("sort_key", { - data %>% - arrange(TRT01P, AGE) %>% - sort_key(spec) %>% - expect_equal(data) + data %>% + arrange(TRT01P, AGE) %>% + sort_by_key(spec) %>% + expect_equal(data) })