Add pharmaverse shield and change website

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

README.Rmd

@@ -16,6 +16,7 @@ knitr::opts_chunk$set(
 # metatools <a href='https://github.com/pharmaverse/metatools'><img src="man/figures/metatools.png" align="right" style="height:139px;"/></a>
 
 <!-- badges: start -->
+[<img src="http://pharmaverse.org/shields/metatools.svg">](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)
 [<img src="https://img.shields.io/badge/License-MIT-blue.svg">](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 

README.md

@@ -5,6 +5,7 @@
 
 <!-- badges: start -->
 
+[<img src="http://pharmaverse.org/shields/metatools.svg">](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)
 [<img src="https://img.shields.io/badge/License-MIT-blue.svg">](https://github.com/pharmaverse/metatools/blob/main/LICENSE)

_pkgdown.yml

@@ -1 +1,4 @@
 url: https://pharmaverse.github.io/metatools
+template:
+  bootstrap: 5
+  bootswatch: sandstone

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)
 })