Merge pull request #313 from pharmaverse/covid270

Covid270

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: sdtmchecks
 Title: Data Quality Checks for SDTM Datasets
-Version: 0.1.10.9002
+Version: 0.1.11
 Authors@R: 
     person("Will", "Harris", , "[email protected]", role = c("aut", "cre"))
 Description: Functions to identify common data issues in SDTM data. These checks are intended to be generalizable, actionable, and meaningful for analysis. 

NEWS.md

@@ -1,12 +1,17 @@
+# sdtmchecks 0.1.11 "Light Ice"
 
-# sdtmchecks 0.1.10.9002 -- dev
+
+## Metadata updates
+
+* Re-create sdtmchecksmeta.RData with MedDRA dictionary version 27.0 listed instead of 26.1 ([#312](https://github.com/pharmaverse/sdtmchecks/issues/312))
+
+## Misc package updates
 
 * Unit test accompanying new CE check [`check_ce_missing_month()`](https://pharmaverse.github.io/sdtmchecks/reference/check_ce_missing_month.html) previously created by `@rymarinelli` added into tests/testthat subdirectory
 * Fix minor typo in README ([#299](https://github.com/pharmaverse/sdtmchecks/issues/299))
 * Add cran-comments.md ([#305](https://github.com/pharmaverse/sdtmchecks/pull/305))
 
 
-
 # sdtmchecks 0.1.10 "Light Ice"
 
 ## Refinements of existing data check functions

R/run_all_checks.R

@@ -50,61 +50,61 @@ run_all_checks <- function(metads = sdtmchecksmeta,
                            type = c("ALL", "ONC", "COVID", "PRO", "OPHTH"),
                            verbose = TRUE,
                            ncores = 1) {
-
-    if (!is.null(priority) & !all(priority %in% c("High", "Medium", "Low"))) {
-        stop("priority argument should only take values 'High','Medium', or 'Low'")
-        }
-    if (!is.null(type) & !all(type %in% c("ALL", "ONC", "COVID", "PRO", "OPHTH"))) {
-        stop("type argument should only take values 'ALL', 'ONC', 'COVID', 'PRO', 'OPHTH'")
-        }
-
-    # subset meta dataset for specific Type and Priority
-    if (!is.null(priority)) {
-        metads <-subset(metads,metads$priority %in% priority)
-        }
-
-    if (!is.null(type) ) {
-        metads <-subset(metads, metads$category %in% type)
-        }
-
-    #Identify missing expected domains to cat out to the user later
-    expected.domains = sort(unique(strsplit(gsub(" ", "", paste(unique(metads$domains),
-                                                                collapse=",")), ",")[[1]]))
-    missing.domains = expected.domains[!(expected.domains %in% ls(envir = .GlobalEnv))]
-
-    # Run checks
-
-    all_rec <- mcmapply(
-        FUN = run_check,
-        metads$check, metads$fxn_in, metads$xls_title, metads$pdf_title, metads$pdf_subtitle, metads$pdf_return, 
-        verbose,
-        SIMPLIFY = FALSE,  # forces mcmapply to return a list
-        USE.NAMES = TRUE,  # generates list names
-        mc.cores = ncores
+
+  if (!is.null(priority) & !all(priority %in% c("High", "Medium", "Low"))) {
+    stop("priority argument should only take values 'High','Medium', or 'Low'")
+  }
+  if (!is.null(type) & !all(type %in% c("ALL", "ONC", "COVID", "PRO", "OPHTH"))) {
+    stop("type argument should only take values 'ALL', 'ONC', 'COVID', 'PRO', 'OPHTH'")
+  }
+
+  # subset meta dataset for specific Type and Priority
+  if (!is.null(priority)) {
+    metads <-subset(metads,metads$priority %in% priority)
+  }
+
+  if (!is.null(type) ) {
+    metads <-subset(metads, metads$category %in% type)
+  }
+
+  #Identify missing expected domains to cat out to the user later
+  expected.domains = sort(unique(strsplit(gsub(" ", "", paste(unique(metads$domains),
+                                                              collapse=",")), ",")[[1]]))
+  missing.domains = expected.domains[!(expected.domains %in% ls(envir = .GlobalEnv))]
+
+  # Run checks
+
+  all_rec <- mcmapply(
+    FUN = run_check,
+    metads$check, metads$fxn_in, metads$xls_title, metads$pdf_title, metads$pdf_subtitle, metads$pdf_return, 
+    verbose,
+    SIMPLIFY = FALSE,  # forces mcmapply to return a list
+    USE.NAMES = TRUE,  # generates list names
+    mc.cores = ncores
+  )
+
+  if (verbose == TRUE & length(missing.domains) > 0) {
+    cat(
+      paste0(
+        "\nDomain not found: ",
+        missing.domains,
+        ". Checks requiring this domain were not run."
+      )
     )
-
-    if (verbose == TRUE & length(missing.domains) > 0) {
-        cat(
-            paste0(
-                "\nDomain not found: ",
-                missing.domains,
-                ". Checks requiring this domain were not run."
-            )
-        )
-    }
-
-    cat("\n")
-
-    if(!("covid_df" %in% ls(envir = .GlobalEnv))){
-      warning("An object named 'covid_df' was not found in your global environment so the following checks were not run: 
+  }
+
+  cat("\n")
+
+  if(!("covid_df" %in% ls(envir = .GlobalEnv))){
+    warning("An object named 'covid_df' was not found in your global environment so the following checks were not run: 
               check_ae_aeacn_ds_disctx_covid
               check_ae_aeacnoth_ds_stddisc_covid
               check_dv_ae_aedecod_covid")
-    }
-    
+  }
+
   cat("\n")
-    
+
   # return the final list
   return(all_rec)
-    
-} # end of function
+
+} # end of function

_pkgdown.yml

@@ -80,6 +80,8 @@ reference:
 
 news:
  releases:
+ - text: "sdtmchecks 0.1.11"  
+   href: news/index.html#sdtmchecks-0111-light-ice
  - text: "sdtmchecks 0.1.10"  
    href: news/index.html#sdtmchecks-0110-light-ice
  - text: "sdtmchecks 0.1.8"  

cran-comments.md

@@ -1,5 +1,3 @@
 ## R CMD check results
 
-0 errors | 0 warnings | 1 note
-
-* This is a new release.
+0 errors ✔ | 0 warnings ✔ | 0 notes ✔

inst/sdtmchecksmeta.R

@@ -55,7 +55,7 @@ sdtmchecksmeta <- googlesheets4::read_sheet(sdtmchecksmeta_url)
 # only update this in May and November when updating and re-running covid.R
 ## MedDRA &MEDDRV. COVID-19 SMQ (Narrow) --> MedDRA v23.1 COVID-19 SMQ (Narrow)
 
-MEDDRV <- "v26.1"
+MEDDRV <- "v27.0"
 sdtmchecksmeta$pdf_subtitle <- gsub("&MEDDRV.", MEDDRV, sdtmchecksmeta$pdf_subtitle)
 
 

tests/staging_testthat/empty.txt

@@ -0,0 +1 @@
+