415 visit logic unit tests

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: sdtmchecks
 Title: Data Quality Checks for Study Data Tabulation Model (SDTM) Datasets
-Version: 1.0.0
+Version: 1.0.0.9001
 Authors@R: c(
     person(given="Will", 
            family="Harris",

NEWS.md

@@ -1,20 +1,28 @@
+# sdtmchecks 1.0.0.9001 "CRAN Try"
+
+
+## Refinements of existing data check functions
+* Add more logic to check missing visit post-subsetting the dataframe: 
+[`check_lb_lbdtc_visit_ordinal_error`](https://pharmaverse.github.io/sdtmchecks/reference/check_lb_lbdtc_visit_ordinal_error.html), [`check_rs_rsdtc_visit_ordinal_error`](https://pharmaverse.github.io/sdtmchecks/reference/check_rs_rsdtc_visit_ordinal_error.html), [`check_tr_trdtc_visit_ordinal_error`](https://pharmaverse.github.io/sdtmchecks/reference/check_tr_trdtc_visit_ordinal_error.html), [`check_tu_tudtc_visit_ordinal_error`](https://pharmaverse.github.io/sdtmchecks/reference/check_tu_tudtc_visit_ordinal_error.html)
+
+
 # sdtmchecks 1.0.0 "CRAN Try"
 
 
 ## Refinements of existing data check functions
 
-* Covid related checks have been updated to expect a character vector of terms identifying covid related AEs.  Specifically [`check_ae_aeacn_ds_disctx_covid`](https://pharmaverse.github.io/sdtmchecks/reference/check_ae_aeacn_ds_disctx_covid.html), [`check_ae_aeacnoth_ds_stddisc_covid`](https://pharmaverse.github.io/sdtmchecks/reference/check_ae_aeacnoth_ds_stddisc_covid.html), [`check_dv_ae_aedecod_covid`](https://pharmaverse.github.io/sdtmchecks/reference/check_dv_ae_aedecod_covid.html) are affected.
+* Covid-19 related checks have been updated to expect a character vector of terms identifying Covid related AEs. Specifically [`check_ae_aeacn_ds_disctx_covid`](https://pharmaverse.github.io/sdtmchecks/reference/check_ae_aeacn_ds_disctx_covid.html), [`check_ae_aeacnoth_ds_stddisc_covid`](https://pharmaverse.github.io/sdtmchecks/reference/check_ae_aeacnoth_ds_stddisc_covid.html), [`check_dv_ae_aedecod_covid`](https://pharmaverse.github.io/sdtmchecks/reference/check_dv_ae_aedecod_covid.html) are affected.
 * [`check_vs_height`](https://pharmaverse.github.io/sdtmchecks/reference/check_vs_height.html) minor update to return message [#379](https://github.com/pharmaverse/sdtmchecks/issues/379)
 * [`check_lb_missing_month`](https://pharmaverse.github.io/sdtmchecks/reference/check_lb_missing_month.html) and [`check_mh_missing_month`](https://pharmaverse.github.io/sdtmchecks/reference/check_mh_missing_month.html) were both updated to have flexibility for Roche functions parsing `--SPID`
 
 ## Misc package updates
 
 * General updates for CRAN compliance, e.g. to DESCRIPTION file, Roxygen headers, etc.
 * Remove `rm(list=ls())` from sdtmchecksmeta.R ([#375](https://github.com/pharmaverse/sdtmchecks/issues/375))
-* Removed `xls2list()` function.  If working with the results of `run_all_checks()` it's recommended to output results to to .rds instead of parsing .xlsx files.
+* Removed `xls2list()` function.  If working with the results of `run_all_checks()` it's recommended to output results to .rds instead of parsing .xlsx files.
 
 
-# sdtmchecks 0.1.11.9008 "Light Ice"
+# sdtmchecks 0.1.12 "Light Ice"
 
 
 ## Refinements of existing data check functions

R/check_lb_lbdtc_visit_ordinal_error.R

@@ -84,7 +84,16 @@ check_lb_lbdtc_visit_ordinal_error <- function(LB){
         subsetdf = subset(LB, LB$LBSTAT != "NOT DONE"  & !grepl("UNSCHEDU|TREATMENT OR OBSERVATION FU COMP EARLY DISC", toupper(LB$VISIT)))
 
 
-        if(nrow(subsetdf)>0){
+        ### re-check if the subset has VISITNUM all missing 
+        if (length(unique(subsetdf[["VISITNUM"]]))<=1) {
+
+            fail(msg="VISITNUM exists but only a single value. ")
+
+        }
+
+
+
+        else if(nrow(subsetdf)>0){
 
             mydf2 <- dtc_dupl_early(
                 dts = subsetdf,

R/check_rs_rsdtc_visit_ordinal_error.R

@@ -54,7 +54,14 @@ check_rs_rsdtc_visit_ordinal_error <- function(RS){
         #only keep INV overall responses not indicated as Not Done
         subsetdf = subset(RS,RS$RSTESTCD=="OVRLRESP" & RS$RSEVAL=="INVESTIGATOR" & RS$RSSTAT != "NOT DONE" & !grepl("UNSCHEDU",toupper(RS$VISIT)),)
 
-        if(nrow(subsetdf)>0){
+        ### re-check if the subset has VISITNUM all missing 
+        if (length(unique(subsetdf[["VISITNUM"]]))<=1) {
+
+            fail("VISITNUM exists but only a single value. ")
+
+        } 
+
+        else if(nrow(subsetdf)>0){
 
             mydf2 <- dtc_dupl_early(dts = subsetdf, vars = vars,
                                     ### groupby variables used for grouping and visit.order derivation

R/check_tr_trdtc_visit_ordinal_error.R

@@ -53,8 +53,17 @@ check_tr_trdtc_visit_ordinal_error <- function(TR){
     } else {
 
         subsetdf = subset(TR, TR$TREVAL=="INVESTIGATOR" & TR$TRSTAT !="NOT DONE" & !grepl("UNSCHEDU",toupper(TR$VISIT)),)
+
+        ### re-check if the subset has VISITNUM all missing 
+        if (length(unique(subsetdf[["VISITNUM"]]))<=1) {
+
+            fail(msg="VISITNUM exists but only a single value. ")
+
+        }
+
+
 
-        if(nrow(subsetdf)>0){
+        else if(nrow(subsetdf)>0){
 
         mydf2 <- dtc_dupl_early(dts = subsetdf, vars = vars,
                                 ### groupby variables used for grouping and visit.order derivation

R/check_tu_tudtc_visit_ordinal_error.R

@@ -55,7 +55,16 @@ check_tu_tudtc_visit_ordinal_error <- function(TU){
 
         subsetdf = subset(TU, TU$TUEVAL=="INVESTIGATOR" & !grepl("UNSCHEDU",toupper(TU$VISIT)),)
 
-        if(nrow(subsetdf)>0){
+        ### re-check if the subset has VISITNUM all missing 
+        if (length(unique(subsetdf[["VISITNUM"]]))<=1) {
+
+            fail(msg="VISITNUM exists but only a single value. ")
+
+        }
+
+
+
+        else if(nrow(subsetdf)>0){
 
         mydf2 <- dtc_dupl_early(
             dts = subsetdf,

_pkgdown.yml

@@ -69,7 +69,7 @@ reference:
   # - convert_var_to_ascii 
   # - truncate_var_strings
   # - create_R_script
-  # - xlsx2list
+  # - xlsx2list (no longer in the package)
 
 - title: "Company-specific utility functions"
   desc: Helper functions for data checks tailored to company-specific data inputs.
@@ -79,8 +79,10 @@ reference:
 
 news:
  releases:
+ - text: "sdtmchecks 1.0.0"  
+   href: news/index.html#sdtmchecks-100-cran-try
  - text: "sdtmchecks 0.1.12"  
-   href: news/index.html#sdtmchecks-0112-cran-try
+   href: news/index.html#sdtmchecks-0112-light-ice
  - text: "sdtmchecks 0.1.11"  
    href: news/index.html#sdtmchecks-0111-light-ice
  - text: "sdtmchecks 0.1.10"  

tests/testthat/test-check_lb_lbdtc_visit_ordinal_error.R

@@ -108,3 +108,28 @@ test_that("Function returns false when expected column not present", {
   expect_false(check_lb_lbdtc_visit_ordinal_error(LB1))
 })
 
+
+
+test_that("Function returns false when subset has VISITNUM all missing ", {
+
+  LB2 <- data.frame(USUBJID = c(rep("101", 5), rep("102", 5)),
+                    LBCAT = "Hematology",
+                    LBDTC = rep(c(
+                      "2017-01-01T08:25",
+                      "2017-01-05T09:25",
+                      "2017-01-15T10:25",
+                      "2017-01-20T08:25",
+                      "2017-01-25T08:25"), 2),
+                    VISITNUM = rep(c(rep(1, 4), 2),2), 
+                    VISIT = rep(c(
+                      "Visit 1",
+                      "Visit 2",
+                      "Visit 3",
+                      "VIsit 5",
+                      "UNSCheduled!!!"), 2),
+                    LBSTAT = c(rep("", 9), "NOT DONE"),
+                    stringsAsFactors = FALSE)
+
+
+  expect_false(check_lb_lbdtc_visit_ordinal_error(LB2))
+})

tests/testthat/test-check_rs_rsdtc_visit_ordinal_error.R

@@ -104,3 +104,19 @@ test_that("Function returns false when Investigator (INV) records but not OVRLRE
   expect_false(check_rs_rsdtc_visit_ordinal_error(RS))
 })
 
+
+
+test_that("Function returns false when subset has VISITNUM all missing", {
+
+  RS2<- data.frame(USUBJID = 101:102,
+                   RSDTC=rep(c("2017-01-01T08:25", "2017-01-05T09:25",
+                               "2017-01-15T10:25","2017-01-20T08:25","2017-01-25T08:25"), 2),
+                   VISITNUM=rep(c(rep(1, 4), 2),2), 
+                   VISIT=rep(c("Screening", "Cycle 1", "Cycle 2","Cycle 3","UNSCHEDULED"),2),
+                   RSTESTCD="OVRLRESP",
+                   RSEVAL="INVESTIGATOR",
+                   RSSTAT="",
+                   stringsAsFactors=FALSE)
+
+  expect_false(check_rs_rsdtc_visit_ordinal_error(RS2))
+})

tests/testthat/test-check_tr_trdtc_visit_ordinal_error.R

@@ -260,3 +260,20 @@ test_that("Returns false when VISITNUM exists but only a single non-missing valu
 })
 
 
+
+test_that("Function returns false when subset has VISITNUM all missing", {
+
+  TR <- data.frame(USUBJID = 101:102,
+                   TRSEQ=rep(1:5,2),
+                   TRDTC = rep(c("2017-01-01T08:25", "2017-01-05T09:25",
+                                 "2017-01-15T10:25","2017-01-20T08:25","2017-01-25T08:25"), 2),
+                   VISITNUM = rep(c(rep(1, 4), 2),2),
+                   VISIT = rep(c( "Visit 1", "Visit 2", "Visit 3", "Visit 4","Unscheduled"), 2),
+                   TREVAL="INVESTIGATOR",
+                   TRSTAT = "",
+                   stringsAsFactors = FALSE)
+
+  expect_false(check_tr_trdtc_visit_ordinal_error(TR))
+})
+
+

tests/testthat/test-check_tu_tudtc_visit_ordinal_error.R

@@ -222,3 +222,18 @@ test_that("Returns false when VISITNUM exists but only a single non-missing valu
 })
 
 
+
+test_that("Function returns false when subset has VISITNUM all missing", {
+
+  TU <- data.frame(USUBJID = 101:102,
+                   TUORRES = rep(c("NEW", "TARGET"), 5),
+                   TULOC=rep(c("BONE","LIVER"),5),
+                   TUDTC = rep(c("2017-01-01T08:25", "2017-01-05T09:25",
+                                 "2017-01-15T10:25","2017-01-20T08:25","2017-01-25T08:25"), 2),
+                   VISITNUM = rep(c(rep(1, 4), 2),2),
+                   VISIT = rep(c( "Visit 1", "Visit 2", "Visit 3", "Visit 4","UNSCHEDULED"), 2),
+                   TUEVAL="INVESTIGATOR",
+                   stringsAsFactors = FALSE)
+
+  expect_false(check_tu_tudtc_visit_ordinal_error(TU))
+})