v0.1.2

OHDSI · Feb 5, 2025 · 670eaff · 670eaff
1 parent 8da93a8
commit 670eaff
Show file tree

Hide file tree

Showing 6 changed files with 12 additions and 4 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -9,3 +9,4 @@
 ^doc$
 ^Meta$
 ^cran-comments\.md$
+^CRAN-SUBMISSION$
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -0,0 +1,3 @@
+Version: 0.1.2
+Date: 2025-02-05 11:52:25 UTC
+SHA: 8da93a816e8e51f59309a69859cffad54fe8dc65
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PhenotypeR
 Type: Package
 Title: Assess Study Cohorts Using a Common Data Model
-Version: 0.1.1.900
+Version: 0.1.2
 Authors@R: c(
     person("Edward", "Burn", , "edward.burn@ndorms.ox.ac.uk", 
     role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9286-1128")),

diff --git a/tests/testthat/test-codelistDiagnostics.R b/tests/testthat/test-codelistDiagnostics.R
@@ -1,4 +1,6 @@
 test_that("missing codelist attribute", {
+  skip_on_cran()
+
   testthat::skip_on_cran()
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(nPerson = 100) |>

diff --git a/tests/testthat/test-phenotypeDiagnostics.R b/tests/testthat/test-phenotypeDiagnostics.R
@@ -1,5 +1,7 @@
 test_that("overall diagnostics function", {
 
+  skip_on_cran()
+
   cdm_local <- omock::mockCdmReference() |>
     omock::mockPerson(nPerson = 100) |>
     omock::mockObservationPeriod() |>

diff --git a/vignettes/a04_MatchedDiagnostics.Rmd b/vignettes/a04_MatchedDiagnostics.Rmd
@@ -1,5 +1,5 @@
 ---
-title: "a04_MatchedDiagnostics"
+title: "Matched diagnostics"
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{a04_MatchedDiagnostics}
@@ -30,7 +30,7 @@ if (!eunomia_is_available()) downloadEunomiaData(datasetName = "synpuf-1k")
 ## Introduction
 In this example we're going to again create cohorts of individuals with an ankle sprain, ankle fracture, forearm fracture, or a hip fracture using the Eunomia synthetic data. 
 
-```{r}
+```{r, eval=FALSE}
 library(CDMConnector)
 library(CohortConstructor)
 library(CodelistGenerator)
@@ -60,7 +60,7 @@ cdm$injuries <- conceptCohort(cdm = cdm,
 
 ## Matched diagnostics
 Running the `matchedDiagnostics()` will compare the individuals in our cohorts with age and sex matched controls from the data source. This helps us to find features of our cohort that are particularly distinctive.
-```{r}
+```{r, eval=FALSE}
 matched_diag <- matchedDiagnostics(cdm$injuries)
 ```
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,3 +9,4 @@ @@
     ^doc$
     ^Meta$
     ^cran-comments\.md$
+    ^CRAN-SUBMISSION$