fix bug with unknown classifications

sigven · Jan 30, 2024 · 0f2b046 · 0f2b046
1 parent 7f1c1ef
commit 0f2b046
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Showing 7 changed files with 11 additions and 10 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.5.5
+current_version = 1.5.4
 commit = True
 tag = False
 

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -10,7 +10,7 @@ on:
 name: pkgdown
 
 env:
-  VERSION: '1.5.5'
+  VERSION: '1.5.4'
 jobs:
   pkgdown:
     if: "startsWith(github.event.head_commit.message, 'Bump version:')"

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: pharmOncoX
 Type: Package
 Title: Molecularly targeted cancer drugs and biomarkers
-Version: 1.5.5
+Version: 1.5.4
 Date: 2024-01-30
 Authors@R: 
     c(person(given = "Sigve",

diff --git a/R/helpers.R b/R/helpers.R
@@ -9,9 +9,10 @@ get_targeted_drugs <- function(cache_dir = NA) {
 
 
   onco_drugs <- 
-    pharmOncoX::get_drugs(treatment_category = c("targeted_therapy_classified",
-                                     "targeted_therapy_unclassified",
-                                     "hormone_therapy_classified"),
+    pharmOncoX::get_drugs(
+      treatment_category = c("targeted_therapy_classified",
+                             "targeted_therapy_unclassified",
+                             "hormone_therapy_classified"),
               cache_dir = cache_dir,
               drug_classified_cancer = TRUE,
               drug_cancer_indication = TRUE,
@@ -301,7 +302,7 @@ get_targeted_drugs <- function(cache_dir = NA) {
   all_tt_records <- all_tt_records |>
     dplyr::filter(!(.data$atc_treatment_category == "cancer_unclassified" & 
                     .data$drug_cancer_relevance == "by_cancer_condition_otp" & 
-                    .data$drug_frac_cancer_indications < 0.7 & 
+                    .data$drug_frac_cancer_indications < 0.6 & 
                     .data$approved_indication == F)) |>
     dplyr::filter(!stringr::str_detect(.data$symbol,"^RRM"))
 

diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/data-raw/drug_utilities.R b/data-raw/drug_utilities.R
@@ -2663,7 +2663,7 @@ assign_drug_category <- function(drug_df = NULL,
       !is.na(target_symbol) &
       !is.na(atc_code_level3) &
         stringr::str_detect(
-          atc_code_level3, "(\\|L01XX[A-J])|(^L01XX[A-J])"
+          atc_code_level3, "(\\|L01XX[A-J]?)|(^L01XX[A-J]?)"
         ) ~ "cancer_targeted_therapy",
       !is.na(target_symbol) &
         !is.na(atc_code_level3) &

diff --git a/inst/CITATION b/inst/CITATION
@@ -5,10 +5,10 @@ citEntry(
   title    = "pharmOncoX: Targeted and non-targeted anti-cancer drugs and drug regimens",
   author   = "Sigve Nakken",
   year     = "2023",
-  note     = "R package version 1.5.5",
+  note     = "R package version 1.5.4",
   url      = "https://github.com/sigven/pharmOncoX",
   textVersion = paste("Nakken S. ","(2023)",
   " pharmOncoX: Targeted and non-targeted anti-cancer drugs and drug regimens.",
-  " R package version 1.5.5.",
+  " R package version 1.5.4.",
   " (https://github.com/sigven/pharmOncoX)")
 )