Merge pull request #106 from ramses-antibiotics/develop

Ramses 0.6.0
ramses-antibiotics · Oct 23, 2022 · e15bf24 · e15bf24
2 parents 0aa1c48 + 5f7c2b9
commit e15bf24
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -6,6 +6,9 @@ on:
       - 'feature/**'
       - 'bug_fix/**'
       - 'bugfix/**'
+  schedule:
+    # run release on the 8th of every month to detect problems with new packages/R releases
+    - cron:  '19 3 8 * *'
 
 name: R-CMD-check
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: Ramses
 Type: Package
 Title: R Package for Antimicrobial Stewardship & Surveillance 
-Version: 0.5.2
+Version: 0.6.0
 Authors@R: c(
     person(given = "Peter",
            family = "Dutey-Magni",
@@ -32,6 +32,7 @@ Imports:
     rlang,
     dplyr (>= 1.0.1),
     dbplyr (>= 2.2.0),
+    tidyselect,
     magrittr,
     duckdb (>= 0.4.0),
     Rdpack (>= 0.7),

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,22 @@
 
+# Ramses 0.6.0
+
+*23 October 2022* 
+
+## Improvements
+
+- Changed `validate_inpatient_diagnoses()` to accept two optional fields `diagnosis_start`
+and `diagnosis_end` and take advantage of clinical systems such as problem lists
+- Changed `therapy_timeline()` to take advantage of `diagnosis_start` and `diagnosis_end`
+variables if present
+- Changed the `inpatient_diagnoses` mock dataset to removed episode start and end fields [#103](https://github.com/ramses-antibiotics/ramses-package/issues/103) which 
+duplicated information in `inpatient_episodes`
+- Changed `bridge_*()` functions to add a field `antiinfective_type` to bridge tables [#76](https://github.com/ramses-antibiotics/ramses-package/issues/76) and prevent 
+unrelated generation issues [#104](https://github.com/ramses-antibiotics/ramses-package/issues/104)
+- General code maintenance and adaptation to ongoing changes to the `dplyr` data masking
+approach [#105](https://github.com/ramses-antibiotics/ramses-package/issues/105).
+
+
 # Ramses 0.5.2
 
 *13 September 2022*

diff --git a/R/clinical_features.R b/R/clinical_features.R
@@ -23,20 +23,20 @@
   if ( !is.null(observation_code_system) ) {
   db_observation_codes <- dplyr::filter(
     dplyr::tbl(conn, "inpatient_investigations"), 
-    observation_code %in% !!observation_code & 
-      observation_code_system == !!observation_code_system
+    .data$observation_code %in% !!observation_code & 
+      .data$observation_code_system == !!observation_code_system
     )
   } else {
     db_observation_codes <- dplyr::filter(
       dplyr::tbl(conn, "inpatient_investigations"),
-      observation_code %in% !!observation_code
+      .data$observation_code %in% !!observation_code
     ) 
   }
 
   db_observation_codes <- dplyr::distinct(db_observation_codes,
-                                          observation_code_system, 
-                                          observation_code) %>% 
-    dplyr::group_by(observation_code) %>% 
+                                          .data$observation_code_system, 
+                                          .data$observation_code) %>% 
+    dplyr::group_by(.data$observation_code) %>% 
     dplyr::summarise(n = dplyr::n()) %>% 
     dplyr::collect() 
 
@@ -99,14 +99,14 @@
   operation <- tolower(operation)
   if ( is.null(observation_code_system) ) {
     parameter_name <- tbl(conn, "inpatient_investigations") %>% 
-      dplyr::filter(observation_code == !!observation_code) %>% 
-      dplyr::distinct(observation_display) %>% 
+      dplyr::filter(.data$observation_code == !!observation_code) %>% 
+      dplyr::distinct(.data$observation_display) %>% 
       dplyr::collect()
   } else {
     parameter_name <- tbl(conn, "inpatient_investigations") %>% 
-      dplyr::filter(observation_code == !!observation_code &
-                      observation_code_system == !!observation_code_system) %>% 
-      dplyr::distinct(observation_display) %>% 
+      dplyr::filter(.data$observation_code == !!observation_code &
+                      .data$observation_code_system == !!observation_code_system) %>% 
+      dplyr::distinct(.data$observation_display) %>% 
       dplyr::collect()
   }
   if ( nrow(parameter_name) == 0 ) {
@@ -162,21 +162,21 @@
   observations_linked <- dplyr::inner_join(
     LT, 
     dplyr::select(tbl(x@conn, "inpatient_investigations"),
-                  patient_id, observation_datetime,
-                  observation_code, observation_value_numeric,
-                  status, observation_code_system),
+                  "patient_id", "observation_datetime",
+                  "observation_code", "observation_value_numeric",
+                  "status", "observation_code_system"),
     by = "patient_id"
   ) %>% 
     dplyr::filter(
       dplyr::sql(sql_condition_1) &
-        status %in% c("final", "preliminary", "corrected", "amended") &
-        observation_code %in% !!observation_code & 
-        !is.na(observation_value_numeric)
+        .data$status %in% c("final", "preliminary", "corrected", "amended") &
+        .data$observation_code %in% !!observation_code & 
+        !is.na(.data$observation_value_numeric)
     )
 
   if ( !is.null(observation_code_system) ) {
     observations_linked <- observations_linked %>% 
-      dplyr::filter(observation_code_system == !!observation_code_system)
+      dplyr::filter(.data$observation_code_system == !!observation_code_system)
   }
 
   observations_linked
@@ -207,7 +207,7 @@
     observation_code_system = observation_code_system
   ) %>% 
     dplyr::group_by(.data$patient_id, .data[[x_entity_id_field_name]], .data$t) %>% 
-    dplyr::mutate(keep = dplyr::row_number(dplyr::desc(observation_datetime))) %>% 
+    dplyr::mutate(keep = dplyr::row_number(dplyr::desc(.data$observation_datetime))) %>% 
     dplyr::ungroup() %>% 
     dplyr::filter(.data$keep == 1) %>% 
     dplyr::transmute(.data$t,