Merge pull request #110 from ramses-antibiotics/develop

Ramses 0.7.0
ramses-antibiotics · Apr 11, 2023 · ebd423f · ebd423f
2 parents e15bf24 + e4e2888
commit ebd423f
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -6,6 +6,7 @@ on:
       - 'feature/**'
       - 'bug_fix/**'
       - 'bugfix/**'
+      - 'maint/**'
   schedule:
     # run release on the 8th of every month to detect problems with new packages/R releases
     - cron:  '19 3 8 * *'
@@ -37,7 +38,7 @@ jobs:
           # container action is not supported on windows or macOS
           # - {os: windows-latest, r: 'release'}
           # - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-20.04, r: '4.0.0', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
@@ -82,14 +83,16 @@ jobs:
 
       - name: Install dependencies
         run: |
+          remotes::install_github("msberends/AMR", build = TRUE)
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        run: |
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
       - name: Code coverage

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: Ramses
 Type: Package
 Title: R Package for Antimicrobial Stewardship & Surveillance 
-Version: 0.6.0
+Version: 0.7.0
 Authors@R: c(
     person(given = "Peter",
            family = "Dutey-Magni",
@@ -25,14 +25,14 @@ BugReports: https://github.com/ramses-antibiotics/ramses-package/issues
 Encoding: UTF-8
 LazyData: true
 Depends: 
-    R (>= 3.6.0),
+    R (>= 4.0.0),
     AMR (>= 1.8.0)
 Imports: 
     DBI,
     rlang,
-    dplyr (>= 1.0.1),
-    dbplyr (>= 2.2.0),
-    tidyselect,
+    dplyr (>= 1.1.0),
+    dbplyr (>= 2.3.2),
+    tidyselect (>= 1.2.0),
     magrittr,
     duckdb (>= 0.4.0),
     Rdpack (>= 0.7),

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,17 @@
 
+# Ramses 0.7.0
+
+*11 April 2023* 
+
+## Changed
+
+- Now requires minimum R v4.0.0, `dplyr` v1.1.0, `dbplyr` v2.3.2 and `tidyselect` v1.2.0.
+- Internal code maintenance in line with new tidy programming practice.
+- Tolerance built into the timeline for handling of no growth results. Ramses does not 
+currently prescribe whether no growth should be loaded into `microbiology_isolates` or not ([#108](https://github.com/ramses-antibiotics/ramses-package/issues/108)).
+The timeline will now show specimens without an isolate record at the time of collection.
+
+
 # Ramses 0.6.0
 
 *23 October 2022* 

diff --git a/R/metadata.R b/R/metadata.R
@@ -30,8 +30,9 @@ download_icd10cm <- function(silent = FALSE) {
   icd_source$level <- nchar(icd_source$icd_code)
 
   icd3 <- dplyr::filter(icd_source, .data$level == 3) %>% 
-    dplyr::transmute(category_code = .data$icd_code,
-                     category_description = .data$icd_description)
+    dplyr::mutate(category_code = .data$icd_code,
+                  category_description = .data$icd_description,
+                  .keep = "none")
 
   icd5 <- dplyr::filter(icd_source, .data$header_indicator == 1) %>% 
     dplyr::mutate(category_code = substring(.data$icd_code, 0, 3))
@@ -113,8 +114,9 @@ import_icd <- function(archive, version) {
   icd_source$level <- nchar(icd_source[["alt_code"]])
 
   icd3 <- dplyr::filter(icd_source, .data$level == 3) %>% 
-    dplyr::transmute(category_code = .data$alt_code,
-                     category_description = .data$description)
+    dplyr::mutate(category_code = .data$alt_code,
+                  category_description = .data$description,
+                  .keep = "none")
 
   icd5 <- dplyr::filter(icd_source, .data$level > 3) %>% 
     dplyr::mutate(category_code = substring(.data$alt_code, 0, 3))
@@ -127,9 +129,9 @@ import_icd <- function(archive, version) {
   icd$edition <- version
 
   icd <- dplyr::rename(icd,
-                       icd_display = .data$code,
-                       icd_code = .data$alt_code,
-                       icd_description = .data$description)
+                       icd_display = "code",
+                       icd_code = "alt_code",
+                       icd_description = "description")
   icd <- arrange_variables(icd, 
                            first_column_names = c(
                              "icd_code",

diff --git a/R/objects.R b/R/objects.R
@@ -185,7 +185,7 @@ Encounter <- function(conn, id, extend_table_start = NULL) {
   if(is(conn, "PqConnection") | is(conn, "duckdb_connection")) {
     tbl(conn, "ramses_tally") %>%
       dplyr::mutate(t = .data$t - as.integer(extend_table_start)) %>% 
-      dplyr::full_join(longitudinal_table, by = character()) %>%
+      dplyr::cross_join(longitudinal_table) %>%
       dplyr::mutate(t_start = dplyr::sql("admission_date + interval '1h' * t ")) %>% 
       dplyr::filter(.data$t_start < .data$discharge_date) %>% 
       dplyr::mutate(t_end = dplyr::sql("admission_date + interval '1h' * (t + 1)")) %>% 
@@ -369,7 +369,7 @@ setGeneric(name = "TherapyEpisode", def = TherapyEpisode)
   if(is(conn, "PqConnection") | is(conn, "duckdb_connection")) {
     tbl(conn, "ramses_tally") %>%
       dplyr::mutate(t = .data$t - as.integer(extend_table_start)) %>% 
-      dplyr::full_join(longitudinal_table, by = character()) %>%
+      dplyr::cross_join(longitudinal_table) %>%
       dplyr::mutate(t_start = dplyr::sql("therapy_start + interval '1h' * t "))%>% 
       dplyr::filter(.data$t_start < .data$therapy_end) %>% 
       dplyr::mutate(t_end = dplyr::sql("therapy_start + interval '1h' * (t + 1)")) %>% 

diff --git a/R/reference.R b/R/reference.R
@@ -205,7 +205,6 @@
 #'     \item{\code{pt_term}}{SNOMED CT Preferred Term}
 #'     \item{\code{snomed_release_version}}{SNOMED CT RF2 release date}
 #' }
-#' @seealso \url{https://snomedizer.web.app}
 #' @format A data frame.
 #' @docType data
 #' @name reference_specimen_type

diff --git a/R/timeline.R b/R/timeline.R
@@ -409,6 +409,11 @@ setMethod(
       dplyr::mutate(className = dplyr::if_else(is.na(.data$organism_code),
                                                "micro-report-no-growth", 
                                                "micro-report")) %>% 
+      dplyr::mutate(isolation_datetime = dplyr::if_else(
+        is.na(.data$isolation_datetime),
+        .data$specimen_datetime,
+        .data$isolation_datetime
+      )) %>% 
       dplyr::group_by(.data$specimen_id, .data$className) %>% 
       dplyr::summarise(
         id = paste0("Specimen ID:",

diff --git a/man/reference_specimen_type.Rd b/man/reference_specimen_type.Rd
diff --git a/tests/testthat/test-objects.R b/tests/testthat/test-objects.R
@@ -790,7 +790,9 @@ test_that("Encounter..constructor", {
     fake_db_conn, 
     dplyr::tibble(
       patient_id = "9",
-      encounter_id = "999999"
+      encounter_id = "999999", 
+      admission_date = Sys.Date(), 
+      discharge_date = Sys.Date()
     ),
     "inpatient_episodes", 
     temporary = FALSE
@@ -812,7 +814,9 @@ test_that("Encounter..constructor", {
     fake_db_conn, 
     dplyr::tibble(
       patient_id = 9,
-      encounter_id = 999999
+      encounter_id = 999999,
+      admission_date = Sys.Date(), 
+      discharge_date = Sys.Date()
     ),
     "inpatient_episodes", 
     temporary = FALSE
@@ -828,7 +832,9 @@ test_that("Encounter..constructor", {
     fake_db_conn, 
     dplyr::tibble(
       patient_id = 9L,
-      encounter_id = 999999L
+      encounter_id = 999999L,
+      admission_date = Sys.Date(), 
+      discharge_date = Sys.Date()
     ),
     "inpatient_episodes", 
     temporary = FALSE

diff --git a/tests/testthat/test-warehousing-duckdb.R b/tests/testthat/test-warehousing-duckdb.R
@@ -31,7 +31,7 @@ test_that(".create_sql_index on DuckDB", {
   expect_equal(
     DBI::dbGetQuery(db_conn, "SELECT * FROM pg_catalog.pg_indexes") %>% 
       dplyr::filter(.data$tablename == "test_table") %>% 
-      dplyr::select(.data$tablename, .data$indexname) %>% 
+      dplyr::select("tablename", "indexname") %>% 
       dplyr::collect(),
     data.frame(
       tablename = "test_table",
@@ -103,8 +103,8 @@ test_that("drug_prescriptions_edges on DuckDB", {
   load_medications(db_conn, records_rx, overwrite = T)
 
   output <- dplyr::distinct(tbl(db_conn, "drug_prescriptions_edges"), 
-                            patient_id, edge_type, relation_type) %>%
-    dplyr::arrange(patient_id) %>% 
+                            .data$patient_id, .data$edge_type, .data$relation_type) %>%
+    dplyr::arrange(.data$patient_id) %>% 
     dplyr::collect()
 
   records_edges <- read.csv(system.file("test_cases", "prescription_linkage_edges_classes.csv", 
@@ -131,8 +131,8 @@ test_that("create_mock_database on DuckDB", {
     dplyr::filter(prescription_id %in% c("592a738e4c2afcae6f625c01856151e0", 
                                          "89ac870bc1c1e4b2a37cec79d188cb08",
                                          "0bf9ea7732dd6e904ab670a407382d95")) %>% 
-    dplyr::select(prescription_id, combination_id, therapy_id) %>% 
-    dplyr::arrange(therapy_id, prescription_id) %>% 
+    dplyr::select("prescription_id", "combination_id", "therapy_id") %>% 
+    dplyr::arrange(.data$therapy_id, .data$prescription_id) %>% 
     dplyr::collect()
   expect_equal(
     test_output, 
@@ -226,8 +226,8 @@ test_that("Ramses on DuckDB (system test)", {
     dplyr::filter(prescription_id %in% c("592a738e4c2afcae6f625c01856151e0", 
                                          "89ac870bc1c1e4b2a37cec79d188cb08",
                                          "0bf9ea7732dd6e904ab670a407382d95")) %>% 
-    dplyr::select(prescription_id, combination_id, therapy_id) %>% 
-    dplyr::arrange(therapy_id, prescription_id) %>% 
+    dplyr::select("prescription_id", "combination_id", "therapy_id") %>% 
+    dplyr::arrange(.data$therapy_id, .data$prescription_id) %>% 
     dplyr::collect()
   expect_equal(
     test_output, 

diff --git a/tests/testthat/test-warehousing-postgres.R b/tests/testthat/test-warehousing-postgres.R
@@ -50,7 +50,7 @@ test_that(".create_sql_index on Postgres", {
   expect_equal(
     DBI::dbGetQuery(pq_conn, "SELECT * FROM pg_catalog.pg_indexes") %>% 
       dplyr::filter(.data$tablename == "test_table") %>% 
-      dplyr::select(.data$tablename, .data$indexname) %>% 
+      dplyr::select("tablename", "indexname") %>% 
       dplyr::collect(),
     data.frame(
       tablename = "test_table",
@@ -152,8 +152,8 @@ test_that("drug_prescriptions_edges on Postgres", {
   load_medications(pq_conn, records_rx, overwrite = T)
 
   output <- dplyr::distinct(tbl(pq_conn, "drug_prescriptions_edges"), 
-                            patient_id, edge_type, relation_type) %>% 
-    dplyr::arrange(patient_id) %>% 
+                            .data$patient_id, .data$edge_type, .data$relation_type) %>% 
+    dplyr::arrange(.data$patient_id) %>% 
     dplyr::collect()
 
   records_edges <- read.csv(system.file("test_cases", "prescription_linkage_edges_classes.csv", 
@@ -253,8 +253,8 @@ test_that("Ramses on PosgreSQL (system test)", {
     dplyr::filter(prescription_id %in% c("592a738e4c2afcae6f625c01856151e0", 
                                          "89ac870bc1c1e4b2a37cec79d188cb08",
                                          "0bf9ea7732dd6e904ab670a407382d95")) %>% 
-    dplyr::select(prescription_id, combination_id, therapy_id) %>% 
-    dplyr::arrange(therapy_id, prescription_id) %>% 
+    dplyr::select("prescription_id", "combination_id", "therapy_id") %>% 
+    dplyr::arrange(.data$therapy_id, .data$prescription_id) %>% 
     dplyr::collect()
   expect_equal(
     test_output,