Merge pull request #7 from oxford-pharmacoepi/dev_cc

shine and code updated
oxford-pharmacoepi · Jan 13, 2025 · 7a49f62 · 7a49f62
2 parents d37d75b + ddc07ab
commit 7a49f62
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Showing 23 changed files with 2,105 additions and 4,930 deletions.
diff --git a/CharacterisationCode/RunCharacterisation.R b/CharacterisationCode/RunCharacterisation.R
@@ -16,9 +16,10 @@ log_message("Start time recorded.")
 tableName <- c("observation_period", "visit_occurrence", "condition_occurrence", "drug_exposure", "procedure_occurrence", 
                "device_exposure", "measurement" , "observation", "death")
 sex <- TRUE # FALSE
-ageGroup <- list(c(0,19), c(20, 39),c(40, 59), c(60, 79), c(80, Inf) ) # NULL
+ageGroup <- list(c(0,19), c(20, 39),c(40, 59), c(60, 79), c(80, Inf) ) 
 ageGroup <- omopgenerics::validateAgeGroupArgument(ageGroup, ageGroupName = "")[[1]]
 dateRange <- as.Date(c("2012-01-01", NA))
+
 # Snapshot
 log_message("Getting cdm snapshot")
 snapshot <- OmopSketch::summariseOmopSnapshot(cdm) 
@@ -30,6 +31,7 @@ result_populationCharacteristics <- CohortConstructor::demographicsCohort(cdm, "
   CohortConstructor::requireInDateRange(dateRange = dateRange)|>
   CohortCharacteristics::summariseCharacteristics(strata = list("sex", "age_group") )
 
+# Summarise missing data
 log_message("Summarising missing data")
 result_missingData <- OmopSketch::summariseMissingData(cdm ,
                                                        omopTableName = tableName, 
@@ -38,15 +40,16 @@ result_missingData <- OmopSketch::summariseMissingData(cdm ,
                                                        year = TRUE, 
                                                        dateRange = dateRange)
 
-log_message("Summarising all concept counts")
-result_allConceptCount <- OmopSketch::summariseAllConceptCounts(cdm, 
-                                                                omopTableName = tableName, 
-                                                                sex = sex, 
-                                                                ageGroup = ageGroup, 
-                                                                year = TRUE, 
-                                                                dateRange = dateRange)
+# Summarise concept counts
+log_message("Summarising concept id counts")
+result_conceptIdCount <- OmopSketch::summariseConceptIdCounts(cdm, 
+                                                              omopTableName = tableName, 
+                                                              sex = sex, 
+                                                              ageGroup = ageGroup, 
+                                                              year = TRUE, 
+                                                              dateRange = dateRange)
 
-# Summarize clinical records
+# Summarise clinical records
 log_message("Summarising clinical records")
 result_clinicalRecords<- OmopSketch::summariseClinicalRecords(cdm, 
                                                   omopTableName = tableName, 
@@ -77,15 +80,15 @@ result_inObservation <- OmopSketch::summariseInObservation(cdm$observation_perio
 
 
 
-# Summarize observation period
+# Summarise observation period
 log_message("Summarising observation period")
 result_observationPeriod <- OmopSketch::summariseObservationPeriod(cdm$observation_period, 
                                                                    sex = sex, 
                                                                    ageGroup = ageGroup, 
                                                                    dateRange = dateRange)
 
 # Combine results and export
-result <- omopgenerics::bind(snapshot, result_populationCharacteristics, result_missingData, result_allConceptCount, result_clinicalRecords, result_recordCounts, result_inObservation, result_observationPeriod)
+result <- omopgenerics::bind(snapshot, result_populationCharacteristics, result_missingData, result_conceptIdCount, result_clinicalRecords, result_recordCounts, result_inObservation, result_observationPeriod)
 omopgenerics::exportSummarisedResult(result, minCellCount = minCellCount, path = outputFolder, fileName = paste0(
   "result_characterisation_", dbName, ".csv"))
 
@@ -96,7 +99,7 @@ dur <- abs(as.numeric(Sys.time() - start_time, units = "secs"))
 log_message(paste("Study code finished. Code ran in", floor(dur / 60), "min and", dur %% 60 %/% 1, "sec"))
 
 # Close connection
-cdm_disconnect(cdm)
+CDMConnector::cdmDisconnect(cdm)
 log_message("Database connection closed")
 
 # Zip the results

diff --git a/CharacterisationCode/codeLocal.R b/CharacterisationCode/codeLocal.R
diff --git a/CharacterisationCode/renv.lock b/CharacterisationCode/renv.lock
@@ -11,7 +11,7 @@
   "Packages": {
     "CDMConnector": {
       "Package": "CDMConnector",
-      "Version": "1.6.1",
+      "Version": "1.7.0",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -21,7 +21,6 @@
         "cli",
         "dbplyr",
         "dplyr",
-        "fs",
         "generics",
         "glue",
         "jsonlite",
@@ -35,10 +34,9 @@
         "stringr",
         "tidyr",
         "tidyselect",
-        "waldo",
         "withr"
       ],
-      "Hash": "1b6e550b3f742dab03099f3768595b98"
+      "Hash": "5233515358b0c45cd01e0d19573f0709"
     },
     "CohortCharacteristics": {
       "Package": "CohortCharacteristics",
@@ -99,13 +97,9 @@
     },
     "OmopSketch": {
       "Package": "OmopSketch",
-      "Version": "0.1.1",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteRepo": "OmopSketch",
-      "RemoteUsername": "OHDSI",
-      "RemoteSha": "24bcfb26100b03f55579ac973a3d8ca6a1bbe1c5",
+      "Version": "0.2.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
       "Requirements": [
         "CDMConnector",
         "CohortConstructor",
@@ -114,19 +108,20 @@
         "cli",
         "clock",
         "dplyr",
+        "glue",
+        "lifecycle",
         "omopgenerics",
         "purrr",
         "rlang",
         "stringr",
         "tibble",
-        "tidyr",
-        "visOmopResults"
+        "tidyr"
       ],
-      "Hash": "e26a42bbb901e8d9d3e972df3b9dddda"
+      "Hash": "0c37ddc951ee1dafd9ef3ef7998db507"
     },
     "PatientProfiles": {
       "Package": "PatientProfiles",
-      "Version": "1.2.2",
+      "Version": "1.2.3",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -141,7 +136,7 @@
         "stringr",
         "tidyr"
       ],
-      "Hash": "87b3c5ddb1c4bc1f464115f610325c0e"
+      "Hash": "4f2cb7324f2d1d4f04a4aeb52fc6a200"
     },
     "R6": {
       "Package": "R6",
@@ -165,13 +160,13 @@
     },
     "bit": {
       "Package": "bit",
-      "Version": "4.5.0",
+      "Version": "4.5.0.1",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R"
       ],
-      "Hash": "5dc7b2677d65d0e874fc4aaf0e879987"
+      "Hash": "f89f074e0e49bf1dbe3eba0a15a91476"
     },
     "bit64": {
       "Package": "bit64",
@@ -250,13 +245,13 @@
     },
     "cpp11": {
       "Package": "cpp11",
-      "Version": "0.5.0",
+      "Version": "0.5.1",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "R"
       ],
-      "Hash": "91570bba75d0c9d3f1040c835cee8fba"
+      "Hash": "9df43854f1c84685d095ed6270b52387"
     },
     "crayon": {
       "Package": "crayon",
@@ -298,21 +293,6 @@
       ],
       "Hash": "39b2e002522bfd258039ee4e889e0fd1"
     },
-    "diffobj": {
-      "Package": "diffobj",
-      "Version": "0.3.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "crayon",
-        "methods",
-        "stats",
-        "tools",
-        "utils"
-      ],
-      "Hash": "bcaa8b95f8d7d01a5dedfd959ce88ab8"
-    },
     "dplyr": {
       "Package": "dplyr",
       "Version": "1.1.4",
@@ -361,17 +341,6 @@
       ],
       "Hash": "962174cf2aeb5b9eea581522286a911f"
     },
-    "fs": {
-      "Package": "fs",
-      "Version": "1.6.5",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "methods"
-      ],
-      "Hash": "7f48af39fa27711ea5fbd183b399920d"
-    },
     "generics": {
       "Package": "generics",
       "Version": "0.1.3",
@@ -453,13 +422,9 @@
     },
     "omopgenerics": {
       "Package": "omopgenerics",
-      "Version": "0.4.0",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "RemoteHost": "api.github.com",
-      "RemoteRepo": "omopgenerics",
-      "RemoteUsername": "darwin-eu",
-      "RemoteSha": "3778bbd2cd5510a817dbac411b10af401fd25965",
+      "Version": "0.4.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
       "Requirements": [
         "R",
         "cli",
@@ -476,24 +441,23 @@
         "tidyr",
         "vctrs"
       ],
-      "Hash": "28e55bb219ef063055c3775a57ad60a0"
+      "Hash": "072f4e363174ababd20aeab7926d5797"
     },
     "pillar": {
       "Package": "pillar",
-      "Version": "1.9.0",
+      "Version": "1.10.0",
       "Source": "Repository",
-      "Repository": "CRAN",
+      "Repository": "RSPM",
       "Requirements": [
         "cli",
-        "fansi",
         "glue",
         "lifecycle",
         "rlang",
         "utf8",
         "utils",
         "vctrs"
       ],
-      "Hash": "15da5a8412f317beeee6175fbc76f4bb"
+      "Hash": "101ca350beea21261a15ba169d7a8513"
     },
     "pkgconfig": {
       "Package": "pkgconfig",
@@ -778,21 +742,6 @@
       ],
       "Hash": "390f9315bc0025be03012054103d227c"
     },
-    "waldo": {
-      "Package": "waldo",
-      "Version": "0.6.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "cli",
-        "diffobj",
-        "glue",
-        "methods",
-        "rlang"
-      ],
-      "Hash": "52f574062a7b66e56926988c3fbdb3b7"
-    },
     "withr": {
       "Package": "withr",
       "Version": "3.0.2",

diff --git a/README.md b/README.md
@@ -15,16 +15,25 @@ This repository contains code for the characterisation of a database.
 
 1.  **Download the Repository**\
     Download this repository:
+
     -   Either download as a ZIP file using `Code -> Download ZIP`, then unzip.
     -   Or, use GitHub Desktop to clone the repository.
+
 2.  **Open the R Project**
+
     -   Navigate to the `CharacterisationCode` folder and open the project file `CharacterisationCode.Rproj` in RStudio.
     -   You should see the project name in the top-right corner of your RStudio session.
+
 3.  **Run the Analysis Code**
+
     -   Open the `CodeToRun.R` file. This is the main script you’ll use.
     -   Follow the instructions within the file to add your database-specific information.
     -   Run the code as directed. This will generate a `Results` folder containing the outputs, including a ZIP file with the results for sharing.
-4.  **Visualize Results in Shiny**
+
+4.  **OPTIONAL: Visualize Results in Shiny**
+
+    -   Navigate to the `shiny` folder and open the project file `shiny.Rproj` in RStudio.
+    -   You should see the project name in the top-right corner of your RStudio session.
     -   Copy the generated result files (in .csv format) into the `Data` folder located within the `Shiny` folder.
-    -   Open the `global.R` script in the `Shiny` folder.
+    -   Open the `global.R` script in the `shiny` folder.
     -   Click the *Run App* button in RStudio to launch the local Shiny app for interactive exploration of the results.
diff --git a/Shiny/.Rprofile b/Shiny/.Rprofile
diff --git a/Shiny/background.md b/Shiny/background.md
diff --git a/Shiny/data/README b/Shiny/data/README
diff --git a/Shiny/global.R b/Shiny/global.R