Merge pull request #227 from OHDSI/v0.1.2

v0.1.2
OHDSI · Nov 13, 2024 · 0abd870 · 0abd870
2 parents e5d68a1 + 46bc63a
commit 0abd870
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diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -13,6 +13,8 @@ permissions: read-all
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - uses: actions/checkout@v4
@@ -42,7 +44,7 @@ jobs:
           file: ./cobertura.xml
           plugin: noop
           disable_search: true
-          token: 8e3843c1-7a05-4c43-89ac-ddc8f0edff7d
+          token: ${{ secrets.CODECOV_TOKEN }}
 
       - name: Show testthat output
         if: always()

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: OmopSketch
 Title: Characterise Tables of an OMOP Common Data Model Instance
-Version: 0.1.1
+Version: 0.1.2
 Authors@R: c(
     person( 
         "Marta", "Alcalde-Herraiz", 
@@ -15,10 +15,6 @@ Authors@R: c(
         "Elin", "Rowlands", email = "[email protected]", 
         role = c("aut"), comment = c(ORCID = "0009-0005-5166-0417")
     ),
-    person(
-        "Cecilia", "Campanile", email = "[email protected]", 
-        role = c("aut"), comment = c(ORCID = "0009-0007-6629-4661")
-    ),
     person(
         "Edward", "Burn", email = "[email protected]", 
         role = c("aut"), comment = c(ORCID = "0000-0002-9286-1128")
@@ -34,45 +30,27 @@ Description: Summarises key information in data mapped to the Observational
     to obtain feasibility counts and trends.
 License: Apache License (>= 2)
 Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-Suggests:
-    CodelistGenerator,
-    DBI,
-    duckdb,
-    flextable,
-    gt,
-    here,
-    knitr,
-    odbc,
-    remotes,
-    rmarkdown,
-    RPostgres,
-    testthat (>= 3.0.0),
-    withr,
-    omock (>= 0.3.0),
-    covr
+Suggests: CodelistGenerator, DBI, here, knitr, odbc, remotes,
+        rmarkdown, RPostgres, testthat (>= 3.0.0), withr
 Config/testthat/edition: 3
 Config/testthat/parallel: true
-Imports: 
-    CDMConnector (>= 1.3.0),
-    cli,
-    clock,
-    CohortConstructor (>= 0.3.1),
-    dplyr,
-    ggplot2,
-    omopgenerics (>= 0.3.1),
-    PatientProfiles (>= 1.2.1),
-    purrr,
-    rlang,
-    stringr,
-    tibble,
-    tidyr,
-    visOmopResults (>= 0.4.0)
-Depends: 
-    R (>= 2.10)
+Imports: CDMConnector (>= 1.3.0), cli, clock, gt, flextable,
+        CohortCharacteristics (>= 0.3.0), CohortConstructor (>= 0.3.1),
+        dplyr, ggplot2, omock (>= 0.3.0), omopgenerics (>= 0.3.1),
+        PatientProfiles (>= 1.2.0), purrr, rlang, stringr, tibble,
+        tidyr, visOmopResults (>= 0.4.0), duckdb
+Depends: R (>= 2.10)
 URL: https://OHDSI.github.io/OmopSketch/
 BugReports: https://github.com/OHDSI/OmopSketch/issues
 VignetteBuilder: knitr
-Remotes: 
-    darwin-eu-dev/omopgenerics
+NeedsCompilation: no
+Packaged: 2024-11-12 21:14:36 UTC; martaa
+Author: Marta Alcalde-Herraiz [aut, cre]
+    (<https://orcid.org/0009-0002-4405-1814>),
+  Kim Lopez-Guell [aut] (<https://orcid.org/0000-0002-8462-8668>),
+  Elin Rowlands [aut] (<https://orcid.org/0009-0005-5166-0417>),
+  Edward Burn [aut] (<https://orcid.org/0000-0002-9286-1128>),
+  Martí Català [aut] (<https://orcid.org/0000-0003-3308-9905>)
+Repository: CRAN
+Date/Publication: 2024-11-12 21:40:07 UTC
diff --git a/NAMESPACE b/NAMESPACE
@@ -9,20 +9,18 @@ export(plotInObservation)
 export(plotObservationPeriod)
 export(plotRecordCount)
 export(settings)
-export(summariseAllConceptCounts)
 export(summariseClinicalRecords)
 export(summariseConceptCounts)
 export(summariseInObservation)
-export(summariseMissingData)
 export(summariseObservationPeriod)
 export(summariseOmopSnapshot)
+export(summarisePopulationCharacteristics)
 export(summariseRecordCount)
 export(suppress)
-export(tableAllConceptCounts)
 export(tableClinicalRecords)
-export(tableMissingData)
 export(tableObservationPeriod)
 export(tableOmopSnapshot)
+export(tablePopulationCharacteristics)
 importFrom(dplyr,"%>%")
 importFrom(omopgenerics,bind)
 importFrom(omopgenerics,exportSummarisedResult)

diff --git a/R/checks.R b/R/checks.R
@@ -1,32 +1,12 @@
 #' @noRd
-checkInterval <- function(interval, call = parent.frame()){
-  omopgenerics::assertCharacter(interval, length = 1, na = FALSE, null = FALSE, call = call)
+checkUnit <- function(unit, call = parent.frame()){
+  omopgenerics::assertCharacter(unit, length = 1, na = FALSE, null = FALSE, call = call)
 
-  if(!interval %in% c("year","month")){
-    cli::cli_abort("Interval argument {interval} is not valid. Valid options are either `year` or `month`.", call = call)
+  if(!unit %in% c("year","month")){
+    cli::cli_abort("Unit argument {unit} is not valid. Valid options are either `year` or `month`.", call = call)
   }
 }
 
-validateIntervals <- function(interval, call = parent.frame()){
-
-  omopgenerics::assertCharacter(interval, length = 1, na = FALSE, null = FALSE, call = call)
-
-  if(!interval %in% c("overall","years","months","quarters")){
-    cli::cli_abort("Interval argument {interval} is not valid. Valid options are either `overall`, `years`, `quarters` or `months`.", call = call)
-  }
-
-  unitInterval <- dplyr::case_when(
-    interval == "overall" ~ NA,
-    interval == "quarters" ~ 4,
-    interval == "months" ~ 1,
-    interval == "years" ~ 1
-  )
-
-  if(interval == "quarters"){quarters <- "month"}else{interval <- gsub("s$","",interval)}
-
-  return(list("interval" = interval, "unitInterval" = unitInterval))
-}
-
 #' @noRd
 checkCategory <- function(category, overlap = FALSE, type = "numeric", call = parent.frame()) {
   omopgenerics::assertList(

diff --git a/R/mockOmopSketch.R b/R/mockOmopSketch.R
@@ -14,7 +14,10 @@
 #' @return A mock cdm_reference object.
 #' @export
 #' @examples
+#' \donttest{
+#' library(OmopSketch)
 #' mockOmopSketch(numberIndividuals = 100)
+#' }
 mockOmopSketch <- function(con = NULL,
                            writeSchema = NULL,
                            numberIndividuals = 100,

diff --git a/R/plotConceptCounts.R b/R/plotConceptCounts.R
@@ -9,7 +9,7 @@
 #' @export
 #' @examples
 #' \donttest{
-#' library(dplyr)
+#' library(dplyr, warn.conflicts = FALSE)
 #'
 #' cdm <- mockOmopSketch()
 #'
@@ -22,8 +22,8 @@
 #'   )
 #'
 #' result |>
-#'   filter(variable_name == "Number subjects") |>
-#'   plotConceptCounts(facet = "codelist_name", colour = "standard_concept_name")
+#'   filter(estimate_name == "person_count", variable_name == "overall") |>
+#'   plotConceptCounts(facet = "codelist_name", colour = "codelist_name")
 #'
 #' PatientProfiles::mockDisconnect(cdm)
 #' }
@@ -36,55 +36,29 @@ plotConceptCounts <- function(result,
   # subset to results of interest
   result <- result |>
     visOmopResults::filterSettings(.data$result_type == "summarise_concept_counts")
-
   if (nrow(result) == 0) {
     cli::cli_abort(c("!" = "No records found with result_type == summarise_concept_counts"))
   }
 
   # check only one estimate is contained
- variable <- unique(result$variable_name)
-  if (length(variable) > 1) {
+  estimate <- unique(result$estimate_name)
+  if (length(estimate) > 1) {
     cli::cli_abort(c(
-      "!" = "Subset to the variable of interest, there are results from: {variable}.",
-      "i" = "result |> dplyr::filter(variable_name == '{variable[1]}')"
+      "!" = "Subset to the estimate of interest, there are results from: {estimate}.",
+      "i" = "result |> dplyr::filter(estimate_name == '{estimate[1]}')"
     ))
   }
 
-  result1 <- result |> visOmopResults::splitAdditional()
-  # Detect if there are several time intervals
-  if("time_interval" %in% colnames(result1)){
-    # Line plot where each concept is a different line
-    p <- result1 |>
-      dplyr::filter(.data$time_interval != "overall") |>
-      visOmopResults::uniteAdditional(cols = c("time_interval", "standard_concept_name", "standard_concept_id", "source_concept_name", "source_concept_id", "domain_id")) |>
-      visOmopResults::scatterPlot(x = "time_interval",
-                                  y = "count",
-                                  line   = TRUE,
-                                  point  = TRUE,
-                                  ribbon = TRUE,
-                                  group  = "standard_concept_name",
-                                  facet  = facet,
-                                  colour = colour)
-  }else{
-    if("standard_concept_name" %in% colnames(result1)){
-      p <- result |>
-        visOmopResults::barPlot(x = "standard_concept_name",
-                                y = "count",
-                                facet = facet,
-                                colour = colour)
-    }else{
-      p <- result |>
-        visOmopResults::barPlot(x = "codelist_name",
-                                y = "count",
-                                facet = facet,
-                                colour = colour)
-    }
-    p <- p +
-      ggplot2::labs(
-        x = "Concept name"
-      )
-  }
-
- p +
+  order <- c("overall", sort(unique(result$variable_name[result$variable_name != "overall"])))
+  result |>
+    dplyr::mutate(variable_name = factor(.data$variable_name,
+                                         levels = order)) |>
+    visOmopResults::barPlot(x = "variable_name",
+                            y = estimate,
+                            facet = facet,
+                            colour = colour) +
+    ggplot2::labs(
+      x = "Concept name"
+    ) +
     ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, vjust = 0.5, hjust = 1))
 }
diff --git a/R/plotInObservation.R b/R/plotInObservation.R
@@ -10,7 +10,7 @@
 #' @export
 #' @examples
 #' \donttest{
-#' library(dplyr)
+#' library(dplyr, warn.conflicts = FALSE)
 #'
 #' cdm <- mockOmopSketch()
 #'
@@ -52,35 +52,27 @@ plotInObservation <- function(result,
   }
 
   # warn
-  warnFacetColour(result, list(facet = asCharacterFacet(facet), colour = colour, "additional_level"))
+  warnFacetColour(result, list(facet = asCharacterFacet(facet), colour = colour, "variable_level"))
 
   # plot
-  if(length(unique(result$additional_level)) > 1 ){
-    result |>
-      dplyr::mutate(additional_level = as.character(gsub("-01$","",as.Date(gsub(" to.*","",.data$additional_level))))) |>
-      dplyr::filter(.data$estimate_name == "count") |>
-      visOmopResults::scatterPlot(
-        x = "time_interval",
-        y = "count",
-        line = TRUE,
-        point = TRUE,
-        ribbon = FALSE,
-        ymin = NULL,
-        ymax = NULL,
-        facet = facet,
-        colour = colour,
-        group = c("cdm_name", "omop_table", visOmopResults::strataColumns(result))
-      ) +
-      ggplot2::labs(
-        y = variable,
-        x = "Date"
-      )
-  }else{
-    result |>
-      dplyr::filter(.data$estimate_name == "count") |>
-      visOmopResults::barPlot(x = "variable_name",
-                              y = "count",
-                              facet  = facet,
-                              colour = colour)
-  }
+  result |>
+    dplyr::mutate(variable_level = as.Date(stringr::str_extract(
+      .data$variable_level, "^[^ to]+"))) |>
+    dplyr::filter(.data$estimate_name == "count") |>
+    visOmopResults::scatterPlot(
+      x = "variable_level",
+      y = "count",
+      line = TRUE,
+      point = TRUE,
+      ribbon = FALSE,
+      ymin = NULL,
+      ymax = NULL,
+      facet = facet,
+      colour = colour,
+      group = c("cdm_name", "omop_table", visOmopResults::strataColumns(result))
+    ) +
+    ggplot2::labs(
+      y = variable,
+      x = "Date"
+    )
 }
diff --git a/R/plotObservationPeriod.R b/R/plotObservationPeriod.R
@@ -57,9 +57,9 @@ plotObservationPeriod <- function(result,
 
   validateFacet(facet, result)
 
-  optFacetColour <- c("cdm_name", "observation_period_ordinal",
-                      visOmopResults::strataColumns(result))
-  omopgenerics::assertChoice(facet, optFacetColour, null = TRUE)
+  optFacetColour <- visOmopResults::tidyColumns(result)
+  optFacetColour <- optFacetColour[optFacetColour %in% visOmopResults::tidyColumns(result)]
+  omopgenerics::assertChoice(facet, optFacetColour, null = TRUE, call = call)
 
   # this is due to bug in visOmopResults to remove in next release
   # https://github.com/darwin-eu/visOmopResults/issues/246
@@ -68,7 +68,8 @@ plotObservationPeriod <- function(result,
 
   if(length(visOmopResults::groupColumns(result)) == 0){
     result <- result |>
-      dplyr::mutate(group_name  = "observation_period_ordinal")
+      dplyr::mutate(group_name  = "observation_period_ordinal",
+             group_level = "Overall")
   }
 
   if (plotType == "barplot") {
@@ -85,7 +86,7 @@ plotObservationPeriod <- function(result,
       x = "observation_period_ordinal",
       facet = facet,
       colour = colour)
-  } else if (plotType == "densityplot") {
+  } else {
     p <- visOmopResults::scatterPlot(
       result = result,
       x = "density_x",
@@ -95,8 +96,7 @@ plotObservationPeriod <- function(result,
       ribbon = FALSE,
       facet = facet,
       colour = colour,
-      group = optFacetColour
-    ) +
+      group = optFacetColour) +
       ggplot2::xlab(stringr::str_to_sentence(unique(result$variable_name))) +
       ggplot2::ylab("Density")
   }