v0.6.1

darwin-eu · Nov 28, 2024 · d336f68 · d336f68
1 parent c8444d6
commit d336f68
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Showing 6 changed files with 43 additions and 26 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: CohortSurvival
 Title: Estimate Survival from Common Data Model Cohorts
-Version: 0.6.0
+Version: 0.6.1
 Authors@R: c(
     person("Edward", "Burn", email = "[email protected]", 
     role = c("aut", "cre"), 
@@ -27,7 +27,7 @@ Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 Imports: 
     CDMConnector (>= 1.3.0),
-    omopgenerics (>= 0.2.0),
+    omopgenerics (>= 0.4.0),
     checkmate,
     cli,
     DBI,
@@ -37,10 +37,8 @@ Imports:
     lubridate,
     broom,
     PatientProfiles,
-    visOmopResults (>= 0.3.0),
     rlang (>= 0.4.11),
     survival (>= 3.7.0),
-    scales,
     stringr,
     tibble,
     tidyr,
@@ -58,7 +56,9 @@ Suggests:
     cmprsk,
     duckdb,
     gt,
-    flextable
+    flextable,
+    scales,
+    visOmopResults (>= 0.5.0)
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 VignetteBuilder: knitr

diff --git a/R/asSurvivalResult.R b/R/asSurvivalResult.R
@@ -43,15 +43,16 @@ asSurvivalResult <- function(result) {
     cli::cli_abort("result is not a valid `summarised_result` object.")
   }
   result <- result %>%
-     visOmopResults::addSettings() %>%
+     omopgenerics::addSettings(
+       settingsColumn = c("result_type",omopgenerics::settingsColumns(result))) %>%
      dplyr::select(c("cdm_name", "group_name", "group_level", "strata_name",
                      "strata_level", "variable_name", "variable_level",
                      "estimate_name", "estimate_type", "estimate_value",
                      "additional_name", "additional_level", "result_type",
                      "outcome", "competing_outcome",
                      "eventgap")) %>%
-    visOmopResults::splitAdditional() %>%
-    visOmopResults::splitGroup() %>%
+    omopgenerics::splitAdditional() %>%
+    omopgenerics::splitGroup() %>%
     dplyr::mutate(estimate_value = as.numeric(.data$estimate_value))
 
   estimates <- result %>%

diff --git a/R/deathDiagnostics.R b/R/deathDiagnostics.R
@@ -96,6 +96,7 @@ deathDiagnostics <- function(cdm,
   output <- output %>%
     dplyr::mutate(
       cdm_name = attr(cdm, "cdm_name"),
+      result_id = 1,
       result_type = "death_diagnostics",
       package_name = "CohortSurvival",
       package_version = as.character(utils::packageVersion("CohortSurvival")),
@@ -178,6 +179,7 @@ deathDiagnostics <- function(cdm,
       output_w <- output_w %>%
         dplyr::mutate(
           cdm_name = attr(cdm, "cdm_name"),
+          result_id = 1,
           result_type = "death_diagnostics",
           package_name = "CohortSurvival",
           package_version = as.character(utils::packageVersion("CohortSurvival")),
@@ -208,5 +210,14 @@ deathDiagnostics <- function(cdm,
     }
   }
 
+  settings <- output %>%
+    dplyr::select("result_id", "result_type", "package_name", "package_version") %>%
+    dplyr::distinct()
+
+  output <- output %>%
+    dplyr::select(-c("result_type", "package_name", "package_version"))
+
+  output <- omopgenerics::newSummarisedResult(output, settings = settings)
+
   return(output)
 }
diff --git a/R/estimateSurvival.R b/R/estimateSurvival.R
@@ -189,8 +189,8 @@ estimateSingleEventSurvival <- function(cdm,
       "estimate_type" = "integer",
       competing_outcome = "none"
     ) %>%
-    visOmopResults::uniteStrata("reason") %>%
-    visOmopResults::uniteAdditional("reason_id")
+    omopgenerics::uniteStrata("reason") %>%
+    omopgenerics::uniteAdditional("reason_id")
 
   if(attrition %>% dplyr::group_by("target_cohort") %>% dplyr::tally() %>% dplyr::pull("n") ==
      attrition %>% dplyr::group_by("target_cohort", "cohort_definition_id") %>% dplyr::tally() %>% dplyr::pull("n")) {
@@ -288,8 +288,7 @@ estimateSingleEventSurvival <- function(cdm,
       censor_on_date = .env$censorOnDate,
       follow_up_days = .env$followUpDays,
       restricted_mean_follow_up = .env$restrictedMeanFollowUp,
-      minimum_survival_days = .env$minimumSurvivalDays,
-      min_cell_count = .env$minCellCount
+      minimum_survival_days = .env$minimumSurvivalDays
     )
 
   surv_estimates <- omopgenerics::newSummarisedResult(complete_results,
@@ -520,8 +519,8 @@ estimateCompetingRiskSurvival <- function(cdm,
       "estimate_value" = as.character(.data$estimate_value),
       "estimate_type" = "integer"
     ) %>%
-    visOmopResults::uniteStrata("reason") %>%
-    visOmopResults::uniteAdditional("reason_id")
+    omopgenerics::uniteStrata("reason") %>%
+    omopgenerics::uniteAdditional("reason_id")
 
   if(attrition %>% dplyr::group_by("target_cohort") %>% dplyr::tally() %>% dplyr::pull("n") ==
      attrition %>% dplyr::group_by("target_cohort", "cohort_definition_id") %>% dplyr::tally() %>% dplyr::pull("n")) {
@@ -621,8 +620,7 @@ estimateCompetingRiskSurvival <- function(cdm,
       censor_on_date = .env$censorOnDate,
       follow_up_days = .env$followUpDays,
       restricted_mean_follow_up = .env$restrictedMeanFollowUp,
-      minimum_survival_days = .env$minimumSurvivalDays,
-      min_cell_count = .env$minCellCount
+      minimum_survival_days = .env$minimumSurvivalDays
     )
 
   surv_estimates <- omopgenerics::newSummarisedResult(complete_results,

diff --git a/R/plotSurvival.R b/R/plotSurvival.R
@@ -53,6 +53,9 @@ plotSurvival <- function(result,
                          riskTable = FALSE,
                          riskInterval = 30) {
 
+  rlang::check_installed("ggplot2")
+  rlang::check_installed("scales")
+
   # Missing input checks
    omopgenerics::assertNumeric(xlim, min = 1, length = 1, integerish = TRUE, null = TRUE)
   if(is.null(xlim)) {xlim <- "Inf"}

diff --git a/R/tableSurvival.R b/R/tableSurvival.R
@@ -52,6 +52,8 @@ tableSurvival <- function(x,
                           groupColumn = NULL,
                           .options = list()){
 
+  rlang::check_installed("visOmopResults", version = "0.5.0")
+
   # initial checks
   omopgenerics::assertNumeric(times, min = 0, null = TRUE)
   omopgenerics::assertCharacter(timeScale, length = 1)
@@ -65,10 +67,12 @@ tableSurvival <- function(x,
   }
 
   # check times in x
-  x_clean <- x %>% visOmopResults::splitAdditional() %>%
+  x_clean <- x %>%
     dplyr::filter(.data$result_id %in% (omopgenerics::settings(x) %>%
                     dplyr::filter(grepl("probability", .data$result_type) | grepl("summary", .data$result_type)) %>%
-                    dplyr::pull("result_id")))
+                    dplyr::pull("result_id"))) %>%
+    omopgenerics::splitAdditional() %>%
+    dplyr::select(-"reason_id")
 
   if (!is.null(times)) {
     times_final <- dplyr::tibble(
@@ -136,7 +140,7 @@ tableSurvival <- function(x,
           bigMark = .options$bigMark
         ) %>%
         visOmopResults::formatEstimateName(
-          estimateNameFormat =
+          estimateName =
             c(" survival estimate" =
                 "<estimate> (<estimate_95CI_lower>, <estimate_95CI_upper>)")
         ) %>%
@@ -216,9 +220,10 @@ tableSurvival <- function(x,
       "Outcome type" = "variable_name",
       "Outcome name" = "variable_level"
     )
+    excludeCols = c("time", "reason_id", "reason")
     formatEstimateName = c("Restricted mean survival" = "<restricted_mean_survival>")
   } else {
-    excludeCols = c(excludeCols, "variable_name")
+    excludeCols = c(excludeCols, "variable_name","time", "reason_id", "reason")
     renameCols = c("Outcome name" = "variable_level")
     formatEstimateName = c("Restricted mean survival (SE)" =
                              "<restricted_mean_survival> (<restricted_mean_survival_se>)")
@@ -233,19 +238,18 @@ tableSurvival <- function(x,
 
   # to SR
   summary_table <- summary_table %>%
-    visOmopResults::uniteAdditional() %>%
+    omopgenerics::uniteAdditional() %>%
     dplyr::select(omopgenerics::resultColumns())
 
   summary_table <- visOmopResults::visOmopTable(
     summary_table,
-    formatEstimateName = formatEstimateName,
+    estimateName = formatEstimateName,
     header = header,
-    split = split,
     groupColumn = groupColumn,
     type = type,
-    renameColumns = renameCols,
+    rename = renameCols,
     showMinCellCount = TRUE,
-    excludeColumns = excludeCols,
+    hide = excludeCols,
     .options = c(.options, list(useFormatOrder = FALSE)) # to keep order set when factoring
   )
 
@@ -270,7 +274,7 @@ tableSurvival <- function(x,
 #'
 #'
 optionsTableSurvival <- function() {
-  default <- visOmopResults::optionsVisOmopTable()
+  default <- visOmopResults::tableOptions()
   default <- default[!names(default) %in% c("useFormatOrder", "keepNotFormatted")]
   return(default)
 }