v0.8.0

darwin-eu · Oct 14, 2024 · 2f96bb8 · 2f96bb8
1 parent cfbc27a
commit 2f96bb8
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: IncidencePrevalence
 Title: Estimate Incidence and Prevalence using the OMOP Common Data Model
-Version: 0.7.4
+Version: 0.8.0
 Authors@R: c(
     person("Edward", "Burn", email = "[email protected]", 
     role = c("aut", "cre"), 
@@ -25,7 +25,7 @@ Authors@R: c(
 Description: Calculate incidence and prevalence using data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. Incidence and prevalence can be estimated for the total population in a database or for a stratification cohort.
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Depends: 
     R (>= 4.0)
 Imports: 
@@ -36,16 +36,15 @@ Imports:
     dbplyr (>= 2.5.0),
     dplyr (>= 1.1.0),
     glue (>= 1.5.0),
-    omopgenerics (>= 0.1.2),
-    lifecycle,
+    omopgenerics (>= 0.3.1),
     lubridate (>= 1.0.0),
     magrittr (>= 2.0.0),
     PatientProfiles (>= 1.1.0),
     purrr (>= 0.3.5),
     rlang (>= 1.0.0),
     stringr (>= 1.5.0),
     tidyr (>= 1.2.0),
-    visOmopResults
+    visOmopResults (>= 0.4.0)
 Suggests: 
     knitr,
     rmarkdown,

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,10 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(attrition,IncidenceResult)
-S3method(attrition,PrevalenceResult)
-S3method(participants,IncidencePrevalenceResult)
-S3method(settings,IncidenceResult)
-S3method(settings,PrevalenceResult)
 export("%>%")
 export(attrition)
 export(benchmarkIncidencePrevalence)
@@ -17,20 +12,25 @@ export(estimatePointPrevalence)
 export(exportSummarisedResult)
 export(generateDenominatorCohortSet)
 export(generateTargetDenominatorCohortSet)
+export(importSummarisedResult)
 export(mockIncidencePrevalenceRef)
 export(optionsTableIncidence)
 export(optionsTablePrevalence)
-export(participants)
 export(plotIncidence)
 export(plotPrevalence)
 export(settings)
 export(suppress)
+export(tableIncidence)
+export(tableIncidenceAttrition)
+export(tablePrevalence)
+export(tablePrevalenceAttrition)
 importFrom(magrittr,"%>%")
 importFrom(omopgenerics,attrition)
 importFrom(omopgenerics,bind)
 importFrom(omopgenerics,cohortCodelist)
 importFrom(omopgenerics,cohortCount)
 importFrom(omopgenerics,exportSummarisedResult)
+importFrom(omopgenerics,importSummarisedResult)
 importFrom(omopgenerics,settings)
 importFrom(omopgenerics,suppress)
 importFrom(rlang,":=")

diff --git a/R/benchmarkIncidencePrevalence.R b/R/benchmarkIncidencePrevalence.R
@@ -19,7 +19,6 @@
 #' @param cdm A CDM reference object
 #' @param analysisType A string of the following: "all", "only incidence",
 #' "only prevalence"
-#' @param returnParticipants Whether to return participants
 #'
 #' @return a tibble with time taken for different analyses
 #' @export
@@ -38,7 +37,6 @@
 #' timings <- benchmarkIncidencePrevalence(cdm)
 #' }
 benchmarkIncidencePrevalence <- function(cdm,
-                                         returnParticipants = FALSE,
                                          analysisType = "all") {
   errorMessage <- checkmate::makeAssertCollection()
   cdmCheck <- inherits(cdm, "cdm_reference")
@@ -116,7 +114,6 @@ benchmarkIncidencePrevalence <- function(cdm,
     tictoc::tic()
     pointPrev <- estimatePointPrevalence(
       cdm = cdm,
-      returnParticipants = returnParticipants,
       denominatorTable = "denominator_typical",
       outcomeTable = "bench_outcome",
       interval = "years"
@@ -133,7 +130,6 @@ benchmarkIncidencePrevalence <- function(cdm,
     tictoc::tic()
     period_prev <- estimatePeriodPrevalence(
       cdm = cdm,
-      returnParticipants = returnParticipants,
       denominatorTable = "denominator_typical",
       outcomeTable = "bench_outcome",
       interval = "years",
@@ -153,7 +149,6 @@ benchmarkIncidencePrevalence <- function(cdm,
     tictoc::tic()
     incTypicalYears <- estimateIncidence(
       cdm = cdm,
-      returnParticipants = returnParticipants,
       denominatorTable = "denominator_typical",
       outcomeTable = "bench_outcome",
       interval = "years"
@@ -192,24 +187,11 @@ benchmarkIncidencePrevalence <- function(cdm,
       ) %>%
       dplyr::pull())
 
-  if (isFALSE(returnParticipants)) {
-    timings <- timings %>%
-      dplyr::mutate(with_participants = "No")
-  } else {
-    timings <- timings %>%
-      dplyr::mutate(with_participants = "Yes")
-  }
 
   CDMConnector::dropTable(cdm = cdm,
                           name = dplyr::contains("denominator_typical"))
   CDMConnector::dropTable(cdm = cdm,
                           name = dplyr::contains("bench_outcome"))
-  CDMConnector::dropTable(cdm = cdm,
-                          name = dplyr::contains("point_prev_participants"))
-  CDMConnector::dropTable(cdm = cdm,
-                          name = dplyr::contains("period_prev_participants"))
-  CDMConnector::dropTable(cdm = cdm,
-                          name = dplyr::contains("inc_participants"))
 
   # as a summarised result
   timings <- timings %>%
@@ -230,13 +212,11 @@ benchmarkIncidencePrevalence <- function(cdm,
                   estimate_value = as.character(.data$time_taken_mins),
                   additional_name = paste0("dbms &&& person_n &&& ",
                                           "min_observation_start &&& ",
-                                          "max_observation_end &&& ",
-                                          "with_participants"),
+                                          "max_observation_end"),
                   additional_level = paste0(.data$dbms, " &&& ",
                                             .data$person_n, " &&& ",
                                             .data$min_observation_start, " &&& ",
-                                            .data$max_observation_end, " &&& ",
-                                            .data$with_participants)
+                                            .data$max_observation_end)
                   ) %>%
     dplyr::select(dplyr::all_of(
       colnames(omopgenerics::emptySummarisedResult()))) %>%

diff --git a/R/dateUtilities.R b/R/dateUtilities.R
@@ -17,7 +17,7 @@ addDaysQuery <- function(cdm,
     }
 
   if(type == "year"){
-    if(omopgenerics::cdmSourceType(cdm) == "spark"){
+    if(omopgenerics::sourceType(cdm) == "spark"){
       # https://github.com/darwin-eu-dev/IncidencePrevalence/issues/395
       number_days_to_years <- as.integer(number*365)
       q <- glue::glue("clock::add_days({variable}, {(number_days_to_years)}L)")
@@ -49,7 +49,7 @@ minusDaysQuery <- function(cdm,
       q <- glue::glue("clock::add_days({variable} , {(number)}L)")
     }
   if(type == "year"){
-    if(omopgenerics::cdmSourceType(cdm) == "spark"){
+    if(omopgenerics::sourceType(cdm) == "spark"){
       # https://github.com/darwin-eu-dev/IncidencePrevalence/issues/395
       number_days_to_years <- as.integer(number*365)
       q <- glue::glue("clock::add_days({variable}, {(number_days_to_years)}L)")