v0.2.5

.Rbuildignore

@@ -6,3 +6,4 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
+^cran-comments\.md$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: CohortSurvival
-Title: Estimate survival using the OMOP Common Data Model
-Version: 0.2.4
+Title: Estimate Survival from Common Data Model Cohorts
+Version: 0.2.5
 Authors@R: c(
     person("Edward", "Burn", email = "[email protected]", 
     role = c("aut", "cre"), 
@@ -16,7 +16,7 @@ Authors@R: c(
     person("Danielle", "Newby", email = "[email protected]", 
     role = c("ctb"), 
     comment = c(ORCID = "0000-0002-3001-1478")))
-Description: Estimate survival using data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model. Survival can be estimated based on user-defined study cohorts.
+Description: Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.
 License: Apache License (>= 2)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
@@ -51,4 +51,4 @@ Suggests:
 Config/testthat/edition: 3
 Config/testthat/parallel: true
 VignetteBuilder: knitr
-URL: https://darwin-eu.github.io/CohortSurvival/
+URL: https://darwin-eu-dev.github.io/CohortSurvival/

R/addCohortSurvival.R

@@ -1,4 +1,18 @@
-
+# Copyright 2023 DARWIN EU®
+#
+# This file is part of CohortSurvival
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 
 #' Add survival information to a cohort table
 #' @param x cohort table to add survival information
@@ -21,6 +35,7 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' cohort <- dplyr::tibble(
 #' cohort_definition_id = c(1,1,1),
 #' subject_id = c(1,2,3),
@@ -38,6 +53,7 @@
 #'     outcomeCohortTable = "cohort2",
 #'     outcomeCohortId = 1
 #'   )
+#'   }
 #'
 addCohortSurvival <- function(x,
                               cdm,

R/benchmarkCohortSurvival.R

@@ -1,3 +1,20 @@
+# Copyright 2023 DARWIN EU®
+#
+# This file is part of CohortSurvival
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 #' Estimate performance of estimateSurvival function for benchmarking
 #'
 #' @param cdm CDM reference
@@ -29,15 +46,16 @@
 #' @return tibble with performance of estimateSurvival function information,
 #' according to the selected input parameters
 #' @export
-#' @importFrom tictoc
 #'
 #' @examples
+#' \donttest{
 #' cdm <- mockMGUS2cdm()
 #' cdm$condition_occurrence <- cdm$death_cohort %>%
 #' dplyr::rename("condition_start_date" = "cohort_start_date",
 #'              "condition_end_date" = "cohort_end_date")
 #' surv_timings <- benchmarkCohortSurvival(
 #' cdm, targetSize = 100, outcomeSize = 20)
+#'}
 #'
 benchmarkCohortSurvival <- function(cdm,
                                     targetSize,

R/estimateSurvival.R

@@ -1,3 +1,20 @@
+# Copyright 2023 DARWIN EU®
+#
+# This file is part of CohortSurvival
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 #' Estimate survival for a given event of interest using cohorts in the OMOP Common Data Model
 #'
 #' @param cdm CDM reference
@@ -31,6 +48,7 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' cdm <- mockMGUS2cdm()
 #' surv <- estimateSingleEventSurvival(
 #'   cdm = cdm,
@@ -40,6 +58,7 @@
 #'   outcomeCohortId = 1,
 #'   timeGap = 7
 #' )
+#' }
 #'
 estimateSingleEventSurvival <- function(cdm,
                                         targetCohortTable,
@@ -157,6 +176,7 @@ estimateSingleEventSurvival <- function(cdm,
 #' @export
 #'
 #' @examples
+#' \donttest{
 #' cdm <- mockMGUS2cdm()
 #' surv <- estimateCompetingRiskSurvival(
 #'   cdm = cdm,
@@ -168,6 +188,7 @@ estimateSingleEventSurvival <- function(cdm,
 #'   competingOutcomeCohortId = 1,
 #'   timeGap = 7
 #' )
+#' }
 #'
 estimateCompetingRiskSurvival <- function(cdm,
                                           targetCohortTable,

R/generateDeathCohort.R

@@ -1,3 +1,18 @@
+# Copyright 2023 DARWIN EU®
+#
+# This file is part of CohortSurvival
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 
 #' To create a death cohort
 #'
@@ -14,6 +29,24 @@
 #' @export
 #'
 #' @examples
+#' \donttest{
+#' library(CDMConnector)
+#' library(CohortSurvival)
+#' cdm <- PatientProfiles::mockPatientProfiles()
+#' deathTable <- dplyr::tibble(
+#'   person_id = c(1,2,3),
+#'   death_date = c(as.Date("2020-01-01"),
+#'                  as.Date("2020-01-02"),
+#'                  as.Date("2020-01-01")))
+#' DBI::dbWithTransaction(attr(cdm, "dbcon"), {
+#'   DBI::dbWriteTable(attr(cdm, "dbcon"), "death",
+#'                     deathTable, overwrite = TRUE)
+#' })
+#' cdm$death <- dplyr::tbl(attr(cdm, "dbcon"), "death")
+#' cdm <- generateDeathCohortSet(cdm=cdm,
+#'                               name = "death_cohort")
+#' }
+
 generateDeathCohortSet <- function(
     cdm,
     name,

R/inputValidation.R

@@ -1,3 +1,18 @@
+# Copyright 2023 DARWIN EU®
+#
+# This file is part of CohortSurvival
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 
 checkCdm <- function(cdm, tables = NULL) {
   if (!isTRUE(inherits(cdm, "cdm_reference"))) {

R/mockMGUS2cdm.R

@@ -1,9 +1,29 @@
+# Copyright 2023 DARWIN EU®
+#
+# This file is part of CohortSurvival
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 #' Create mock CDM reference with survival::mgus2 dataset
 #'
 #' @return CDM reference containing data from the survival::mgus2 dataset
 #' @export
 #'
 #' @examples
+#'  \donttest{
+#' cdm <- mockMGUS2cdm()
+#' cdm$person
+#' }
 mockMGUS2cdm <- function() {
   mgus2 <- survival::mgus2 %>%
     dplyr::mutate(

R/plotSurvival.R

@@ -1,3 +1,19 @@
+# Copyright 2023 DARWIN EU®
+#
+# This file is part of CohortSurvival
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 #' Plot survival results
 #'
 #' @param result Survival results
@@ -9,10 +25,19 @@
 #' @param colour Variables to use for colours
 #' @param colour_name Colour legend name
 #'
-#' @return A ggplot with the survival results plotted
+#' @return A plot of survival probabilities over time
 #' @export
 #'
 #' @examples
+#' \donttest{
+#' cdm <- mockMGUS2cdm()
+#' surv <- estimateSingleEventSurvival(cdm,
+#'                                     targetCohortTable = "mgus_diagnosis",
+#'                                     outcomeCohortTable = "death_cohort")
+#' plot <- plotSurvival(surv)
+#' plot
+#'}
+#'
 plotSurvival <- function(result,
                          x = "time",
                          xscale = "days",
@@ -63,10 +88,18 @@ plotSurvival <- function(result,
 #' @param colour Variables to use for colours
 #' @param colour_name Colour legend name
 #'
-#' @return
+#' @return A plot of cumulative incidence over time
 #' @export
 #'
 #' @examples
+#' \donttest{
+#' cdm <- mockMGUS2cdm()
+#' surv <- estimateSingleEventSurvival(cdm,
+#'                                     targetCohortTable = "mgus_diagnosis",
+#'                                     outcomeCohortTable = "death_cohort")
+#' plot <- plotCumulativeIncidence(surv)
+#' plot
+#'}
 plotCumulativeIncidence <- function(result,
                                     x = "time",
                                     xscale = "days",

R/recordAttrition.R

@@ -1,6 +1,6 @@
 # Copyright 2023 DARWIN EU®
 #
-# This file is part of IncidencePrevalence
+# This file is part of CohortSurvival
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.

R/summariseSurvivalParticipants.R

@@ -1,3 +1,18 @@
+# Copyright 2023 DARWIN EU®
+#
+# This file is part of CohortSurvival
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 
 #' @importFrom PatientProfiles summariseCharacteristics
 #' @export

R/suppressSurvivalCounts.R

@@ -1,3 +1,19 @@
+# Copyright 2023 DARWIN EU®
+#
+# This file is part of CohortSurvival
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
 suppressSurvivalCounts <- function(result,
                            minCellCount = 5) {
 

R/survivalSummary.R

@@ -1,11 +1,35 @@
+# Copyright 2023 DARWIN EU®
+#
+# This file is part of CohortSurvival
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+
 #' Survival summary
 #'
 #' @param x Result from estimateSingleEventSurvival
 #'
-#' @return
+#' @return A tibble containing a summary of observed survival
 #' @export
 #'
 #' @examples
+#' \donttest{
+#' cdm <- mockMGUS2cdm()
+#' surv <- estimateSingleEventSurvival(cdm,
+#'                                     targetCohortTable = "mgus_diagnosis",
+#'                                     outcomeCohortTable = "death_cohort")
+#' survivalSummary(surv)
+#'}
 survivalSummary <- function(x){
 attr(x, "summary")
 }