Merge pull request #93 from OHDSI/adding_descriptions

adding descriptions

R/addCodelistAttribute.R

@@ -1,5 +1,13 @@
 #' Adds the cohort_codelist attribute to a cohort
 #'
+#' @description
+#' `addCodelistAttribute()` allows the users to add a codelist to a cohort in
+#' OMOP CDM.
+#'
+#' This is particularly important for the use of `codelistDiagnostics()`, as the
+#' underlying assumption is that the cohort that is fed into
+#' `codelistDiagnostics()` has a cohort_codelist attribute attached to it.
+#'
 #' @inheritParams cohortDoc
 #' @param codelist Named list of concepts
 #' @param cohortName For each element of the codelist, the name of the cohort in

R/codelistDiagnostics.R

@@ -1,5 +1,14 @@
 #' Run codelist-level diagnostics
 #'
+#' @description
+#' `codelistDiagnostics()` runs phenotypeR diagnostics on the cohort_codelist
+#' attribute on the cohort. Thus codelist attribute of the cohort must be
+#' populated. If it is missing then it could be populated using
+#' `addCodelistAttribute()` function.
+#'
+#' Furthermore `codelistDiagnostics()` requires achilles tables to be present in
+#' the cdm so that concept counts could be derived.
+#'
 #' @param cohort A cohort table in a cdm reference. The cohort_codelist
 #' attribute must be populated. The cdm reference must contain achilles
 #' tables as these will be used for deriving concept counts.

R/cohortDiagnostics.R

@@ -1,5 +1,14 @@
 #' Run cohort-level diagnostics
 #'
+#' @description
+#' Runs phenotypeR diagnostics on the cohort.
+#' The diganotics include:
+#' * Age groups and sex summarised.
+#' * A summary of visits of everyone in the cohort using visit_occurrence table.
+#' * A summary of age and sex density of the cohort.
+#' * Attritions of the cohorts.
+#' * Overlap between cohorts (if more than one cohort is being used).
+#'
 #' @inheritParams cohortDoc
 #'
 #' @return A summarised result

R/databaseDiagnostics.R

@@ -1,5 +1,12 @@
 #' Database diagnostics
 #'
+#' @description
+#' phenotypeR diagnostics on the cdm object.
+#'
+#' Diagnostics include:
+#' * Summarise a cdm_reference object, creating a snapshot with the metadata of the cdm_reference object.
+#' * Summarise the observation period table getting some overall statistics in a summarised_result object.
+#'
 #' @param cdm CDM reference
 #'
 #' @return A summarised result

R/matchedDiagnostics.R

@@ -1,5 +1,18 @@
 #' Compare characteristics of cohort matched to database population
 #'
+#' @description
+#' A summary of the cohort that is matched to the original cohort that has been
+#' given by the user. Such summary contains basic cohort summary including
+#' number of visits within one year prior of the cohort_start_date, as well as
+#' a large scale charactersitics using the following domians of OMOP CDM:
+#'
+#' * condition_occurrence
+#' * visit_occurrence
+#' * measurement
+#' * procedure_occurrence
+#' * observation
+#' * drug_exposure
+#'
 #' @inheritParams cohortDoc
 #' @inheritParams matchedSampleDoc
 #'

R/phenotypeDiagnostics.R

@@ -1,5 +1,15 @@
 #' Phenotype a cohort
 #'
+#' @description
+#' This comprises all the diagnostics that are being offered in this package,
+#' this includes:
+#'
+#' * A diagnostics on the database via `databaseDiagnostics`.
+#' * A diagnostics on the cohort_codelist attribute of the cohort via `codelistDiagnostics`.
+#' * A diagnostics on the cohort via `cohortDiagnostics`.
+#' * A diagnostics on the population via `populationDiagnostics`.
+#' * A diagnostics on the matched cohort via `matchedDiagnostics`.
+#'
 #' @inheritParams cohortDoc
 #' @param databaseDiagnostics If TRUE, database diagnostics will be run.
 #' @param codelistDiagnostics If TRUE, codelist diagnostics will be run.

R/populationDiagnostics.R

@@ -1,5 +1,12 @@
 #' Population-level diagnostics
 #'
+#' @description
+#' phenotypeR diagnostics on the cohort of input with relation to a denomination
+#' population. Diagnostics include:
+#'
+#' * Incidence
+#' * Prevalence
+#'
 #' @inheritParams cohortDoc
 #' @inheritParams populationSampleDoc
 #'
@@ -10,7 +17,6 @@
 #' \donttest{
 #' library(IncidencePrevalence)
 #' cdm <- mockIncidencePrevalenceRef(sampleSize = 1000)
-#' cdm <- generateDenominatorCohortSet(cdm, name = "denom")
 #' pop_diag <- populationDiagnostics(cohort = cdm$outcome,
 #'                                   populationSample = 250)
 #' CDMConnector::cdm_disconnect(cdm)

R/reportDiagnostics.R

@@ -1,4 +1,3 @@
-
 #' Create a report summarising your phenotyping results
 #'
 #' @inheritParams resultDoc

R/shinyDiagnostics.R

@@ -1,5 +1,16 @@
 #' Create a shiny app summarising your phenotyping results
 #'
+#' @description
+#' A shiny app that is designed for any diagnostics results from phenotypeR, this
+#' includes:
+#'
+#' * A diagnostics on the database via `databaseDiagnostics`.
+#' * A diagnostics on the cohort_codelist attribute of the cohort via `codelistDiagnostics`.
+#' * A diagnostics on the cohort via `cohortDiagnostics`.
+#' * A diagnostics on the population via `populationDiagnostics`.
+#' * A diagnostics on the matched cohort via `matchedDiagnostics`.
+#'
+#'
 #' @inheritParams resultDoc
 #' @inheritParams directoryDoc
 #'