spelling and eunomia

Author: edward-burn

R/generateIntersectCohorts.R

@@ -178,7 +178,7 @@ generateIntersectCohortSet <- function(cdm,
 #' @export
 #'
 #' @return Table in the cdm with start, end and by as columns. Periods are not
-#' going to overlpa between each other.
+#' going to overlap between each other.
 #'
 splitOverlap <- function(x,
                          start = "cohort_start_date",
@@ -244,7 +244,7 @@ splitOverlap <- function(x,
 #' @export
 #'
 #' @return Table in the cdm with start, end and by as columns. Periods are not
-#' going to overlpa between each other.
+#' going to overlap between each other.
 #'
 joinOverlap <- function(x,
                         start = "cohort_start_date",
@@ -302,7 +302,7 @@ joinOverlap <- function(x,
     CDMConnector::computeQuery()
 }
 
-#' Get ramdon identifies not present in a table based on a prefix.
+#' Get random identifiers not present in a table based on a prefix.
 #'
 #' @param x Table.
 #' @param len Number of identifiers.

R/requireDemographics.R

@@ -8,7 +8,7 @@
 #' @param ageRange A list of minimum and maximum age
 #' @param sex Can be "Both", "Male" or "Female". If one of the latter, only
 #' those with that sex will be included.
-#' @param minPriorObservation A mimimum number of prior observation days in
+#' @param minPriorObservation A minimum number of prior observation days in
 #' the database.
 #' @param minFutureObservation A minimum number of future observation days in
 #' the database.
@@ -147,7 +147,7 @@ requireSex <- function(cohort,
 #' @param cohort A cohort table in a cdm reference
 #' @param indexDate Variable in cohort that contains the date to compute the
 #' demographics characteristics on which to restrict on.
-#' @param minPriorObservation A mimimum number of prior observation days in
+#' @param minPriorObservation A minimum number of prior observation days in
 #' the database.
 #'
 #' @return The cohort table with only records for individuals satisfying the

README.Rmd

@@ -16,8 +16,6 @@ knitr::opts_chunk$set(
 # CohortConstructor
 
 <!-- badges: start -->
-[![CRAN status](https://www.r-pkg.org/badges/version/CohortConstructor)](https://CRAN.R-project.org/package=CohortConstructor)
-[![codecov.io](https://codecov.io/github/oxford-pharmacoepi/CohortConstructor/coverage.svg?branch=main)](https://app.codecov.io/github/oxford-pharmacoepi/CohortConstructor?branch=main)
 [![R-CMD-check](https://github.com/oxford-pharmacoepi/CohortConstructor/workflows/R-CMD-check/badge.svg)](https://github.com/oxford-pharmacoepi/CohortConstructor/actions)
 [![Lifecycle:Experimental](https://img.shields.io/badge/Lifecycle-Experimental-339999)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 <!-- badges: end -->

README.md

@@ -5,9 +5,6 @@
 
 <!-- badges: start -->
 
-[![CRAN
-status](https://www.r-pkg.org/badges/version/CohortConstructor)](https://CRAN.R-project.org/package=CohortConstructor)
-[![codecov.io](https://codecov.io/github/oxford-pharmacoepi/CohortConstructor/coverage.svg?branch=main)](https://app.codecov.io/github/oxford-pharmacoepi/CohortConstructor?branch=main)
 [![R-CMD-check](https://github.com/oxford-pharmacoepi/CohortConstructor/workflows/R-CMD-check/badge.svg)](https://github.com/oxford-pharmacoepi/CohortConstructor/actions)
 [![Lifecycle:Experimental](https://img.shields.io/badge/Lifecycle-Experimental-339999)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 <!-- badges: end -->
@@ -214,7 +211,7 @@ Both diclofenac and acetaminophen
 Generate a combination cohort.
 
 ``` r
-cdm <- generateCombinationCohortSet(cdm = cdm, 
+cdm <- generateIntersectCohortSet(cdm = cdm, 
                                     name = "combinations", 
                                     targetCohortName = "medications")
 

inst/WORDLIST

@@ -0,0 +1,17 @@
+CDMConnector
+CMD
+DrugUtilisation
+Eunomia
+Lifecycle
+OMOP
+ORCID
+cdm
+codecov
+diclofenac
+generateDrugUtilisationCohortSet
+indexDate
+individuals’
+io
+matchSex
+matchYearOfBirth
+overlaping

man/getIdentifier.Rd

@@ -14,6 +14,10 @@ knitr::opts_chunk$set(
   warning = FALSE,
   comment = "#>"
 )
+
+if (Sys.getenv("EUNOMIA_DATA_FOLDER") == "") Sys.setenv("EUNOMIA_DATA_FOLDER" = file.path(tempdir(), "eunomia"))
+if (!dir.exists(Sys.getenv("EUNOMIA_DATA_FOLDER"))) dir.create(Sys.getenv("EUNOMIA_DATA_FOLDER"))
+if (!eunomia_is_available()) downloadEunomiaData()
 ```
 
 For this example we'll use the Eunomia synthetic data from the CDMConnector package.