diff --git a/DESCRIPTION b/DESCRIPTION index 41127e6..c6bf8f7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,4 +1,4 @@ -Package: phenotypeR +Package: PhenotypeR Type: Package Title: Assess Study Cohorts Using a Common Data Model Version: 0.0.900 @@ -52,7 +52,7 @@ Imports: vctrs, visOmopResults, glue -URL: https://ohdsi.github.io/phenotypeR/ +URL: https://ohdsi.github.io/PhenotypeR/ VignetteBuilder: knitr Remotes: OHDSI/OmopViewer, diff --git a/R/reportDiagnostics.R b/R/reportDiagnostics.R index 1674bc0..eb560f8 100644 --- a/R/reportDiagnostics.R +++ b/R/reportDiagnostics.R @@ -10,7 +10,7 @@ reportDiagnostics <- function(result, directory = here::here()){ input <- system.file("rmd", "phenotype_report.Rmd", - package = "phenotypeR") + package = "PhenotypeR") cohortNames <- result |> visOmopResults::addSettings() |> @@ -20,7 +20,7 @@ reportDiagnostics <- function(result, dplyr::distinct() |> dplyr::pull() cohortNames <- paste0(cohortNames, collapse = "; ") - workingTitle <- paste('phenotypeR results for cohort', cohortNames) + workingTitle <- paste('PhenotypeR results for cohort', cohortNames) rmarkdown::render(input = input, params = list(title = workingTitle, diff --git a/R/shinyDiagnostics.R b/R/shinyDiagnostics.R index 67d470a..8a2f882 100644 --- a/R/shinyDiagnostics.R +++ b/R/shinyDiagnostics.R @@ -128,11 +128,11 @@ getBackground <- function(result) { } c( - "header" = "phenotypeR Diagnostics", + "header" = "PhenotypeR Diagnostics", cohorts, codelists, databases, resTypes, - "footer" = "This Shiny App presents results generated using the [phenotypeR](https://ohdsi.github.io/phenotypeR/) package (version {as.character(utils::packageVersion('phenotypeR'))})." |> glue::glue() + "footer" = "This Shiny App presents results generated using the [PhenotypeR](https://ohdsi.github.io/PhenotypeR/) package (version {as.character(utils::packageVersion('PhenotypeR'))})." |> glue::glue() ) } diff --git a/README.Rmd b/README.Rmd index 1181b4b..d7b87ab 100644 --- a/README.Rmd +++ b/README.Rmd @@ -16,18 +16,18 @@ knitr::opts_chunk$set( ) ``` -# phenotypeR +# PhenotypeR > **This package is under development and not yet ready for use.** -[![R-CMD-check](https://github.com/ohdsi/phenotypeR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ohdsi/phenotypeR/actions/workflows/R-CMD-check.yaml) +[![R-CMD-check](https://github.com/ohdsi/PhenotypeR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ohdsi/PhenotypeR/actions/workflows/R-CMD-check.yaml) [![Lifecycle:Experimental](https://img.shields.io/badge/Lifecycle-Experimental-339999)](https://lifecycle.r-lib.org/articles/stages.html#experimental) -The phenotypeR package helps us to assess the research-readiness of a set of cohorts we have defined. This assessment includes: +The PhenotypeR package helps us to assess the research-readiness of a set of cohorts we have defined. This assessment includes: - ___Database diagnostics___ which help us to better understand the database in which they have been created. This includes information about the size of the data, the time period covered, the number of people in the data as a whole. More granular information that may influence analytic decisions, such as the number of observation periods per person, is also described. - ___Codelist diagnostics___ which help to answer questions like what concepts from our codelist are used in the database? What concepts were present led to individuals' entry in the cohort? Are there any concepts being used in the database that we didn't include in our codelist but maybe we should have? @@ -37,11 +37,11 @@ The phenotypeR package helps us to assess the research-readiness of a set of coh ## Installation -You can install phenotypeR from GitHub: +You can install PhenotypeR from GitHub: ```{r, eval = FALSE} # install.packages("remotes") -remotes::install_github("ohdsi/phenotypeR") +remotes::install_github("ohdsi/PhenotypeR") ``` ## Example usage @@ -49,7 +49,7 @@ remotes::install_github("ohdsi/phenotypeR") ```{r, message=FALSE, warning=FALSE} library(omopgenerics) library(CDMConnector) -library(phenotypeR) +library(PhenotypeR) library(CohortConstructor) library(dplyr) diff --git a/README.md b/README.md index b6e7b40..924fb6e 100644 --- a/README.md +++ b/README.md @@ -1,18 +1,18 @@ -# phenotypeR +# PhenotypeR > **This package is under development and not yet ready for use.** -[![R-CMD-check](https://github.com/ohdsi/phenotypeR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ohdsi/phenotypeR/actions/workflows/R-CMD-check.yaml) +[![R-CMD-check](https://github.com/ohdsi/PhenotypeR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ohdsi/PhenotypeR/actions/workflows/R-CMD-check.yaml) [![Lifecycle:Experimental](https://img.shields.io/badge/Lifecycle-Experimental-339999)](https://lifecycle.r-lib.org/articles/stages.html#experimental) -The phenotypeR package helps us to assess the research-readiness of a +The PhenotypeR package helps us to assess the research-readiness of a set of cohorts we have defined. This assessment includes: - ***Database diagnostics*** which help us to better understand the @@ -42,11 +42,11 @@ set of cohorts we have defined. This assessment includes: ## Installation -You can install phenotypeR from GitHub: +You can install PhenotypeR from GitHub: ``` r # install.packages("remotes") -remotes::install_github("ohdsi/phenotypeR") +remotes::install_github("ohdsi/PhenotypeR") ``` ## Example usage @@ -54,7 +54,7 @@ remotes::install_github("ohdsi/phenotypeR") ``` r library(omopgenerics) library(CDMConnector) -library(phenotypeR) +library(PhenotypeR) library(CohortConstructor) library(dplyr) @@ -73,8 +73,8 @@ result <- cdm$gibleed |> ``` r summary(result) -#> A summarised_result object with 13334 rows, 48 different result_id, 1 different -#> cdm names, and 25 settings. +#> A summarised_result object with 16025 rows, 49 different result_id, 1 different +#> cdm names, and 24 settings. #> CDM names: Synthea synthetic health database. #> Settings: package_name, package_version, result_type, timing, table_name, #> cohort_definition_id, cdm_version, vocabulary_version, diff --git a/_pkgdown.yml b/_pkgdown.yml index 11ae70d..af35030 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,4 +1,4 @@ -url: https://ohdsi.github.io/phenotypeR/ +url: https://ohdsi.github.io/PhenotypeR/ template: bootstrap: 5 diff --git a/man/phenotypeR-package.Rd b/man/PhenotypeR-package.Rd similarity index 82% rename from man/phenotypeR-package.Rd rename to man/PhenotypeR-package.Rd index 318f6ca..44de2a9 100644 --- a/man/phenotypeR-package.Rd +++ b/man/PhenotypeR-package.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/phenotypeR-package.R \docType{package} -\name{phenotypeR-package} -\alias{phenotypeR} -\alias{phenotypeR-package} -\title{phenotypeR: Assess Study Cohorts Using a Common Data Model} +\name{PhenotypeR-package} +\alias{PhenotypeR} +\alias{PhenotypeR-package} +\title{PhenotypeR: Assess Study Cohorts Using a Common Data Model} \description{ \if{html}{\figure{logo.png}{options: style='float: right' alt='logo' width='120'}} @@ -13,7 +13,7 @@ Phenotype study cohorts in data mapped to the Observational Medical Outcomes Par \seealso{ Useful links: \itemize{ - \item \url{https://ohdsi.github.io/phenotypeR/} + \item \url{https://ohdsi.github.io/PhenotypeR/} } } diff --git a/tests/testthat.R b/tests/testthat.R index 3b3fd44..d2c2713 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -7,6 +7,6 @@ # * https://testthat.r-lib.org/articles/special-files.html library(testthat) -library(phenotypeR) +library(PhenotypeR) -test_check("phenotypeR") +test_check("PhenotypeR") diff --git a/vignettes/a02_CodelistDiagnostics.Rmd b/vignettes/a02_CodelistDiagnostics.Rmd index efdd833..413d821 100644 --- a/vignettes/a02_CodelistDiagnostics.Rmd +++ b/vignettes/a02_CodelistDiagnostics.Rmd @@ -30,7 +30,7 @@ We'll begin by creating our study cohorts. library(CDMConnector) library(CohortConstructor) library(CodelistGenerator) -library(phenotypeR) +library(PhenotypeR) library(dplyr) library(ggplot2) diff --git a/vignettes/a03_CohortDiagnostics.Rmd b/vignettes/a03_CohortDiagnostics.Rmd index 444abfd..c3c21a8 100644 --- a/vignettes/a03_CohortDiagnostics.Rmd +++ b/vignettes/a03_CohortDiagnostics.Rmd @@ -38,7 +38,7 @@ library(CohortConstructor) library(CodelistGenerator) library(PatientProfiles) library(CohortCharacteristics) -library(phenotypeR) +library(PhenotypeR) library(dplyr) library(ggplot2) diff --git a/vignettes/a04_MatchedDiagnostics.Rmd b/vignettes/a04_MatchedDiagnostics.Rmd index c5e01bb..85a0d3d 100644 --- a/vignettes/a04_MatchedDiagnostics.Rmd +++ b/vignettes/a04_MatchedDiagnostics.Rmd @@ -15,5 +15,5 @@ knitr::opts_chunk$set( ``` ```{r setup} -library(phenotypeR) +library(PhenotypeR) ``` diff --git a/vignettes/a05_PopulationDiagnostics.Rmd b/vignettes/a05_PopulationDiagnostics.Rmd index 65d68b8..4a01647 100644 --- a/vignettes/a05_PopulationDiagnostics.Rmd +++ b/vignettes/a05_PopulationDiagnostics.Rmd @@ -15,5 +15,5 @@ knitr::opts_chunk$set( ``` ```{r setup} -library(phenotypeR) +library(PhenotypeR) ```