Merge pull request #90 from OHDSI/PhenotypeR

rename pkg
OHDSI · Oct 18, 2024 · 24363db · 24363db
2 parents 623b372 + 0cb65ee
commit 24363db
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diff --git 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
@@ -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
@@ -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
@@ -16,18 +16,18 @@ knitr::opts_chunk$set(
 )
 ```
 
-# phenotypeR <img src="man/figures/logo.png" align="right" height="180"/>
+# PhenotypeR <img src="man/figures/logo.png" align="right" height="180"/>
 
 <!-- badges: start -->
 
 > **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)
 
 <!-- badges: end -->
 
-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?  
@@ -37,19 +37,19 @@ 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
 
 ```{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
@@ -1,18 +1,18 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# phenotypeR <img src="man/figures/logo.png" align="right" height="180"/>
+# PhenotypeR <img src="man/figures/logo.png" align="right" height="180"/>
 
 <!-- badges: start -->
 
 > **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)
 
 <!-- badges: end -->
 
-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
@@ -42,19 +42,19 @@ 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
 
 ``` 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
@@ -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 → man/PhenotypeR-package.Rd b/man/phenotypeR-package.Rd → man/PhenotypeR-package.Rd
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -15,5 +15,5 @@ knitr::opts_chunk$set(
 ```
 
 ```{r setup}
-library(phenotypeR)
+library(PhenotypeR)
 ```