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rename pkg #90

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4 changes: 2 additions & 2 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
Package: phenotypeR
Package: PhenotypeR
Type: Package
Title: Assess Study Cohorts Using a Common Data Model
Version: 0.0.900
Expand Down Expand Up @@ -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,
Expand Down
4 changes: 2 additions & 2 deletions R/reportDiagnostics.R
Original file line number Diff line number Diff line change
Expand Up @@ -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() |>
Expand All @@ -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,
Expand Down
4 changes: 2 additions & 2 deletions R/shinyDiagnostics.R
Original file line number Diff line number Diff line change
Expand Up @@ -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()
)
}
12 changes: 6 additions & 6 deletions README.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -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?
Expand All @@ -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)

Expand Down
16 changes: 8 additions & 8 deletions README.md
Original file line number Diff line number Diff line change
@@ -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
Expand Down Expand Up @@ -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)

Expand All @@ -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,
Expand Down
2 changes: 1 addition & 1 deletion _pkgdown.yml
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
url: https://ohdsi.github.io/phenotypeR/
url: https://ohdsi.github.io/PhenotypeR/
template:
bootstrap: 5

Expand Down
10 changes: 5 additions & 5 deletions man/phenotypeR-package.Rd → man/PhenotypeR-package.Rd

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

4 changes: 2 additions & 2 deletions tests/testthat.R
Original file line number Diff line number Diff line change
Expand Up @@ -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")
2 changes: 1 addition & 1 deletion vignettes/a02_CodelistDiagnostics.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -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)

Expand Down
2 changes: 1 addition & 1 deletion vignettes/a03_CohortDiagnostics.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ library(CohortConstructor)
library(CodelistGenerator)
library(PatientProfiles)
library(CohortCharacteristics)
library(phenotypeR)
library(PhenotypeR)
library(dplyr)
library(ggplot2)

Expand Down
2 changes: 1 addition & 1 deletion vignettes/a04_MatchedDiagnostics.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -15,5 +15,5 @@ knitr::opts_chunk$set(
```

```{r setup}
library(phenotypeR)
library(PhenotypeR)
```
2 changes: 1 addition & 1 deletion vignettes/a05_PopulationDiagnostics.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -15,5 +15,5 @@ knitr::opts_chunk$set(
```

```{r setup}
library(phenotypeR)
library(PhenotypeR)
```
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