Merge pull request #165 from OHDSI/issue_128

Issue 128
OHDSI · Oct 14, 2024 · 5de340f · 5de340f
2 parents 77e7ce3 + 341be85
commit 5de340f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,4 +1,4 @@
-Package: omopViewer
+Package: OmopViewer
 Type: Package
 Title: Visualise OMOP Results in a Shiny App 
 Version: 0.0.0.900

diff --git a/R/about.R b/R/about.R
@@ -13,11 +13,11 @@ createAbout <- function(logo) {
       ),
       "This shiny app was generated with ",
       shiny::a(
-        "omopViewer",
-        href = "https://github.com/OHDSI/omopViewer",
+        "OmopViewer",
+        href = "https://github.com/OHDSI/OmopViewer",
         target = "_blank"
       ),
-      shiny::strong("v{as.character(utils::packageVersion("omopViewer"))}")
+      shiny::strong("v{as.character(utils::packageVersion("OmopViewer"))}")
     )
   )' |>
     glue::glue() |>

diff --git a/R/appDynamic.R b/R/appDynamic.R
@@ -14,7 +14,7 @@ createDynamicUi <- function(choices) {
   c(
     'bslib::page_navbar(',
     c(
-      pageTitle("omopViewer App", logo),
+      pageTitle("OmopViewer App", logo),
       loadDataUi(),
       createUi(choices),
       'bslib::nav_spacer()',
@@ -174,13 +174,13 @@ messageProcessFiles <- function(x) {
 }
 mergeData <- function(newData, originalData) {
   if (is.null(newData)) return(originalData)
-  id0 <- getOption("omopViewer.number_ids", 0L)
+  id0 <- getOption("OmopViewer.number_ids", 0L)
   newData <- newData |>
     dplyr::mutate(
       id = .env$id0 + dplyr::row_number(),
       upload_datetime = Sys.time() |> format("%Y-%m-%d %H:%M:%S")
     )
-  options("omopViewer.number_ids" = id0 + nrow(newData))
+  options("OmopViewer.number_ids" = id0 + nrow(newData))
   if (is.null(originalData)) {
     return(newData)
   } else {

diff --git a/R/appStatic.R b/R/appStatic.R
@@ -139,8 +139,8 @@ exportStaticApp <- function(result,
 messageShiny <- function() {
   c(
     paste0(
-      "# Generated by omopViewer ",
-      as.character(utils::packageVersion("omopViewer"))
+      "# Generated by OmopViewer ",
+      as.character(utils::packageVersion("OmopViewer"))
     ),
     "# Be careful editing this file",
     ""
@@ -179,7 +179,7 @@ logoPath <- function(logo) {
   lowLogo <- stringr::str_to_lower(logo)
   # add more logoKeywords in data-raw/internalData
   if (lowLogo %in% logoKeywords) {
-    system.file(file.path("logos", paste0(lowLogo, "_logo.svg")), package = "omopViewer")
+    system.file(file.path("logos", paste0(lowLogo, "_logo.svg")), package = "OmopViewer")
   } else {
     logo
   }

diff --git a/R/background.R b/R/background.R
@@ -96,7 +96,7 @@ createBackground <- function(background) {
   'bslib::nav_panel(
     title = "Background",
     icon = shiny::icon("disease"),
-    omopViewer::cardFromMd("background.md")
+    OmopViewer::cardFromMd("background.md")
   )'
 }
 

diff --git a/R/createServer.R b/R/createServer.R
@@ -22,7 +22,7 @@ selectiseServer <- function(resultTypes, data) {
   c(
     '# fill selectise variables ----',
     paste0('shiny::observe({
-      choices <- omopViewer::getChoices(', data, ', flatten = TRUE)
+      choices <- OmopViewer::getChoices(', data, ', flatten = TRUE)
       for (k in seq_along(choices)) {
         shiny::updateSelectizeInput(
           session,

diff --git a/R/panelFormatted.R b/R/panelFormatted.R
@@ -211,7 +211,7 @@ formattedServer <- function(rt, data) {
       c(
       'getFormattedData[formatCamel(rt)] <- shiny::reactive({
         [data] |>
-          omopViewer::filterData("[rt]", input) |>
+          OmopViewer::filterData("[rt]", input) |>
           [fun](
             [args]
           )

diff --git a/R/panelPlot.R b/R/panelPlot.R
@@ -108,7 +108,7 @@ plotsServer <- function(rt, data) {
   plotServer <- purrr::map_chr(plots, \(id) {
     c('createPlot[id] <- shiny::reactive({
         result <- [data] |>
-          omopViewer::filterData("[rt]", input)
+          OmopViewer::filterData("[rt]", input)
         [createPlotFunction(id)]
       })',
       'output$[rt]_plot_[id] <- [renderPlotFunction(id)]({

diff --git a/R/panelRaw.R b/R/panelRaw.R
@@ -19,7 +19,7 @@ downloadRawDataServer <- function(data) {
   output$download_raw <- shiny::downloadHandler(
     filename = "results.csv",
     content = function(file) {
-      omopViewer::exportSummarisedResult([data], fileName = file)
+      OmopViewer::exportSummarisedResult([data], fileName = file)
     }
   )' |>
     glue::glue(.open = "[", .close = "]") |>

diff --git a/R/panelTidy.R b/R/panelTidy.R
@@ -30,8 +30,8 @@ tidyUi <- function(tab) {
 tidyServer <- function(rt, data) {
   c(paste0('getTidyData', formatCamel(rt), ' <- shiny::reactive({
       res <- ', data, ' |>
-        omopViewer::filterData("', rt, '", input) |>
-        omopViewer::tidyData()
+        OmopViewer::filterData("', rt, '", input) |>
+        OmopViewer::tidyData()
 
       # columns to eliminate
       colsEliminate <- colnames(res)

diff --git a/R/summary.R b/R/summary.R
@@ -146,6 +146,6 @@ summaryTab <- function(summary) {
   'bslib::nav_panel(
     title = "Summary",
     icon = shiny::icon("file-alt"),
-    omopViewer::cardSummary(data)
+    OmopViewer::cardSummary(data)
   )'
 }
diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/README.Rmd b/README.Rmd
@@ -13,33 +13,33 @@ knitr::opts_chunk$set(
 )
 ```
 
-# omopViewer
+# OmopViewer
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/OHDSI/omopViewer/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/OHDSI/omopViewer/actions/workflows/R-CMD-check.yaml)
-[![CRAN status](https://www.r-pkg.org/badges/version/omopViewer)](https://CRAN.R-project.org/package=omopViewer)
+[![R-CMD-check](https://github.com/OHDSI/OmopViewer/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/OHDSI/OmopViewer/actions/workflows/R-CMD-check.yaml)
+[![CRAN status](https://www.r-pkg.org/badges/version/OmopViewer)](https://CRAN.R-project.org/package=OmopViewer)
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
-[![Codecov test coverage](https://codecov.io/gh/OHDSI/omopViewer/branch/main/graph/badge.svg)](https://app.codecov.io/gh/OHDSI/omopViewer?branch=main)
+[![Codecov test coverage](https://codecov.io/gh/OHDSI/OmopViewer/branch/main/graph/badge.svg)](https://app.codecov.io/gh/OHDSI/OmopViewer?branch=main)
 <!-- badges: end -->
 
 > [!IMPORTANT]
 > This package is under construction and this is just a first Beta release, please use it carefully and report any issue that you encounter using it.
 
-The goal of omopViewer is to allow the user to easily create Shiny Apps to visualise study results in `<summarised_result>` format.
+The goal of OmopViewer is to allow the user to easily create Shiny Apps to visualise study results in `<summarised_result>` format.
 
 ## Installation
 
-You can install the development version of omopViewer from [GitHub](https://github.com/OHDSI/omopViewer) with:
+You can install the development version of OmopViewer from [GitHub](https://github.com/OHDSI/OmopViewer) with:
 
 ``` {r, eval = FALSE}
 install.packages("pak")
-pak::pkg_install("OHDSI/omopViewer")
+pak::pkg_install("OHDSI/OmopViewer")
 ```
 
 ## Main functionalities
 
 ```{r}
-library(omopViewer)
+library(OmopViewer)
 ```
 
 The package can be divided in 3 main functionalities:

diff --git a/README.md b/README.md
@@ -1,40 +1,40 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# omopViewer
+# OmopViewer
 
 <!-- badges: start -->
 
-[![R-CMD-check](https://github.com/OHDSI/omopViewer/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/OHDSI/omopViewer/actions/workflows/R-CMD-check.yaml)
+[![R-CMD-check](https://github.com/OHDSI/OmopViewer/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/OHDSI/OmopViewer/actions/workflows/R-CMD-check.yaml)
 [![CRAN
-status](https://www.r-pkg.org/badges/version/omopViewer)](https://CRAN.R-project.org/package=omopViewer)
+status](https://www.r-pkg.org/badges/version/OmopViewer)](https://CRAN.R-project.org/package=OmopViewer)
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![Codecov test
-coverage](https://codecov.io/gh/OHDSI/omopViewer/branch/main/graph/badge.svg)](https://app.codecov.io/gh/OHDSI/omopViewer?branch=main)
+coverage](https://codecov.io/gh/OHDSI/OmopViewer/branch/main/graph/badge.svg)](https://app.codecov.io/gh/OHDSI/OmopViewer?branch=main)
 <!-- badges: end -->
 
 > \[!IMPORTANT\] This package is under construction and this is just a
 > first Beta release, please use it carefully and report any issue that
 > you encounter using it.
 
-The goal of omopViewer is to allow the user to easily create Shiny Apps
+The goal of OmopViewer is to allow the user to easily create Shiny Apps
 to visualise study results in `<summarised_result>` format.
 
 ## Installation
 
-You can install the development version of omopViewer from
-[GitHub](https://github.com/OHDSI/omopViewer) with:
+You can install the development version of OmopViewer from
+[GitHub](https://github.com/OHDSI/OmopViewer) with:
 
 ``` r
 install.packages("pak")
-pak::pkg_install("OHDSI/omopViewer")
+pak::pkg_install("OHDSI/OmopViewer")
 ```
 
 ## Main functionalities
 
 ``` r
-library(omopViewer)
+library(OmopViewer)
 ```
 
 The package can be divided in 3 main functionalities: - Static shiny
@@ -50,22 +50,18 @@ results and can be modified later locally.
 # lets generate some results
 library(CohortCharacteristics)
 cdm <- mockCohortCharacteristics()
-#> Note: method with signature 'DBIConnection#Id' chosen for function 'dbExistsTable',
-#>  target signature 'duckdb_connection#Id'.
-#>  "duckdb_connection#ANY" would also be valid
 result <- summariseCharacteristics(cdm$cohort1) |>
   bind(summariseCohortAttrition(cdm$cohort1))
 #> ℹ adding demographics columns
 #> ℹ summarising data
 #> ✔ summariseCharacteristics finished!
 
 exportStaticApp(result = result)
-#> ℹ shiny folder will be overwritten.
 #> ℹ Processing data
 #> ✔ Data processed: 2 result types idenfied: `summarise_characteristics` and
 #>   `summarise_cohort_attrition`.
 #> ℹ Creating shiny from provided data
-#> ✔ Shiny created in: /Users/martics/Documents/GitHub/omopViewer/shiny
+#> ✔ Shiny created in: C:/Users/martics/Documents/GitHub/omopViewer/shiny
 ```
 
 ## Dynamic shiny app

diff --git a/data-raw/internalData.R b/data-raw/internalData.R
@@ -45,7 +45,7 @@ omopViewerPlotArguments <- dplyr::tribble(
 
 omopViewerTables <- dplyr::tribble(
   ~table_id, ~result_tab_id, ~title, ~fun, ~output,
-  0L, 0L, "Formatted", "omopViewer::omopViewerTable", "gt",
+  0L, 0L, "Formatted", "OmopViewer::omopViewerTable", "gt",
   1L, 1L, "Table cohort overlap", "tableCohortOverlap", "gt",
   2L, 2L, "Table cohort attrition", "tableCohortAttrition", "gt",
   3L, 3L, "Table cohort timing", "tableCohortTiming", "gt",
@@ -127,8 +127,8 @@ omopViewerProj <- c(
 )
 
 omopViewerGlobal <- c(
-  "data <- omopViewer::importSummarisedResult(here::here(\"data\")) |>",
-  "omopViewer::correctSettings()"
+  "data <- OmopViewer::importSummarisedResult(here::here(\"data\")) |>",
+  "OmopViewer::correctSettings()"
 ) |>
   styleCode()
 

diff --git a/man/omopViewer-package.Rd → man/OmopViewer-package.Rd b/man/omopViewer-package.Rd → man/OmopViewer-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(omopViewer)
+library(OmopViewer)
 
-test_check("omopViewer")
+test_check("OmopViewer")