new ignore

.Rbuildignore

@@ -6,7 +6,10 @@
 ^CODE_OF_CONDUCT\.md$
 ^app/
 ^publish_shiny.R
+^publish_cran.R
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
 ^\.github$
+^data/prioritized_sample\.xlsx$
+^sample_data$

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

.gitignore

@@ -5,3 +5,6 @@
 .DS_Store
 .quarto
 docs
+data/prioritized_sample.xlsx
+sample_data
+app/rsconnect

DESCRIPTION

@@ -13,30 +13,27 @@ License: GPL (>= 3)
 Imports: 
     dplyr,
     ggplot2,
-    magrittr,
     ompr,
     ompr.roi,
-    openxlsx,
+    openxlsx2,
     patchwork,
-    renv,
-    ROI,
-    ROI.plugin.symphony,
     shiny,
-    tidyr,
     viridisLite,
-    shinylive,
-    httpuv,
-    here,
-    cpp11,
-    ROI.plugin.alabama,
     assertthat,
-    readODS
+    readODS,
+    tibble
 Suggests:
     pak,
     usethis,
     styler,
     roxygen2,
-    devtools
+    devtools,
+    rhub,
+    here,
+    cpp11,
+    renv,
+    ROI,
+    ROI.plugin.symphony
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2

NAMESPACE

@@ -4,3 +4,4 @@ S3method(plot,prioritized_groups_list)
 export(file_extension)
 export(grouping_plot)
 export(prioritized_grouping)
+export(read_input)

R/prioritized_grouping.R

@@ -16,9 +16,12 @@ utils::globalVariables(c("group", "grp", "i", "j", "value"))
 #' @export
 #'
 #' @examples
-#' prioritized_grouping(
+#' # prioritized_grouping(
-#' data=read.csv(here::here("data/prioritized_sample.csv")),
+#' # data=read.csv(here::here("data/prioritized_sample.csv")),
-#' pre_grouped=read.csv(here::here("data/pre_grouped.csv"))) |> plot()
+#' # pre_grouped=read.csv(here::here("data/pre_grouped.csv"))) |> plot()
+#' data.frame(id=paste0("id",1:100),
+#' matrix(replicate(100,sample(c(1:5,rep(NA,15)),10)),ncol=10,byrow = TRUE)) |>
+#' prioritized_grouping()
 prioritized_grouping <-
   function(data,
            cap_classes = NULL,
@@ -191,7 +194,7 @@ prioritized_grouping <-
 
     class(out) <- c("prioritized_groups_list", class(out))
 
-    return(out)
+    invisible(out)
   }
 
 #' Assessment performance overview
@@ -203,7 +206,7 @@ prioritized_grouping <-
 #'
 #' @param data A "prioritized_groups_list" class list from
 #' 'prioritized_grouping()'
-#' @param columns number of columns in plot
+#' @param columns number of columns in plot. Default=4.
 #' @param overall logical to only print overall groups mean priority/cost
 #' @param viridis.option option value passed on to 'viridisLite::viridis'.
 #' Default="D".
@@ -217,8 +220,11 @@ prioritized_grouping <-
 #' #read.csv(here::here("data/prioritized_sample.csv")) |>
 #' #  prioritized_grouping(cap_classes = sample(4:12, 17, TRUE)) |>
 #' #  grouping_plot()
+#' data.frame(id=paste0("id",1:100),
+#' matrix(replicate(100,sample(c(1:5,rep(NA,15)),10)),ncol=10,byrow = TRUE)) |>
+#' prioritized_grouping() |> grouping_plot(overall=TRUE)
 grouping_plot <- function(data,
-                          columns = NULL,
+                          columns = 4,
                           overall = FALSE,
                           viridis.option="D",
                           viridis.direction=-1) {
@@ -286,18 +292,19 @@ grouping_plot <- function(data,
 
 #' Plot extension for easy groupings plot
 #'
-#' @param data data of class 'prioritized_groups_list'
+#' @param x data of class 'prioritized_groups_list'
 #' @param ... passed on to 'grouping_plot()'
 #'
 #' @return ggplot2 list object
 #' @export
 #'
 #' @examples
-#' read.csv(here::here("data/prioritized_sample.csv")) |>
+#' # read.csv(here::here("data/prioritized_sample.csv")) |>
-#'   prioritized_grouping() |>
+#' #   prioritized_grouping() |>
-#'   plot(overall = TRUE, viridis.option="D",viridis.direction=-1)
+#' #   plot(overall = TRUE, viridis.option="D",viridis.direction=-1)
-plot.prioritized_groups_list <- function(data, ...) {
+#'
-  grouping_plot(data, ...)
+plot.prioritized_groups_list <- function(x, ...) {
+  grouping_plot(x, ...)
 }
 
 ## Helper function for Shiny
@@ -317,3 +324,39 @@ file_extension <- function(filenames) {
     filenames, perl = TRUE
   )
 }
+
+
+#' Flexible file import based on extension
+#'
+#' @param file file name
+#' @param consider.na character vector of strings to consider as NAs
+#'
+#' @return tibble
+#' @export
+#'
+#' @examples
+#' read_input("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv")
+read_input <- function(file, consider.na = c("NA", '""', "")) {
+  ext <- file_extension(file)
+
+  tryCatch(
+    {
+      if (ext == "csv") {
+        df <- utils::read.csv(file = file, na = consider.na)
+      } else if (ext %in% c("xls", "xlsx")) {
+        df <- openxlsx2::read_xlsx(file = file, na.strings = consider.na)
+      } else if (ext == "ods") {
+        df <- readODS::read_ods(file = file)
+      } else {
+        stop("Input file format has to be on of:
+             '.csv', '.xls', '.xlsx', '.dta' or '.ods'")
+      }
+    },
+    error = function(e) {
+      # return a safeError if a parsing error occurs
+      stop(shiny::safeError(e))
+    }
+  )
+
+  df
+}

app/rsconnect/shinyapps.io/agdamsbo/prioritized-grouping.dcf

@@ -1,10 +0,0 @@
-name: prioritized-grouping
-title:
-username: agdamsbo
-account: agdamsbo
-server: shinyapps.io
-hostUrl: https://api.shinyapps.io/v1
-appId: 12977223
-bundleId: 9205937
-url: https://agdamsbo.shinyapps.io/prioritized-grouping/
-version: 1

app/server.R

@@ -22,6 +22,9 @@ utils::globalVariables(c("group", "grp", "i", "j", "value"))
 
 
 
+
+
+
 
 
 
@@ -197,7 +200,7 @@ prioritized_grouping <-
 
     class(out) <- c("prioritized_groups_list", class(out))
 
-    return(out)
+    invisible(out)
   }
 
 
@@ -219,12 +222,15 @@ prioritized_grouping <-
 
 
 
+
+
+
 
 
 
 
 grouping_plot <- function(data,
-                          columns = NULL,
+                          columns = 4,
                           overall = FALSE,
                           viridis.option="D",
                           viridis.direction=-1) {
@@ -302,8 +308,9 @@ grouping_plot <- function(data,
 
 
 
-plot.prioritized_groups_list <- function(data, ...) {
+
-  grouping_plot(data, ...)
+plot.prioritized_groups_list <- function(x, ...) {
+  grouping_plot(x, ...)
 }
 
 ## Helper function for Shiny
@@ -325,6 +332,42 @@ file_extension <- function(filenames) {
 }
 
 
+
+
+
+
+
+
+
+
+
+
+read_input <- function(file, consider.na = c("NA", '""', "")) {
+  ext <- file_extension(file)
+
+  tryCatch(
+    {
+      if (ext == "csv") {
+        df <- utils::read.csv(file = file, na = consider.na)
+      } else if (ext %in% c("xls", "xlsx")) {
+        df <- openxlsx2::read_xlsx(file = file, na.strings = consider.na)
+      } else if (ext == "ods") {
+        df <- readODS::read_ods(file = file)
+      } else {
+        stop("Input file format has to be on of:
+             '.csv', '.xls', '.xlsx', '.dta' or '.ods'")
+      }
+    },
+    error = function(e) {
+      # return a safeError if a parsing error occurs
+      stop(shiny::safeError(e))
+    }
+  )
+
+  df
+}
+
+
 ########
 #### Current file: app/server_raw.R 
 ########
@@ -341,27 +384,7 @@ server <- function(input, output, session) {
 
     req(input$file1)
     # Make laoding dependent of file name extension (file_ext())
-    ext <- file_extension(input$file1$datapath)
+    df <- read_input(input$file1$datapath)
-
-    tryCatch(
-      {
-        if (ext == "csv") {
-          df <- utils::read.csv(input$file1$datapath,na.strings = c("NA", '""',""))
-        } else if (ext %in% c("xls", "xlsx")) {
-          df <- openxlsx::read.xlsx(input$file1$datapath,na.strings = c("NA", '""',""))
-        } else if (ext == "ods") {
-          df <- readODS::read_ods(file = file)
-        } else {
-          stop("Input file format has to be on of:
-             '.csv', '.xls', '.xlsx' or '.ods'")
-        }
-      },
-      error = function(e) {
-        # return a safeError if a parsing error occurs
-        stop(safeError(e))
-      }
-    )
-
     return(df)
   })
 
@@ -370,18 +393,7 @@ server <- function(input, output, session) {
     # req(input$file2)
     # Make laoding dependent of file name extension (file_ext())
     if (!is.null(input$file2$datapath)){
-      ext <- file_extension(input$file2$datapath)
+      df <- read_input(input$file2$datapath)
-
-      if (ext == "csv") {
-        df <- utils::read.csv(input$file2$datapath,na.strings = c("NA", '""',""))
-      } else if (ext %in% c("xls", "xlsx")) {
-        df <- openxlsx::read.xlsx(input$file2$datapath,na.strings = c("NA", '""',""))
-      } else if (ext == "ods") {
-        df <- readODS::read_ods(file = file)
-      } else {
-        stop("Input file format has to be on of:
-             '.csv', '.xls', '.xlsx' or '.ods'")
-      }
 
       return(df)
     } else {

app/server_raw.R

@@ -10,27 +10,7 @@ server <- function(input, output, session) {
 
     req(input$file1)
     # Make laoding dependent of file name extension (file_ext())
-    ext <- file_extension(input$file1$datapath)
+    df <- read_input(input$file1$datapath)
-
-    tryCatch(
-      {
-        if (ext == "csv") {
-          df <- utils::read.csv(input$file1$datapath,na.strings = c("NA", '""',""))
-        } else if (ext %in% c("xls", "xlsx")) {
-          df <- openxlsx::read.xlsx(input$file1$datapath,na.strings = c("NA", '""',""))
-        } else if (ext == "ods") {
-          df <- readODS::read_ods(file = file)
-        } else {
-          stop("Input file format has to be on of:
-             '.csv', '.xls', '.xlsx' or '.ods'")
-        }
-      },
-      error = function(e) {
-        # return a safeError if a parsing error occurs
-        stop(safeError(e))
-      }
-    )
-
     return(df)
   })
 
@@ -39,18 +19,7 @@ server <- function(input, output, session) {
     # req(input$file2)
     # Make laoding dependent of file name extension (file_ext())
     if (!is.null(input$file2$datapath)){
-      ext <- file_extension(input$file2$datapath)
+      df <- read_input(input$file2$datapath)
-
-      if (ext == "csv") {
-        df <- utils::read.csv(input$file2$datapath,na.strings = c("NA", '""',""))
-      } else if (ext %in% c("xls", "xlsx")) {
-        df <- openxlsx::read.xlsx(input$file2$datapath,na.strings = c("NA", '""',""))
-      } else if (ext == "ods") {
-        df <- readODS::read_ods(file = file)
-      } else {
-        stop("Input file format has to be on of:
-             '.csv', '.xls', '.xlsx' or '.ods'")
-      }
 
       return(df)
     } else {

data/pre_grouped.csv

@@ -1,11 +0,0 @@
-"ID","group"
-"sub36",16
-"sub105",10
-"sub112",3
-"sub61",15
-"sub27",8
-"sub78",7
-"sub110",1
-"sub129",2
-"sub109",12
-"sub46",14

data/prioritized_sample.csv

@@ -1,134 +0,0 @@
-"ID","a","b","c","d","e","f","g","h","i","j","k","l","m","n","o","p","q"
-"sub1",,,3,,,,,5,,,1,4,,,,2,
-"sub2",,,,3,,5,,,,,,1,,2,,,4
-"sub3",4,,,,2,,3,,,,,,,,,5,1
-"sub4",,,,,2,,5,4,,,,1,,3,,,
-"sub5",,,,5,,,2,,4,,1,,,,,3,
-"sub6",,4,,,,,,,2,,1,,5,3,,,
-"sub7",3,,,,,4,,,,,1,,,,2,5,
-"sub8",,,,,2,,4,,1,,3,,,,,5,
-"sub9",,3,,,,,,,1,5,,,4,,,,2
-"sub10",,,,4,,,,,,3,,,5,,2,1,
-"sub11",,5,,4,,,2,,1,,,,,3,,,
-"sub12",,,2,5,,,,,,,,,3,4,,,1
-"sub13",,,,5,,,,,,,,1,,3,2,,4
-"sub14",,3,4,,,5,,,,,,,,,2,,1
-"sub15",4,,,,5,,,2,1,,,,,,,,3
-"sub16",5,,,2,4,,,,,,1,,,,3,,
-"sub17",,4,,,3,1,5,,,,,,,2,,,
-"sub18",,,,,1,2,,,3,5,,,,,,4,
-"sub19",,,4,,,,3,,1,,2,,,,5,,
-"sub20",,,2,,,,1,,,3,4,5,,,,,
-"sub21",5,4,,,,2,,,,,1,,,,,,3
-"sub22",,,,,1,,3,2,,,5,,,,4,,
-"sub23",1,,,,4,,,,,,,,3,,2,,5
-"sub24",,,5,,,,,,,,,1,4,2,,3,
-"sub25",2,5,,,,3,,,,,,,,,,1,4
-"sub26",,2,,5,,,4,,,,,,,,3,,1
-"sub27",,,,,3,2,,,5,,,,,4,,1,
-"sub28",,,5,,,,,4,,,1,,,2,,3,
-"sub29",2,,,,,3,,,1,,5,4,,,,,
-"sub30",,,,,,,1,,,4,,3,,,2,,5
-"sub31",,,3,,,,,,,5,,1,,4,,,2
-"sub32",3,,,,,,,,2,5,,1,,,4,,
-"sub33",,2,,,4,,1,5,,,,,,3,,,
-"sub34",,,3,1,,,,4,,,5,,,,,,2
-"sub35",1,4,,,,,,2,,,,,,,3,5,
-"sub36",,5,,3,,4,1,2,,,,,,,,,
-"sub37",,,4,,3,,,,,,,1,2,5,,,
-"sub38",,,,4,,,,3,,,,2,,1,5,,
-"sub39",5,,,,1,4,,2,,,,,,3,,,
-"sub40",,,,,4,2,5,1,,,,,,,3,,
-"sub41",,1,,,,3,,5,,,,4,2,,,,
-"sub42",,,,,,3,,,,,,1,5,,2,,4
-"sub43",,,,,,,,,,,1,,3,,4,2,5
-"sub44",,4,,,,,,,,,2,,,5,3,,1
-"sub45",2,3,,,,,4,,1,,,,,,,,5
-"sub46",,3,,,4,,,,,5,1,,,,,,2
-"sub47",,2,1,,5,,,,,3,,4,,,,,
-"sub48",,2,,,1,3,,,,,5,4,,,,,
-"sub49",,,,1,,,,3,,,,2,,,,4,5
-"sub50",3,,,,,,,5,,1,,,4,,,2,
-"sub51",,,1,3,4,,,,2,,,,,,,5,
-"sub52",,,1,,,,,,,4,5,,,,2,3,
-"sub53",,,,2,5,,,,,1,,3,,,,4,
-"sub54",,,,3,,,,,4,,,1,,2,,5,
-"sub55",,,2,,,,4,,,,,,1,3,5,,
-"sub56",,,,,,,,,3,,1,5,4,2,,,
-"sub57",,,4,,2,,1,,,,,3,,,,,5
-"sub58",,3,,,,,,,,,,4,,,1,5,2
-"sub59",,,,4,,,1,,3,,5,2,,,,,
-"sub60",,,,,,,,2,,,,1,3,5,,4,
-"sub61",,,1,,,3,,2,4,,,,,5,,,
-"sub62",1,2,,,,,,5,,4,,,,,,3,
-"sub63",,2,,,3,,4,,,,,,,5,,,1
-"sub64",,,5,,,1,2,,,,3,,,,,,4
-"sub65",1,,3,2,,,,,,4,,,5,,,,
-"sub66",,,,,,,1,,,,,2,,4,5,,3
-"sub67",4,5,,,,,2,,1,,,,,3,,,
-"sub68",3,,,2,5,,4,,,1,,,,,,,
-"sub69",5,,1,,,,4,,,,,3,,,2,,
-"sub70",,2,,,,5,1,,,,3,,4,,,,
-"sub71",5,,,,4,2,,1,,,3,,,,,,
-"sub72",5,,,4,1,,,,,,3,,,,,2,
-"sub73",5,3,,,,,,,4,,,1,,,2,,
-"sub74",,5,,2,,3,,,4,,,,,,,,1
-"sub75",,,,,,,,,4,1,,5,2,,,,3
-"sub76",,1,,,,,2,5,4,,,3,,,,,
-"sub77",5,,,,,,3,,,,,,,1,2,,4
-"sub78",4,,,,,,1,3,,2,,,,,,5,
-"sub79",,,,3,,,,,,,4,1,5,,2,,
-"sub80",,2,,,5,4,,,,,,,,,1,3,
-"sub81",,,4,,,,2,,1,,,3,,,,,5
-"sub82",5,,,,,,,2,4,,,3,,,,,1
-"sub83",,2,,,,,4,5,1,,,,,,3,,
-"sub84",,,,3,1,,,,,,2,,4,,,5,
-"sub85",,,,1,4,,,5,,,,,,,2,,3
-"sub86",,,3,,,,,5,1,,,2,4,,,,
-"sub87",,,,,2,5,4,,,,,,1,,,3,
-"sub88",,,,,,,,,,,,2,3,1,,4,5
-"sub89",,,5,2,,,4,,,,,,,1,,3,
-"sub90",,5,,1,,,,,,4,,3,,2,,,
-"sub91",5,,,,,3,,,4,,2,,,1,,,
-"sub92",,,,,,4,,5,,,2,,,,1,3,
-"sub93",,,,,1,,,,,4,2,,5,,,3,
-"sub94",1,,,,,,2,,,,,,4,5,,,3
-"sub95",,,,,4,2,3,,,5,,1,,,,,
-"sub96",,5,,2,,,1,,,,,3,,4,,,
-"sub97",1,3,,,,,,4,2,,,,,,5,,
-"sub98",,,5,,3,,,,,,1,,,2,4,,
-"sub99",,,4,,,,,5,,,,,1,3,2,,
-"sub100",,2,,,,4,5,,,3,,,1,,,,
-"sub101",,3,,1,2,,,,,,4,,,,,,5
-"sub102",1,,,2,,5,,,,,,3,,,,4,
-"sub103",,3,,,,,5,,1,,,,,2,,,4
-"sub104",,5,,4,,1,2,3,,,,,,,,,
-"sub105",,,,2,5,,,3,4,,1,,,,,,
-"sub106",,,,4,5,3,2,,,,,1,,,,,
-"sub107",2,1,3,,,,,,5,,4,,,,,,
-"sub108",,,4,,,,,,,1,,,5,,2,,3
-"sub109",,4,,,,,,2,1,,,5,,3,,,
-"sub110",,,,,3,,,,1,,,,,4,5,,2
-"sub111",,,,,,3,,,4,1,,,,,,2,5
-"sub112",,1,,,,,,,2,5,,,3,,,4,
-"sub113",,,3,,,,,,,,1,5,,4,2,,
-"sub114",,,,,1,3,,,,,5,,4,,2,,
-"sub115",,1,,,4,2,,,,,3,5,,,,,
-"sub116",,2,4,,,3,,5,1,,,,,,,,
-"sub117",,,,,,2,,,,4,,1,,5,,3,
-"sub118",,4,5,,,1,,,3,,,,,2,,,
-"sub119",5,,,3,,,1,,,4,,,2,,,,
-"sub120",1,2,4,,,,,,,,,,5,,,,3
-"sub121",,2,,,,5,,,,,,1,3,,,,4
-"sub122",3,,1,5,,,,,,,,4,,2,,,
-"sub123",,1,3,,,,4,5,,,,,,,,2,
-"sub124",,,2,,,4,,,,3,,,,,5,,1
-"sub125",,,,2,,,,,,,4,1,,5,,,3
-"sub126",,,,2,5,,3,,4,,,,,,,1,
-"sub127",4,,,,,1,2,,,,,,5,3,,,
-"sub128",,,,,1,4,,,,,,3,,,,2,5
-"sub129",,,,3,1,2,,4,,,,5,,,,,
-"sub130",4,,,,1,,,5,,3,2,,,,,,
-"sub131",,,,,1,3,,,,5,2,,,,,,4
-"sub132",,,,,2,,5,,,,3,,1,,,,4
-"sub133",,4,,,,,,3,,,,,,1,,2,5

man/grouping_plot.Rd

@@ -6,7 +6,7 @@
 \usage{
 grouping_plot(
   data,
-  columns = NULL,
+  columns = 4,
   overall = FALSE,
   viridis.option = "D",
   viridis.direction = -1
@@ -16,7 +16,7 @@ grouping_plot(
 \item{data}{A "prioritized_groups_list" class list from
 'prioritized_grouping()'}
 
-\item{columns}{number of columns in plot}
+\item{columns}{number of columns in plot. Default=4.}
 
 \item{overall}{logical to only print overall groups mean priority/cost}
 
@@ -39,4 +39,7 @@ in the group.
 #read.csv(here::here("data/prioritized_sample.csv")) |>
 #  prioritized_grouping(cap_classes = sample(4:12, 17, TRUE)) |>
 #  grouping_plot()
+data.frame(id=paste0("id",1:100),
+matrix(replicate(100,sample(c(1:5,rep(NA,15)),10)),ncol=10,byrow = TRUE)) |>
+prioritized_grouping() |> grouping_plot(overall=TRUE)
 }

man/plot.prioritized_groups_list.Rd

@@ -4,10 +4,10 @@
 \alias{plot.prioritized_groups_list}
 \title{Plot extension for easy groupings plot}
 \usage{
-\method{plot}{prioritized_groups_list}(data, ...)
+\method{plot}{prioritized_groups_list}(x, ...)
 }
 \arguments{
-\item{data}{data of class 'prioritized_groups_list'}
+\item{x}{data of class 'prioritized_groups_list'}
 
 \item{...}{passed on to 'grouping_plot()'}
 }
@@ -18,7 +18,8 @@ ggplot2 list object
 Plot extension for easy groupings plot
 }
 \examples{
-read.csv(here::here("data/prioritized_sample.csv")) |>
+# read.csv(here::here("data/prioritized_sample.csv")) |>
-  prioritized_grouping() |>
+#   prioritized_grouping() |>
-  plot(overall = TRUE, viridis.option="D",viridis.direction=-1)
+#   plot(overall = TRUE, viridis.option="D",viridis.direction=-1)
+
 }

man/prioritized_grouping.Rd

@@ -34,7 +34,10 @@ list of custom class 'prioritized_groups_list'
 Solve grouping based on priorities or costs.
 }
 \examples{
-prioritized_grouping(
+# prioritized_grouping(
-data=read.csv(here::here("data/prioritized_sample.csv")),
+# data=read.csv(here::here("data/prioritized_sample.csv")),
-pre_grouped=read.csv(here::here("data/pre_grouped.csv"))) |> plot()
+# pre_grouped=read.csv(here::here("data/pre_grouped.csv"))) |> plot()
+data.frame(id=paste0("id",1:100),
+matrix(replicate(100,sample(c(1:5,rep(NA,15)),10)),ncol=10,byrow = TRUE)) |>
+prioritized_grouping()
 }

man/read_input.Rd

@@ -0,0 +1,22 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/prioritized_grouping.R
+\name{read_input}
+\alias{read_input}
+\title{Flexible file import based on extension}
+\usage{
+read_input(file, consider.na = c("NA", "\\"\\"", ""))
+}
+\arguments{
+\item{file}{file name}
+
+\item{consider.na}{character vector of strings to consider as NAs}
+}
+\value{
+tibble
+}
+\description{
+Flexible file import based on extension
+}
+\examples{
+read_input("https://raw.githubusercontent.com/agdamsbo/cognitive.index.lookup/main/data/sample.csv")
+}

publish_cran.R

@@ -0,0 +1,36 @@
+# Checks for publishing
+
+# Rhub v2
+
+# rhub::rhub_setup()
+
+# rhub::rhub_doctor()
+
+rhub::rhub_check(platforms = c(
+    "linux",
+    "macos",
+    "macos-arm64",
+    "windows"))
+
+# rhub::rhub_setup(overwrite = TRUE)
+# rhub::rhub_platforms()
+
+# SPELLING - dont use usethis::use_spell_check() - tests create notes on CRAN - not good
+devtools::spell_check()
+spelling::update_wordlist()
+
+
+# Release on CRAN - confirm e-mail
+devtools::release()
+
+# Use the following to publish latest release to GitHub
+usethis::use_github_release()
+
+
+## Testing
+##
+# ds <- data.frame(id=paste0("id",1:100),matrix(replicate(100,sample(c(1:5,rep(NA,15)),10)),ncol=10,byrow = TRUE))
+#
+# ls <- ds|> prioritized_grouping(seed = 7)
+#
+# ls$export |> tibble::as.tibble() |> dplyr::right_join(ds,by = c("ID"="id")) |> View()

renv.lock

@@ -76,33 +76,6 @@
       ],
       "Hash": "42ce9ee4c1cf168869f4386d2cdeadd2"
     },
-    "ROI.plugin.alabama": {
-      "Package": "ROI.plugin.alabama",
-      "Version": "1.0-2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "ROI",
-        "alabama",
-        "methods",
-        "stats",
-        "utils"
-      ],
-      "Hash": "097f1b625baf91f0d8999a1385054250"
-    },
-    "ROI.plugin.symphony": {
-      "Package": "ROI.plugin.symphony",
-      "Version": "1.0-0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "ROI",
-        "Rsymphony",
-        "methods",
-        "slam"
-      ],
-      "Hash": "0d5d6f983334cf25a47eef4b293fb299"
-    },
     "Rcpp": {
       "Package": "Rcpp",
       "Version": "1.0.13",
@@ -114,51 +87,6 @@
       ],
       "Hash": "f27411eb6d9c3dada5edd444b8416675"
     },
-    "Rsymphony": {
-      "Package": "Rsymphony",
-      "Version": "0.1-33",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "3f55239fe534fe91e739c77d99a4ffbf"
-    },
-    "alabama": {
-      "Package": "alabama",
-      "Version": "2023.1.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "numDeriv"
-      ],
-      "Hash": "593db7eb170506e6b61ca0c803201924"
-    },
-    "archive": {
-      "Package": "archive",
-      "Version": "1.1.9",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "rlang",
-        "tibble"
-      ],
-      "Hash": "d26b62e131d4a8b65aba4e9554a4bf74"
-    },
-    "askpass": {
-      "Package": "askpass",
-      "Version": "1.2.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "sys"
-      ],
-      "Hash": "c39f4155b3ceb1a9a2799d700fbd4b6a"
-    },
     "assertthat": {
       "Package": "assertthat",
       "Version": "0.2.1",
@@ -189,16 +117,6 @@
       ],
       "Hash": "543776ae6848fde2f48ff3816d0628bc"
     },
-    "brio": {
-      "Package": "brio",
-      "Version": "1.1.5",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "c1ee497a6d999947c2c224ae46799b1a"
-    },
     "bslib": {
       "Package": "bslib",
       "Version": "0.8.0",
@@ -232,19 +150,6 @@
       ],
       "Hash": "cd9a672193789068eb5a2aad65a0dedf"
     },
-    "callr": {
-      "Package": "callr",
-      "Version": "3.7.6",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "R6",
-        "processx",
-        "utils"
-      ],
-      "Hash": "d7e13f49c19103ece9e58ad2d83a7354"
-    },
     "cellranger": {
       "Package": "cellranger",
       "Version": "1.1.0",
@@ -323,16 +228,6 @@
       ],
       "Hash": "859d96e65ef198fd43e82b9628d593ef"
     },
-    "curl": {
-      "Package": "curl",
-      "Version": "5.2.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "d91263322a58af798f6cf3b13fd56dde"
-    },
     "data.table": {
       "Package": "data.table",
       "Version": "1.16.0",
@@ -344,19 +239,6 @@
       ],
       "Hash": "fb24e05d4a91d8b1c7ff8e284bde834a"
     },
-    "desc": {
-      "Package": "desc",
-      "Version": "1.4.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "R6",
-        "cli",
-        "utils"
-      ],
-      "Hash": "99b79fcbd6c4d1ce087f5c5c758b384f"
-    },
     "digest": {
       "Package": "digest",
       "Version": "0.6.37",
@@ -417,16 +299,6 @@
       "Repository": "RSPM",
       "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8"
     },
-    "filelock": {
-      "Package": "filelock",
-      "Version": "1.0.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "192053c276525c8495ccfd523aa8f2d1"
-    },
     "fontawesome": {
       "Package": "fontawesome",
       "Version": "0.5.2",
@@ -486,34 +358,6 @@
       ],
       "Hash": "44c6a2f8202d5b7e878ea274b1092426"
     },
-    "gh": {
-      "Package": "gh",
-      "Version": "1.4.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "cli",
-        "gitcreds",
-        "glue",
-        "httr2",
-        "ini",
-        "jsonlite",
-        "lifecycle",
-        "rlang"
-      ],
-      "Hash": "fbbbc48eba7a6626a08bb365e44b563b"
-    },
-    "gitcreds": {
-      "Package": "gitcreds",
-      "Version": "0.1.2",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "ab08ac61f3e1be454ae21911eb8bc2fe"
-    },
     "glue": {
       "Package": "glue",
       "Version": "1.8.0",
@@ -540,30 +384,6 @@
       ],
       "Hash": "e18861963cbc65a27736e02b3cd3c4a0"
     },
-    "here": {
-      "Package": "here",
-      "Version": "1.0.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "rprojroot"
-      ],
-      "Hash": "24b224366f9c2e7534d2344d10d59211"
-    },
-    "hms": {
-      "Package": "hms",
-      "Version": "1.1.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "lifecycle",
-        "methods",
-        "pkgconfig",
-        "rlang",
-        "vctrs"
-      ],
-      "Hash": "b59377caa7ed00fa41808342002138f9"
-    },
     "htmltools": {
       "Package": "htmltools",
       "Version": "0.5.8.1",
@@ -595,34 +415,6 @@
       ],
       "Hash": "d55aa087c47a63ead0f6fc10f8fa1ee0"
     },
-    "httr2": {
-      "Package": "httr2",
-      "Version": "1.0.5",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "R6",
-        "cli",
-        "curl",
-        "glue",
-        "lifecycle",
-        "magrittr",
-        "openssl",
-        "rappdirs",
-        "rlang",
-        "vctrs",
-        "withr"
-      ],
-      "Hash": "d84e4c33206aaace37714901ac2b00c3"
-    },
-    "ini": {
-      "Package": "ini",
-      "Version": "0.3.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Hash": "6154ec2223172bce8162d4153cda21f7"
-    },
     "isoband": {
       "Package": "isoband",
       "Version": "0.2.7",
@@ -725,13 +517,6 @@
       ],
       "Hash": "4062982514dd797c7013124da49994c8"
     },
-    "lpSolve": {
-      "Package": "lpSolve",
-      "Version": "5.6.21",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Hash": "730a90bdc519fb0caff03df11218ddd8"
-    },
     "magrittr": {
       "Package": "magrittr",
       "Version": "2.0.3",
@@ -817,16 +602,6 @@
       ],
       "Hash": "ccbb8846be320b627e6aa2b4616a2ded"
     },
-    "numDeriv": {
-      "Package": "numDeriv",
-      "Version": "2016.8-1.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "df58958f293b166e4ab885ebcad90e02"
-    },
     "ompr": {
       "Package": "ompr",
       "Version": "1.0.4",
@@ -859,32 +634,22 @@
       ],
       "Hash": "0f9f0bb7e9cff9da0237c8bd206d40a2"
     },
-    "openssl": {
+    "openxlsx2": {
-      "Package": "openssl",
+      "Package": "openxlsx2",
-      "Version": "2.2.2",
+      "Version": "1.9",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
-      "Requirements": [
-        "askpass"
-      ],
-      "Hash": "d413e0fef796c9401a4419485f709ca1"
-    },
-    "openxlsx": {
-      "Package": "openxlsx",
-      "Version": "4.2.7.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
       "Requirements": [
         "R",
+        "R6",
         "Rcpp",
         "grDevices",
-        "methods",
+        "magrittr",
-        "stats",
         "stringi",
         "utils",
         "zip"
       ],
-      "Hash": "14304e44a0f90fa2d0f905472333c561"
+      "Hash": "f3e00e7d16abb500e63faee67b7dc1a7"
     },
     "patchwork": {
       "Package": "patchwork",
@@ -922,40 +687,6 @@
       ],
       "Hash": "15da5a8412f317beeee6175fbc76f4bb"
     },
-    "pkgbuild": {
-      "Package": "pkgbuild",
-      "Version": "1.4.4",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "R6",
-        "callr",
-        "cli",
-        "desc",
-        "processx"
-      ],
-      "Hash": "a29e8e134a460a01e0ca67a4763c595b"
-    },
-    "pkgcache": {
-      "Package": "pkgcache",
-      "Version": "2.2.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R6",
-        "callr",
-        "cli",
-        "curl",
-        "filelock",
-        "jsonlite",
-        "processx",
-        "tools",
-        "utils"
-      ],
-      "Hash": "502554da4ec4d917b737e6b0fe14dd11"
-    },
     "pkgconfig": {
       "Package": "pkgconfig",
       "Version": "2.0.3",
@@ -966,68 +697,6 @@
       ],
       "Hash": "01f28d4278f15c76cddbea05899c5d6f"
     },
-    "pkgdepends": {
-      "Package": "pkgdepends",
-      "Version": "0.8.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "R6",
-        "callr",
-        "cli",
-        "curl",
-        "desc",
-        "filelock",
-        "jsonlite",
-        "lpSolve",
-        "pkgbuild",
-        "pkgcache",
-        "processx",
-        "ps",
-        "stats",
-        "utils",
-        "zip"
-      ],
-      "Hash": "eb7e3e965327555a527196d26d0643e4"
-    },
-    "prettyunits": {
-      "Package": "prettyunits",
-      "Version": "1.2.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "6b01fc98b1e86c4f705ce9dcfd2f57c7"
-    },
-    "processx": {
-      "Package": "processx",
-      "Version": "3.8.4",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R6",
-        "ps",
-        "utils"
-      ],
-      "Hash": "0c90a7d71988856bad2a2a45dd871bb9"
-    },
-    "progress": {
-      "Package": "progress",
-      "Version": "1.2.3",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "R6",
-        "crayon",
-        "hms",
-        "prettyunits"
-      ],
-      "Hash": "f4625e061cb2865f111b47ff163a5ca6"
-    },
     "promises": {
       "Package": "promises",
       "Version": "1.3.0",
@@ -1044,32 +713,6 @@
       ],
       "Hash": "434cd5388a3979e74be5c219bcd6e77d"
     },
-    "ps": {
-      "Package": "ps",
-      "Version": "1.8.0",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R",
-        "utils"
-      ],
-      "Hash": "4b9c8485b0c7eecdf0a9ba5132a45576"
-    },
-    "purrr": {
-      "Package": "purrr",
-      "Version": "1.0.2",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "lifecycle",
-        "magrittr",
-        "rlang",
-        "vctrs"
-      ],
-      "Hash": "1cba04a4e9414bdefc9dcaa99649a8dc"
-    },
     "rappdirs": {
       "Package": "rappdirs",
       "Version": "0.3.3",
@@ -1136,16 +779,6 @@
       ],
       "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1"
     },
-    "rprojroot": {
-      "Package": "rprojroot",
-      "Version": "2.0.4",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Requirements": [
-        "R"
-      ],
-      "Hash": "4c8415e0ec1e29f3f4f6fc108bef0144"
-    },
     "sass": {
       "Package": "sass",
       "Version": "0.4.9",
@@ -1213,31 +846,6 @@
       ],
       "Hash": "6a293995a66e12c48d13aa1f957d09c7"
     },
-    "shinylive": {
-      "Package": "shinylive",
-      "Version": "0.2.0",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "archive",
-        "brio",
-        "cli",
-        "fs",
-        "gh",
-        "glue",
-        "httr2",
-        "jsonlite",
-        "pkgdepends",
-        "progress",
-        "rappdirs",
-        "renv",
-        "rlang",
-        "tools",
-        "whisker",
-        "withr"
-      ],
-      "Hash": "224c8c0502bb0ead1fd1b4b32ea04a90"
-    },
     "slam": {
       "Package": "slam",
       "Version": "0.1-53",
@@ -1272,30 +880,6 @@
       ],
       "Hash": "39e1144fd75428983dc3f63aa53dfa91"
     },
-    "stringr": {
-      "Package": "stringr",
-      "Version": "1.5.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "glue",
-        "lifecycle",
-        "magrittr",
-        "rlang",
-        "stringi",
-        "vctrs"
-      ],
-      "Hash": "960e2ae9e09656611e0b8214ad543207"
-    },
-    "sys": {
-      "Package": "sys",
-      "Version": "3.4.3",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Hash": "de342ebfebdbf40477d0758d05426646"
-    },
     "tibble": {
       "Package": "tibble",
       "Version": "3.2.1",
@@ -1315,29 +899,6 @@
       ],
       "Hash": "a84e2cc86d07289b3b6f5069df7a004c"
     },
-    "tidyr": {
-      "Package": "tidyr",
-      "Version": "1.3.1",
-      "Source": "Repository",
-      "Repository": "CRAN",
-      "Requirements": [
-        "R",
-        "cli",
-        "cpp11",
-        "dplyr",
-        "glue",
-        "lifecycle",
-        "magrittr",
-        "purrr",
-        "rlang",
-        "stringr",
-        "tibble",
-        "tidyselect",
-        "utils",
-        "vctrs"
-      ],
-      "Hash": "915fb7ce036c22a6a33b5a8adb712eb1"
-    },
     "tidyselect": {
       "Package": "tidyselect",
       "Version": "1.2.1",
@@ -1399,13 +960,6 @@
       ],
       "Hash": "c826c7c4241b6fc89ff55aaea3fa7491"
     },
-    "whisker": {
-      "Package": "whisker",
-      "Version": "0.4.1",
-      "Source": "Repository",
-      "Repository": "RSPM",
-      "Hash": "c6abfa47a46d281a7d5159d0a8891e88"
-    },
     "withr": {
       "Package": "withr",
       "Version": "3.0.1",