all build notes and errors handled

.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$

.gitignore

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

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/server.R

@@ -325,6 +325,44 @@ 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 == "dta") {
+        df <- haven::read_dta(file = file)
+      } 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 +379,7 @@ 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 +388,7 @@ 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 {

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

@@ -76,20 +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",
@@ -124,41 +110,6 @@
       ],
       "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 +140,6 @@
       ],
       "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 +173,6 @@
       ],
       "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 +251,6 @@
       ],
       "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 +262,6 @@
       ],
       "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 +322,6 @@
       "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 +381,6 @@
       ],
       "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 +407,6 @@
       ],
       "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 +438,6 @@
       ],
       "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 +540,6 @@
       ],
       "Hash": "4062982514dd797c7013124da49994c8"
     },
-    "lpSolve": {
-      "Package": "lpSolve",
-      "Version": "5.6.21",
-      "Source": "Repository",
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@@ -817,16 +625,6 @@
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@@ -859,32 +657,22 @@
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@@ -922,40 +710,6 @@
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@@ -966,68 +720,6 @@
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@@ -1044,17 +736,6 @@
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@@ -1136,16 +817,6 @@
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@@ -1213,31 +884,6 @@
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@@ -1289,13 +935,6 @@
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@@ -1399,13 +1038,6 @@
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