From ea768fbba125a6edb9716b0d1c2251e5ff7b7b24 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Thu, 10 Oct 2024 13:22:22 +0200 Subject: [PATCH] all build notes and errors handled --- .Rbuildignore | 3 + .gitignore | 2 + DESCRIPTION | 23 +- NAMESPACE | 1 + R/prioritized_grouping.R | 67 ++++- app/server.R | 73 +++--- app/server_raw.R | 35 +-- man/grouping_plot.Rd | 7 +- man/plot.prioritized_groups_list.Rd | 11 +- man/prioritized_grouping.Rd | 9 +- man/read_input.Rd | 22 ++ publish_cran.R | 36 +++ renv.lock | 382 +--------------------------- 13 files changed, 195 insertions(+), 476 deletions(-) create mode 100644 man/read_input.Rd create mode 100644 publish_cran.R diff --git a/.Rbuildignore b/.Rbuildignore index 96539a6..dec0635 100644 --- a/.Rbuildignore +++ b/.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$ diff --git a/.gitignore b/.gitignore index 457525e..d9b9596 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,5 @@ .DS_Store .quarto docs +data/prioritized_sample.xlsx +sample_data diff --git a/DESCRIPTION b/DESCRIPTION index 6addb68..82be8ca 100644 --- a/DESCRIPTION +++ b/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 diff --git a/NAMESPACE b/NAMESPACE index ff85798..b7905eb 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -4,3 +4,4 @@ S3method(plot,prioritized_groups_list) export(file_extension) export(grouping_plot) export(prioritized_grouping) +export(read_input) diff --git a/R/prioritized_grouping.R b/R/prioritized_grouping.R index d3d0594..cd96070 100644 --- a/R/prioritized_grouping.R +++ b/R/prioritized_grouping.R @@ -16,9 +16,12 @@ utils::globalVariables(c("group", "grp", "i", "j", "value")) #' @export #' #' @examples -#' prioritized_grouping( -#' data=read.csv(here::here("data/prioritized_sample.csv")), -#' pre_grouped=read.csv(here::here("data/pre_grouped.csv"))) |> plot() +#' # prioritized_grouping( +#' # data=read.csv(here::here("data/prioritized_sample.csv")), +#' # 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")) |> -#' prioritized_grouping() |> -#' plot(overall = TRUE, viridis.option="D",viridis.direction=-1) -plot.prioritized_groups_list <- function(data, ...) { - grouping_plot(data, ...) +#' # read.csv(here::here("data/prioritized_sample.csv")) |> +#' # prioritized_grouping() |> +#' # plot(overall = TRUE, viridis.option="D",viridis.direction=-1) +#' +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 +} diff --git a/app/server.R b/app/server.R index 7e6e6a3..82a1a64 100644 --- a/app/server.R +++ b/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$datapath) - - tryCatch( - { - if (ext == "csv") { - df <- utils::read.csv(input$file1$datapath,na.strings = c("NA", '""',"")) - } else if (ext %in% c("xls", "xlsx")) { - df <- openxlsx::read.xlsx(input$file1$datapath,na.strings = c("NA", '""',"")) - } else if (ext == "ods") { - df <- readODS::read_ods(file = file) - } else { - stop("Input file format has to be on of: - '.csv', '.xls', '.xlsx' or '.ods'") - } - }, - error = function(e) { - # return a safeError if a parsing error occurs - stop(safeError(e)) - } - ) - + df <- read_input(input$file1$datapath) return(df) }) @@ -370,18 +388,7 @@ server <- function(input, output, session) { # req(input$file2) # Make laoding dependent of file name extension (file_ext()) if (!is.null(input$file2$datapath)){ - ext <- file_extension(input$file2$datapath) - - 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'") - } + df <- read_input(input$file2$datapath) return(df) } else { diff --git a/app/server_raw.R b/app/server_raw.R index 7f7ca04..e32eb03 100644 --- a/app/server_raw.R +++ b/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$datapath) - - tryCatch( - { - if (ext == "csv") { - df <- utils::read.csv(input$file1$datapath,na.strings = c("NA", '""',"")) - } else if (ext %in% c("xls", "xlsx")) { - df <- openxlsx::read.xlsx(input$file1$datapath,na.strings = c("NA", '""',"")) - } else if (ext == "ods") { - df <- readODS::read_ods(file = file) - } else { - stop("Input file format has to be on of: - '.csv', '.xls', '.xlsx' or '.ods'") - } - }, - error = function(e) { - # return a safeError if a parsing error occurs - stop(safeError(e)) - } - ) - + df <- read_input(input$file1$datapath) return(df) }) @@ -39,18 +19,7 @@ server <- function(input, output, session) { # req(input$file2) # Make laoding dependent of file name extension (file_ext()) if (!is.null(input$file2$datapath)){ - ext <- file_extension(input$file2$datapath) - - 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'") - } + df <- read_input(input$file2$datapath) return(df) } else { diff --git a/man/grouping_plot.Rd b/man/grouping_plot.Rd index eb5a2c8..4d88f9a 100644 --- a/man/grouping_plot.Rd +++ b/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) } diff --git a/man/plot.prioritized_groups_list.Rd b/man/plot.prioritized_groups_list.Rd index 5fb24d9..ebf5ace 100644 --- a/man/plot.prioritized_groups_list.Rd +++ b/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")) |> - prioritized_grouping() |> - plot(overall = TRUE, viridis.option="D",viridis.direction=-1) +# read.csv(here::here("data/prioritized_sample.csv")) |> +# prioritized_grouping() |> +# plot(overall = TRUE, viridis.option="D",viridis.direction=-1) + } diff --git a/man/prioritized_grouping.Rd b/man/prioritized_grouping.Rd index 85f0eb5..b9d2780 100644 --- a/man/prioritized_grouping.Rd +++ b/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( -data=read.csv(here::here("data/prioritized_sample.csv")), -pre_grouped=read.csv(here::here("data/pre_grouped.csv"))) |> plot() +# prioritized_grouping( +# data=read.csv(here::here("data/prioritized_sample.csv")), +# 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() } diff --git a/man/read_input.Rd b/man/read_input.Rd new file mode 100644 index 0000000..12eeaff --- /dev/null +++ b/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") +} diff --git a/publish_cran.R b/publish_cran.R new file mode 100644 index 0000000..214a384 --- /dev/null +++ b/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() diff --git a/renv.lock b/renv.lock index 05e0832..66176d9 100644 --- a/renv.lock +++ b/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" }, - 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"methods", - "stats", + "magrittr", "stringi", "utils", "zip" ], - "Hash": "14304e44a0f90fa2d0f905472333c561" + "Hash": "f3e00e7d16abb500e63faee67b7dc1a7" }, "patchwork": { "Package": "patchwork", @@ -922,40 +710,6 @@ ], "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 +720,6 @@ ], "Hash": "01f28d4278f15c76cddbea05899c5d6f" }, - "pkgdepends": { - "Package": "pkgdepends", - "Version": "0.8.0", - 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