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MarkdownReportsDev is new discontinued.
Further development will be implemented here, in MarkdownReports. MarkdownReportsDev was made when big changes were happening. The development reached its main goals.
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Development/Create_the_MarkdownReports_Package.v4.3.2.R
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| ###################################################################################################### | ||
| # Workflow_to_Create_an_R_Package.R | ||
| # 3- Oct 2021 | ||
| ###################################################################################################### | ||
| # source("~/GitHub/Packages/MarkdownReports/Development/Create_the_MarkdownReports_Package.v4.3.2.R") | ||
| rm(list = ls(all.names = TRUE)); | ||
| try(dev.off(), silent = TRUE) | ||
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| # install.packages("devtools") | ||
| # Functions ------------------------ | ||
| # devtools::install_github(repo = "vertesy/MarkdownReports/MarkdownReports") | ||
| try (source('~/GitHub/Packages/CodeAndRoll/CodeAndRoll.R'),silent= FALSE) | ||
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| # irequire("devtools") | ||
| # install_version("devtools", version = "2.0.2", repos = "http://cran.at.r-project.org") | ||
| irequire("devtools") | ||
| irequire("roxygen2") | ||
| irequire("stringr") | ||
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| kollapse <-function(..., print = TRUE) { | ||
| if (print == TRUE) { | ||
| print(paste0(c(...), collapse = "")) | ||
| } | ||
| paste0(c(...), collapse = "") | ||
| } | ||
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| # Setup ------------------------ | ||
| PackageName = "MarkdownReports" | ||
| setwd("~/GitHub/") | ||
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| RepositoryDir = kollapse("~/GitHub/Packages/", PackageName, "/") | ||
| fname = kollapse(PackageName, ".R") | ||
| Package_FnP = kollapse(RepositoryDir, "R/", fname) | ||
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| BackupDir = "~/GitHub/Packages/MarkdownReports/Development/" | ||
| dir.create(BackupDir) | ||
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| # devtools::use_package("vioplot") | ||
| DESCRIPTION <- list("Title" = "Generate Scientific Figures and Reports Easily" | ||
| , "Author" = person(given = "Abel", family = "Vertesy", email = "a.vertesy@hubrecht.eu", role = c("aut", "cre") ) | ||
| , "Authors@R" = 'person(given = "Abel", family = "Vertesy", email = "a.vertesy@hubrecht.eu", role = c("aut", "cre") )' | ||
| , "Description" = "MarkdownReports is a set of R functions that allows you to generate precise figures easily, | ||
| and create clean markdown reports about what you just discovered with your analysis script. It helps you to: | ||
| 1. Create scientifically accurate (annotated) figures with very short code, making use of variable-, row- and columnnames. | ||
| 2. Save figures automatically as vector graphic (.pdf), that you can use from presentation to posters anywhere. | ||
| 3. Incorporate your figures automatically in a markdown report file. | ||
| 4. Describe your figures & findings in the same report in a clear and nicely formatted way, parsed from your variables into english sentences. | ||
| 5. Share your report, by exporting your report to .pdf, .html or .docx, or via Github or a personal website." | ||
| , "License" = "GPL-3 + file LICENSE" | ||
| , "Version" = "4.3.2" | ||
| , "Packaged" = Sys.time() | ||
| , "Repository" = "CRAN" | ||
| , "Imports" = "stats, methods, sm, graphics, grDevices, gplots, RColorBrewer, colorRamps, clipr, vioplot, VennDiagram, sessioninfo" | ||
| # , "Suggests" = "" | ||
| , "BugReports"= "https://github.com/vertesy/MarkdownReports/issues" | ||
| ) | ||
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| setwd(RepositoryDir) | ||
| if ( !dir.exists(RepositoryDir) ) { create(path = RepositoryDir, description = DESCRIPTION, rstudio = TRUE) | ||
| } else { | ||
| getwd() | ||
| try(file.remove(c("DESCRIPTION","NAMESPACE", "MarkdownReports.Rproj"))) | ||
| create_package(path = RepositoryDir, fields = DESCRIPTION, open = F) | ||
| } | ||
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| # go and write fun's ------------------------------------------------------------------------ | ||
| # file.edit(Package_FnP) | ||
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| # Create Roxygen Skeletons ------------------------ | ||
| # RoxygenReady(Package_FnP) | ||
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| # replace output files ------------------------------------------------ | ||
| BackupOldFile = kollapse(BackupDir, "Development", ".bac", print = FALSE) | ||
| AnnotatedFile = kollapse(BackupDir, "Development", ".annot.R", print = FALSE) | ||
| file.copy(from = Package_FnP, to = BackupOldFile, overwrite = TRUE) | ||
| # file.copy(from = AnnotatedFile, to = Package_FnP, overwrite = TRUE) | ||
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| # Manual editing of descriptors ------------------------------------------------ | ||
| # file.edit(Package_FnP) | ||
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| # Compile a package ------------------------------------------------ | ||
| setwd(RepositoryDir) | ||
| getwd() | ||
| document() | ||
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| # Install your package ------------------------------------------------ | ||
| # # setwd(RepositoryDir) | ||
| install(RepositoryDir) | ||
| # require("MarkdownReports") | ||
| # # remove.packages("MarkdownReports") | ||
| # # Test your package ------------------------------------------------ | ||
| # help("wplot") | ||
| # cat("\014") | ||
| # devtools::run_examples() | ||
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| # Test if you can install from github ------------------------------------------------ | ||
| # devtools::install_github(repo = "vertesy/MarkdownReports") | ||
| # devtools::install_github(repo = "vertesy/MarkdownReports/MarkdownReports") | ||
| # require("MarkdownReports") | ||
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| # Clean up if not needed anymore ------------------------------------------------ | ||
| # View(installed.packages()) | ||
| # remove.packages("MarkdownReports") | ||
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| check(RepositoryDir, cran = TRUE) | ||
| # as.package(RepositoryDir) | ||
| # | ||
| # | ||
| # # source("https://install-github.me/r-lib/desc") | ||
| # # library(desc) | ||
| # # desc$set("MarkdownReports", "foo") | ||
| # # desc$get(MarkdownReports) | ||
| # | ||
| # | ||
| # system("cd ~/GitHub/MarkdownReports/; ls -a; open .Rbuildignore") | ||
| # |
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