added package skeleton, license and updated description quarto doc

.Rbuildignore

@@ -0,0 +1,6 @@
+^speval\.Rproj$
+^\.Rproj\.user$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^LICENSE\.md$

.gitignore

@@ -45,3 +45,5 @@ vignettes/*.pdf
 
 # R Environment Variables
 .Renviron
+.Rproj.user
+docs

DESCRIPTION

@@ -0,0 +1,11 @@
+Package: speval
+Title: What the Package Does (One Line, Title Case)
+Version: 0.0.0.9000
+Authors@R: 
+    person("First", "Last", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "YOUR-ORCID-ID"))
+Description: What the package does (one paragraph).
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: Gael Sola, Lauri Vesa, Javier Garcia Perez

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 Gael Sola, Lauri Vesa, Javier Garcia Perez
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -0,0 +1,2 @@
+# Generated by roxygen2: do not edit by hand
+

R/shiny_run_MCredd.R → R/shiny_run_app.R

@@ -1,10 +1,7 @@
-#' Run Monte Carlo for REDD+ uncertainty's shiny app
+#' Run the species name validation tool
 #'
-#' @description Starts a R Shiny application that guide users to fill in context and
-#'              land use changes for forest related greenhouse gas emissions and removals.
-#'              Inputs include distribution parameters for various distribution then the app
-#'              returns error propagation and sensitivity analysis of the overall uncertainty
-#'              for GHG estimates.
+#' @description Starts a R Shiny application that let users upload a list of species names,
+#'              check them for typos and validate them against several major taxonomic backbones.
 #'
 #' @param ... arguments to pass to shinyApp
 #'
@@ -20,7 +17,7 @@
 #' }
 #'
 #' @export
-shiny_run_MCredd <- function(...) {
+shiny_run_app <- function(...) {
 
   ## GLOBAL ####################################################################
   ## Initiate translation

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: ~
+template:
+  bootstrap: 5
+

app.R

@@ -3,4 +3,4 @@
 # Or use the blue button on top of this file
 
 pkgload::load_all(export_all = FALSE, helpers = FALSE, attach_testthat = FALSE)
-MCredd::shiny_run_MCredd()
+speval::shiny_run_app()

pkg-creation-process.qmd

@@ -0,0 +1,71 @@
+---
+title: "Package creation process"
+format: html
+editor: visual
+execute:
+  eval: false
+---
+
+## Initiate package creation
+
+```{r}
+
+## Create package in current RR project directory
+usethis::create_package(getwd())
+
+## Add pkgdown skeleton
+usethis::use_pkgdown()
+
+```
+
+## Add license
+
+```{r}
+
+usethis::use_mit_license(copyright_holder = "Gael Sola, Lauri Vesa, Javier Garcia Perez")
+```
+
+## Add skeleton
+
+The skeleton includes scripts for shiny modules and translation out of the box i the following directories:
+
+-   home folder:
+
+    -   *app.R*: contains code to launch the app on shinyapps.io
+
+-   R:
+
+    -   functions scripts (file name = function name)
+
+    -   shiny modules scripts (file names like *mod\_\*UI.R* and *mod\_\*\_server.R)*
+
+    -   *helpers.R*: functions useful for the package development but not exported.
+
+    -   zzz.R function to make the asset directory from each user package libriary available to the shiny app
+
+-   inst/assets:
+
+    -   images, translation and other files useful for the app.
+
+------------------------------------------------------------------------
+
+## Quarto
+
+Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
+
+## Running Code
+
+When you click the **Render** button a document will be generated that includes both content and the output of embedded code. You can embed code like this:
+
+```{r}
+1 + 1
+```
+
+You can add options to executable code like this
+
+```{r}
+#| echo: false
+2 * 2
+```
+
+The `echo: false` option disables the printing of code (only output is displayed).

speval.Rproj

@@ -1,7 +1,7 @@
 Version: 1.0
 
-RestoreWorkspace: Default
-SaveWorkspace: Default
+RestoreWorkspace: No
+SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
@@ -11,3 +11,12 @@ Encoding: UTF-8
 
 RnwWeave: Sweave
 LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+LineEndingConversion: Posix
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace