Move from {learndown} to {learnitdown} and start 2021 series

Author: phgrosjean

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: BioDataScience2
-Version: 2020.9.0
+Version: 2021.0.0
 Title: A Series of Learnr Documents for Biological Data Science 2
 Description: Interactive documents using learnr for studying biological data science (second course).
 Authors@R: c(
@@ -9,7 +9,7 @@ Authors@R: c(
   email = "guyliann.engels@umons.ac.be"))
 Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>
 Depends: R (>= 3.5.0)
-Imports: learndown, BioDataScience, shiny, miniUI
+Imports: learnitdown, BioDataScience, shiny, miniUI
 Suggests: SciViews, ggplot2, ggpubr, data.io, flow, chart, covr, knitr, testthat, gradethis
 License: MIT + file LICENSE
 Encoding: UTF-8

NAMESPACE

@@ -9,9 +9,9 @@ export(update_pkg)
 importFrom(BioDataScience,config)
 importFrom(BioDataScience,sign_in)
 importFrom(BioDataScience,sign_out)
-importFrom(learndown,learndownLearnrBanner)
-importFrom(learndown,learndownLearnrServer)
-importFrom(learndown,run)
+importFrom(learnitdown,learnitdownLearnrBanner)
+importFrom(learnitdown,learnitdownLearnrServer)
+importFrom(learnitdown,run)
 importFrom(miniUI,gadgetTitleBar)
 importFrom(miniUI,miniContentPanel)
 importFrom(miniUI,miniPage)

NEWS.md

@@ -1,139 +1,141 @@
 # BioDataScience2 News
 
+## Changes in version 2021.0.0
+
+-   Start of 2021 series.
+
+-   Moved from {learndown} to {learnitdown}.
+
 ## Changes in version 2020.9.0
 
-- A new tutorial B08La_mfa is added.
+-   A new tutorial B08La_mfa is added.
 
 ## Changes in version 2020.8.2
 
-- In the B07La_pca tutorial, chart$<type>() does not work properly in specific cases. A work-around is introduced.
+-   In the B07La_pca tutorial, chart\$<type>() does not work properly in specific cases. A work-around is introduced.
 
 ## Changes in version 2020.8.1
 
-- In the B07La_pca tutorial, chart$<type>() does not work properly in specific cases. This is an attempt to fix it.
+-   In the B07La_pca tutorial, chart\$<type>() does not work properly in specific cases. This is an attempt to fix it.
 
 ## Changes in version 2020.8.0
 
-- New tutorial B07La_pca in version 2.
+-   New tutorial B07La_pca in version 2.
 
-- Praise sentences in English are eliminated from result outputs of {gradethis}.
+-   Praise sentences in English are eliminated from result outputs of {gradethis}.
 
 ## Changes in version 2020.7.0
 
-- Tutorial B06Lc_som migrated to version 2.
+-   Tutorial B06Lc_som migrated to version 2.
 
 ## Changes in version 2020.6.0
 
-- Tutorial B06Lb_mds migrated to version 2.
+-   Tutorial B06Lb_mds migrated to version 2.
 
 ## Changes in version 2020.5.0
 
-- Tutorial B06La_kmeans migrated to version 2.
+-   Tutorial B06La_kmeans migrated to version 2.
 
 ## Changes in version 2020.4.1
 
-- A bug in learnr that cannot run chart$horizontal() in B05La_cah is eliminated.
+-   A bug in learnr that cannot run chart\$horizontal() in B05La_cah is eliminated.
 
 ## Changes in version 2020.4.0
 
-- "Tutorial" B99La_avis added to get a quick feedback from the students.
+-   "Tutorial" B99La_avis added to get a quick feedback from the students.
 
-- Tutorial B05La_cah finalized
+-   Tutorial B05La_cah finalized
 
 ## Changes in version 2020.3.1
 
-- Tutorials that are not in final stage are now placed in the devel/ directory.
+-   Tutorials that are not in final stage are now placed in the devel/ directory.
 
 ## Changes in version 2020.3.0
 
-- New tutorial B04La
+-   New tutorial B04La
 
-- New shinyapps B04Sa, B04Sb, B04Sc, B04Sd, B04Se, B04Sf 
+-   New shinyapps B04Sa, B04Sb, B04Sc, B04Sd, B04Se, B04Sf
 
 ## Changes in version 2020.2.4
 
-- Minor change in B03La_mod_lin
+-   Minor change in B03La_mod_lin
 
 ## Changes in version 2020.2.3
 
-- Update B03La_mod_lin
+-   Update B03La_mod_lin
 
 ## Changes in version 2020.2.2
 
-- Minor change in B02la_reg_multi 
+-   Minor change in B02la_reg_multi
 
 ## Changes in version 2020.2.1
 
-- Minor change in B02lB_reg_poly 
+-   Minor change in B02lB_reg_poly
 
 ## Changes in version 2020.2.0
 
-- Update B02La_reg_multi and B02Lb_reg_poly
+-   Update B02La_reg_multi and B02Lb_reg_poly
 
 ## changes in version 2020.1.1
 
-- Update all tutorials with SciViews Box 2020 and BioDatascience packages
+-   Update all tutorials with SciViews Box 2020 and BioDatascience packages
 
 ## Changes in version 2020.1.0
 
-- Update B01La_rappel and B01Lb_reglin1 for better interaction with gradethis package. 
+-   Update B01La_rappel and B01Lb_reglin1 for better interaction with gradethis package.
 
 ## Changes in version 2020.0.0
 
-- Update all tutorials with SciViews Box 2020, and name change with B01Xa_name,
-with 'B' refers to second course, '01' to first module, 'X' being `L` for learnr
-or `S` for Shiny and 'a' the sequence in case there are several similar items in
-the same module.
+-   Update all tutorials with SciViews Box 2020, and name change with B01Xa_name, with 'B' refers to second course, '01' to first module, 'X' being `L` for learnr or `S` for Shiny and 'a' the sequence in case there are several similar items in the same module.
 
-- RStudio addins.
+-   RStudio addins.
 
 ## Changes in version 2019.11.0
 
-- Tutorial 06b_mds
+-   Tutorial 06b_mds
 
-- Tutorial 06c_som
+-   Tutorial 06c_som
 
 ## Changes in version 2019.11.0
 
-- Tutorial 06a_kmeans
+-   Tutorial 06a_kmeans
 
 ## Changes in version 2019.10.0
 
-- Tutorial 05a_distance_matrix
+-   Tutorial 05a_distance_matrix
 
 ## Changes in version 2019.9.0
 
-- New Shiny app 04e_gompertz
+-   New Shiny app 04e_gompertz
 
 ## Changes in version 2019.8.0
 
-- Shiny app 04c 04d
+-   Shiny app 04c 04d
 
 ## Changes in version 2019.7.0
 
-- Shiny app 04a_michaelis_menten and 04b_exponent
+-   Shiny app 04a_michaelis_menten and 04b_exponent
 
 ## Changes in version 2019.6.0
 
-- Tutorial 03a_mod_lin finalized
+-   Tutorial 03a_mod_lin finalized
 
 ## Changes in version 2019.5.0
 
-- Tutorial 02a_reg_multi finalized
+-   Tutorial 02a_reg_multi finalized
 
 ## Changes in version 2019.4.0
 
-- Tutorial 02b_reg_poly finalized
+-   Tutorial 02b_reg_poly finalized
 
 ## Changes in version 2019.3.0
 
-- Tutorial 01b_reg_lin : minor correction
+-   Tutorial 01b_reg_lin : minor correction
 
 ## Changes in version 2019.2.0
 
-- Tutorial 01b_reg_lin finalized
+-   Tutorial 01b_reg_lin finalized
 
 ## Changes in version 2019.1.0
 
-- Tutorial 01a_rappel finalized
-
+-   Tutorial 01a_rappel finalized

R/BioDataScience2-package.R

@@ -5,7 +5,7 @@
 #' @docType package
 #' @name BioDataScience2-package
 #'
-#' @importFrom learndown run learndownLearnrBanner learndownLearnrServer
+#' @importFrom learnitdown run learnitdownLearnrBanner learnitdownLearnrServer
 #' @importFrom BioDataScience config sign_in sign_out
 #' @importFrom shiny dialogViewer observeEvent selectInput stopApp runGadget
 #' @importFrom miniUI gadgetTitleBar miniContentPanel miniPage miniTitleBarButton miniTitleBarCancelButton

R/addins.R

@@ -47,7 +47,7 @@ run_addin <- function() {
   }
 
   # Update both BioDataScience & BioDataScience2
-  learndown::update_pkg("BioDataScience",
+  learnitdown::update_pkg("BioDataScience",
     github_repos = "BioDataScience-course/BioDataScience")
   update_pkg()
 

R/learnr.R

@@ -1,15 +1,15 @@
-#' Prepare a learnr tutorial for learndown recording
+#' Prepare a learnr tutorial for learnitdown recording
 #'
-#' These functions add recording functionalities through the learndown approach.
+#' These functions add recording features through the learnitdown approach.
 
 #' @param cap The caption of learnr R code widgets.
 #' @param debug Do we issue debugging messages (by default, yes if the
-#' environment variables `LEARNDOWN_DEBUG` is not `0`).
+#' environment variables `LEARNITDOWN_DEBUG` is not `0`).
 #'
 #' @export
 learnr_setup <- function(cap = "Code R",
-  debug = Sys.getenv("LEARNDOWN_DEBUG", 0) != 0) {
-  learndown::learndownLearnrSetup(config = BioDataScience::config(),
+  debug = Sys.getenv("LEARNITDOWN_DEBUG", 0) != 0) {
+  learnitdown::learnitdownLearnrSetup(config = BioDataScience::config(),
     sign_in = BioDataScience::sign_in(), cap = cap, debug = debug)
   # Eliminate praise sentence in English before results
   options(
@@ -25,11 +25,11 @@ learnr_setup <- function(cap = "Code R",
 #' @param simple Do we use a simple banner without title or not?
 learnr_banner <- function(simple = FALSE) {
   if (isTRUE(simple)) {
-    learndownLearnrBanner(
+    learnitdownLearnrBanner(
       msg.nologin = 'Utilisateur anonyme, aucun enregistrement !',
       msg.login = 'Enregistrement actif pour ')
   } else {
-    learndownLearnrBanner(
+    learnitdownLearnrBanner(
       title = "Science des donn\u00e9es biologiques\ II",
       text = "R\u00e9alis\u00e9 par le service d'\u00c9cologie num\u00e9rique, Universit\u00e9 de Mons (Belgique)",
       image = "https://wp.sciviews.org/BioDataScience-96.png",
@@ -45,4 +45,4 @@ learnr_banner <- function(simple = FALSE) {
 #' @param output The Shiny output.
 #' @param session The Shiny session.
 learnr_server <- function(input, output, session)
-  learndownLearnrServer(input, output, session)
+  learnitdownLearnrServer(input, output, session)

R/run.R

@@ -34,7 +34,7 @@
 run <- function(tutorial, ..., update = ask, ask = interactive()) {
   if (missing(tutorial))
     tutorial <- NULL
-  learndown::run(tutorial = tutorial, package = "BioDataScience2",
+  learnitdown::run(tutorial = tutorial, package = "BioDataScience2",
     github_repos = "BioDataScience-course/BioDataScience2",
     ..., update = update, ask = ask)
 }
@@ -45,13 +45,13 @@ run_app <- function(app, ..., update = ask, ask = interactive(),
   in.job = TRUE) {
   if (missing(app))
     app <- NULL
-  learndown::run_app(app = app, package = "BioDataScience2",
+  learnitdown::run_app(app = app, package = "BioDataScience2",
     github_repos = "BioDataScience-course/BioDataScience2",
     ..., update = update, ask = ask, in.job = in.job)
 }
 
 #' @rdname run
 #' @export
 update_pkg <- function()
-  learndown::update_pkg(package = "BioDataScience2",
+  learnitdown::update_pkg(package = "BioDataScience2",
     github_repos = "BioDataScience-course/BioDataScience2")

devel/shiny/B05Sa_cluster/app.R

@@ -1,9 +1,9 @@
-learndown::learndownShinyVersion("0.1.0")
+learnitdown::learnitdownShinyVersion("0.1.0")
 conf <- BioDataScience::config()
 
 library(shiny)
 library(shinyjs)
-library(learndown)
+library(learnitdown)
 library(BioDataScience2)
 library(dplyr)
 library(tidyr)
@@ -396,7 +396,7 @@ score_cah <- function(x, reference = peng_m$species) {
 
 ui <- fluidPage(
   useShinyjs(),
-  learndownShiny("Classification hiérarchique ascendante sur des mesures de manchots d'antarctique."),
+  learnitdownShiny("Classification hiérarchique ascendante sur des mesures de manchots d'antarctique."),
 
   sidebarLayout(
     sidebarPanel(

inst/shiny/B01Sa_reglin/app.R

@@ -1,8 +1,8 @@
-learndown::learndownShinyVersion("1.0.0")
+learnitdown::learnitdownShinyVersion("1.0.0")
 conf <- BioDataScience::config()
 
 library(shiny)
-library(learndown)
+library(learnitdown)
 library(BioDataScience2)
 
 a_init <- -1.5
@@ -19,7 +19,7 @@ model_data <- tibble::tibble(
     rnorm(n = length(x), sd = error_sd))
 
 ui <- fluidPage(
-  learndownShiny("Ajustement manuel d'un modèle : régression linéaire"),
+  learnitdownShiny("Ajustement manuel d'un modèle : régression linéaire"),
 
   sidebarLayout(
     sidebarPanel(

inst/shiny/B04Sa_micmen/app.R

@@ -1,8 +1,8 @@
-learndown::learndownShinyVersion("1.1.0")
+learnitdown::learnitdownShinyVersion("1.1.0")
 conf <- BioDataScience::config()
 
 library(shiny)
-library(learndown)
+library(learnitdown)
 library(BioDataScience2)
 
 vm_init <- 6
@@ -21,7 +21,7 @@ graph <- chart::chart(model_data, y ~ x) +
   ggplot2::ylab("y")
 
 ui <- fluidPage(
-  learndownShiny("Ajustement manuel d'un modèle : Michaelis-Menten"),
+  learnitdownShiny("Ajustement manuel d'un modèle : Michaelis-Menten"),
 
   sidebarLayout(
     sidebarPanel(