Merge pull request #18 from erblast/devel

Devel

.Rbuildignore

@@ -10,3 +10,10 @@
 ^README\.Rmd$
 ^README-.*\.png$
 ^cran-comments\.md$
+^docker-compose\.yml$
+^docker$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^vignettes$
+^tests/figs/$

.gitignore

@@ -4,3 +4,8 @@
 .Ruserdata
 dependencies/
 revdep/
+docs/
+*.rdx
+*.RData
+*.rdb
+vignettes/model_response_cache/

.travis.yml

@@ -2,7 +2,7 @@
 
 language: R
 R:
-  - 3.5.3
+  - 3.6.3
 sudo: false
 cache: packages
 
@@ -16,6 +16,17 @@ matrix:
   - r: release
     after_success:
     - Rscript -e 'covr::codecov()'
+    - Rscript -e 'pkgdown::build_site(run_dont_run = TRUE)'
   - r: release
     name: tidyr-devel
     before_script: Rscript -e "remotes::install_github('tidyverse/tidyr')"
+  - r: release
+    name: dplyr-devel
+    before_script: Rscript -e "remotes::install_github('tidyverse/dplyr')"
+
+deploy:
+  provider: pages
+  skip_cleanup: true
+  github_token: $GITHUB_TOKEN  # Set in the settings page of your repository, as a secure variable
+  keep_history: true
+  local-dir: docs

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: easyalluvial
 Title: Generate Alluvial Plots with a Single Line of Code
-Version: 0.2.2.900
+Version: 0.2.3
 Authors@R: person( "Bjoern", "Koneswarakantha", role = c("aut","cre"), email = "datistics@gmail.com", comment = c(ORCID = "0000-0003-4585-7799") )
 URL: https://github.com/erblast/easyalluvial
 Description: Alluvial plots are similar to sankey diagrams and visualise categorical data 
@@ -25,8 +25,9 @@ Suggests:
     covr,
     ISLR,
     nycflights13,
-    vdiffr (>= 0.3.1)
-RoxygenNote: 7.0.0
+    vdiffr (>= 0.3.1),
+    parcats
+RoxygenNote: 7.1.0
 Imports:
   purrr
   , tidyr (>= 1.0.0)

R/alluvial_model_response.R

@@ -772,6 +772,7 @@ alluvial_model_response_caret = function(train, degree = 4, bins = 5
 #' @return OUTPUT_DESCRIPTION
 #' @seealso \code{\link[e1071]{skewness}}
 #' @rdname use_e1071
+#' @noRd
 #' @importFrom e1071 skewness
 use_e1071 = function(x){
   e1071::skewness(x)

R/manip.R

@@ -202,6 +202,7 @@ manip_bin_numerics = function(x
 
     join_by = names(df_min)[! names(df_min) %in% numerics ]
     join_by = c(join_by, 'easyalluvialid')
+    join_by = unique(join_by)
 
     data_new = df_min %>%
       left_join(df_max, by = join_by )

R/plot_marginal_hist.R

@@ -246,7 +246,6 @@ plot_hist_model_response = function(var, p, data_input, pred_train = NULL, scale
   }
 
   if( ! is_num & is_pred){
-
     var_str = ori_name
 
     df_input = data_input %>%
@@ -259,13 +258,19 @@ plot_hist_model_response = function(var, p, data_input, pred_train = NULL, scale
       select( x, value ) %>%
       rename( variable = x) %>%
       mutate( variable = as.character(variable)
-              , value = fct_drop(value) )
+              , value = fct_drop(value)
+              # p$data does not preserve factor order
+              , value = fct_relevel(value, levels(df_input$value) ) )
+
+    stopifnot(all(levels(df_input$value) == levels(df_resp$value)))
 
+    if(is.ordered(df_input$value)){
+      df_resp$value = as.ordered(df_resp$value)
+    }
+
     df_plot = df_input %>%
       bind_rows(df_resp)
-
-    # df_plot = df_input
-
+
     if( ! is_null(pred_train) ){
       df_plot = df_plot %>%
         bind_rows( tibble(variable = 'pred_train'

README.md

@@ -10,6 +10,7 @@ Status](https://ci.appveyor.com/api/projects/status/github/erblast/easyalluvial?
 
 [![Coverage Status](https://img.shields.io/codecov/c/github/erblast/easyalluvial/master.svg)](https://codecov.io/github/erblast/easyalluvial?branch=master)
 [![CRAN last release](https://www.r-pkg.org/badges/last-release/easyalluvial)](https://CRAN.R-project.org/package=easyalluvial)
+[![CRAN monthly downloads](https://cranlogs.r-pkg.org/badges/easyalluvial)](https://cran.r-project.org/package=easyalluvial)
 [![CRAN total downloads](https://cranlogs.r-pkg.org/badges/grand-total/easyalluvial)](https://CRAN.R-project.org/package=easyalluvial)
 
 

_pkgdown.yml

@@ -0,0 +1,55 @@
+navbar:
+  structure:
+    left:
+    - home
+    - reference
+    - articles
+    - news
+    right: github
+  components:
+    home:
+      icon: fas fa-home fa-lg
+      href: index.html
+    reference:
+      text: Reference
+      href: reference/index.html
+    news:
+      text: Changelog
+      href: news/index.html
+template:
+  params:
+    ganalytics: UA-123997499-2
+url: https://erblast.github.io/easyalluvial/
+reference:
+- title: Main Plot Functions
+  desc: ~
+  contents:
+  - starts_with("alluvial")
+- title: Add Plot Elements
+  desc: ~
+  contents:
+  - starts_with("add_")
+- title: Generate Data for Model Response and Partial Dependence Plots
+  desc: ~
+  contents:
+  - starts_with("get_")
+- title: Helper Functions - Data Manipulation
+  desc: ~
+  contents:
+  - starts_with("manip_")
+  - tidy_imp
+- title: Helper Functions - Plotting
+  desc: ~
+  contents:
+  - starts_with("plot_")
+- title: Helper Functions - Color Palette
+  desc: ~
+  contents:
+  - starts_with("palette_")
+- title: Data Sets
+  desc: ~
+  contents:
+  - mtcars2
+  - titanic
+  - quarterly_flights
+  - quarterly_sunspots

docker-compose.yml

@@ -0,0 +1,47 @@
+
+version: '3.7'
+services:
+  build_latest:
+    build:
+      context: .
+      dockerfile: docker/latest.dockerfile
+    image: 'easyalluvial_latest'
+
+  build_devel:
+    build:
+      context: .
+      dockerfile: docker/devel.dockerfile
+    image: 'easyalluvial_devel'
+
+  rstudio_latest:
+    image: 'easyalluvial_latest'
+    ports: 
+      - '8787:8787'
+    volumes:
+      - '.:/home/rstudio/easyalluvial'
+    command: /init
+    environment:
+      PASSWORD: '123'
+      USER: 'rstudio'
+
+  rstudio_devel:
+    image: 'easyalluvial_devel'
+    ports: 
+      - '8888:8787'
+    volumes:
+      - '.:/home/rstudio/easyalluvial'
+    command: /init
+    environment:
+      PASSWORD: '123'
+      USER: 'rstudio'
+
+  check_devel:
+    image: 'easyalluvial_devel'
+    volumes:
+      - '.:/home/rstudio/easyalluvial'
+
+  check_latest:
+    image: 'easyalluvial_latest'
+    volumes:
+      - '.:/home/rstudio/easyalluvial'
+

docker/devel.dockerfile

@@ -0,0 +1,11 @@
+FROM rocker/verse:devel
+COPY * /home/rstudio/easyalluvial/
+WORKDIR '/home/rstudio/easyalluvial/'
+RUN R -e "devtools::install_dev_deps('.', upgrade = 'never')"
+RUN git clone https://github.com/erblast/parcats.git /home/rstudio/parcats
+RUN git clone https://github.com/tidyverse/tidyr.git /home/rstudio/tidyr
+RUN git clone https://github.com/tidyverse/dplyr.git /home/rstudio/dplyr
+RUN R -e "devtools::install('/home/rstudio/tidyr')"
+RUN R -e "devtools::install('/home/rstudio/dplyr')"
+RUN R -e "devtools::install('/home/rstudio/parcats')"
+CMD R -e "devtools::check('.')" -e "devtools::install('.')" -e "devtools::check('/home/rstudio/parcats')"

docker/latest.dockerfile

@@ -0,0 +1,7 @@
+FROM rocker/verse:latest
+COPY * /home/rstudio/easyalluvial/
+WORKDIR '/home/rstudio/easyalluvial/'
+RUN R -e "devtools::install_dev_deps('.', upgrade = 'never')"
+RUN R -e "remotes::install_cran('parcats', upgrade= 'never')"
+RUN git clone https://github.com/erblast/parcats.git /home/rstudio/parcats
+CMD R -e "devtools::check('.')" -e "devtools::install('.')" -e "devtools::check('/home/rstudio/parcats')"