diff --git a/DESCRIPTION b/DESCRIPTION index 064ec65..2dd6cc8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: easyalluvial Title: Generate Alluvial Plots with a Single Line of Code -Version: 0.3.1.900 +Version: 0.3.2 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 diff --git a/NEWS.md b/NEWS.md index 74c2b8a..b801fe7 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# Version 0.3.2 submitted to CRAN 20231207 +- check for vip pkg installation before executing example of alluvial_model_response_parsnip +- option for using geom_text instead of geom_label (by https://github.com/gernophil) + # Version 0.3.1 submitted to CRAN 20220704 - cleanup package dependencies diff --git a/R/alluvial_model_response.R b/R/alluvial_model_response.R index d9f24be..d75396b 100644 --- a/R/alluvial_model_response.R +++ b/R/alluvial_model_response.R @@ -236,8 +236,8 @@ tidy_imp = function(imp, df, .f = max, resp_var = NULL){ #' \code{\link[easyalluvial]{manip_bin_numerics}}, while leaving categoric #' variables unchanged. The number of bins for each numeric variable is set to #' bins -2. Next the median is picked for each of the bins and the min and the -#' max value is added for each numeric variable So that we get { median(bin) X -#' bins -2, max, min} for each numeric variable. Then all possible combinations +#' max value is added for each numeric variable So that we get (median(bin) X +#' bins -2, max, min) for each numeric variable. Then all possible combinations #' between those values and the categoric factor levels are created. The total #' number of all possible combinations defines the range of the data space. The #' values of the remaining variables are set to mode(factors) or diff --git a/R/alluvial_wide.R b/R/alluvial_wide.R index d2b0c08..6c60131 100644 --- a/R/alluvial_wide.R +++ b/R/alluvial_wide.R @@ -395,7 +395,7 @@ alluvial_wide = function( data data_key = data_new %>% mutate( alluvial_id = manip_factor_2_numeric(alluvial_id) ) %>% - left_join( data_alluvial ) %>% + left_join( data_alluvial, relationship = "many-to-many" ) %>% select( - fill_flow, -fill_value, -fill ) %>% spread( key = x, value = value ) %>% select( one_of(id_str, variables, 'alluvial_id', 'n' ) ) %>% diff --git a/README.Rmd b/README.Rmd index 886bfe9..3b44fd4 100644 --- a/README.Rmd +++ b/README.Rmd @@ -17,7 +17,6 @@ knitr::opts_chunk$set( # easyalluvial -[![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/erblast/easyalluvial?branch=master&svg=true)](https://ci.appveyor.com/project/erblast/easyalluvial) [![R build status](https://github.com/erblast/easyalluvial/workflows/R-CMD-check/badge.svg)](https://github.com/erblast/easyalluvial/actions) [![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) diff --git a/README.md b/README.md index 7630333..c360919 100644 --- a/README.md +++ b/README.md @@ -3,8 +3,6 @@ # easyalluvial -[![AppVeyor Build -Status](https://ci.appveyor.com/api/projects/status/github/erblast/easyalluvial?branch=master&svg=true)](https://ci.appveyor.com/project/erblast/easyalluvial) [![R build status](https://github.com/erblast/easyalluvial/workflows/R-CMD-check/badge.svg)](https://github.com/erblast/easyalluvial/actions) [![Coverage @@ -37,17 +35,17 @@ for data exploration. ## Features -- plot alluvial graph with a single line of code of a given dataframe -- support for wide and long data format [(wiki, wide vs. long/narrow - data)](https://en.wikipedia.org/wiki/Wide_and_narrow_data) -- automatically transforms numerical to categorical data -- helper functions for variable selection -- convenient parameters for coloring and ordering -- marginal histograms -- **model agnostic partial dependence and model response alluvial - plots with 4 dimensions** -- **[interactive plots with `easyalluvial` and - `parcats`](https://erblast.github.io/parcats/articles/parcats.html)** +- plot alluvial graph with a single line of code of a given dataframe +- support for wide and long data format [(wiki, wide vs. long/narrow + data)](https://en.wikipedia.org/wiki/Wide_and_narrow_data) +- automatically transforms numerical to categorical data +- helper functions for variable selection +- convenient parameters for coloring and ordering +- marginal histograms +- **model agnostic partial dependence and model response alluvial plots + with 4 dimensions** +- **[interactive plots with `easyalluvial` and + `parcats`](https://erblast.github.io/parcats/articles/parcats.html)** ## Installation @@ -60,19 +58,20 @@ install.packages('easyalluvial') ### Development Version ``` r + # install.packages("devtools") devtools::install_github("erblast/easyalluvial") ``` ## Documentation -- [pkgdown website](https://erblast.github.io/easyalluvial/) - - [Data Exploration with Alluvial - Plots](https://erblast.github.io/easyalluvial/articles/data_exploration.html) - - [Visualising Model - Response](https://erblast.github.io/easyalluvial/articles/model_response.html) - - [Interactive Plots with - parcats](https://erblast.github.io/easyalluvial/articles/parcats.html) +- [pkgdown website](https://erblast.github.io/easyalluvial/) + - [Data Exploration with Alluvial + Plots](https://erblast.github.io/easyalluvial/articles/data_exploration.html) + - [Visualising Model + Response](https://erblast.github.io/easyalluvial/articles/model_response.html) + - [Interactive Plots with + parcats](https://erblast.github.io/easyalluvial/articles/parcats.html) ## Examples @@ -86,6 +85,7 @@ suppressPackageStartupMessages( require(easyalluvial) ) #### Sample Data ``` r + knitr::kable( head(mtcars2) ) ``` @@ -102,13 +102,14 @@ knitr::kable( head(mtcars2) ) Continuous Variables will be automatically binned as follows. -- High, High (HH) -- Medium, High (MH) -- Medium (M) -- Medium, Low (ML) -- Low, Low (LL) +- High, High (HH) +- Medium, High (MH) +- Medium (M) +- Medium, Low (ML) +- Low, Low (LL) ``` r + alluvial_wide( data = mtcars2 , max_variables = 5 , fill_by = 'first_variable' ) @@ -124,18 +125,19 @@ alluvial_wide( data = mtcars2 knitr::kable( head(quarterly_flights) ) ``` -| tailnum | carrier | origin | dest | qu | mean\_arr\_delay | -|:------------------|:--------|:-------|:-----|:----|:-----------------| -| N0EGMQ LGA BNA MQ | MQ | LGA | BNA | Q1 | on\_time | -| N0EGMQ LGA BNA MQ | MQ | LGA | BNA | Q2 | on\_time | -| N0EGMQ LGA BNA MQ | MQ | LGA | BNA | Q3 | on\_time | -| N0EGMQ LGA BNA MQ | MQ | LGA | BNA | Q4 | on\_time | -| N11150 EWR MCI EV | EV | EWR | MCI | Q1 | late | -| N11150 EWR MCI EV | EV | EWR | MCI | Q2 | late | +| tailnum | carrier | origin | dest | qu | mean_arr_delay | +|:------------------|:--------|:-------|:-----|:----|:---------------| +| N0EGMQ LGA BNA MQ | MQ | LGA | BNA | Q1 | on_time | +| N0EGMQ LGA BNA MQ | MQ | LGA | BNA | Q2 | on_time | +| N0EGMQ LGA BNA MQ | MQ | LGA | BNA | Q3 | on_time | +| N0EGMQ LGA BNA MQ | MQ | LGA | BNA | Q4 | on_time | +| N11150 EWR MCI EV | EV | EWR | MCI | Q1 | late | +| N11150 EWR MCI EV | EV | EWR | MCI | Q2 | late | #### Plot ``` r + alluvial_long( quarterly_flights , key = qu , value = mean_arr_delay @@ -159,6 +161,7 @@ alluvial_wide( data = mtcars2 ### Interactive Graphs ``` r + suppressPackageStartupMessages( require(parcats) ) p = alluvial_wide(mtcars2, max_variables = 5) @@ -166,10 +169,15 @@ p = alluvial_wide(mtcars2, max_variables = 5) parcats(p, marginal_histograms = TRUE, data_input = mtcars2) ``` -![demo](https://raw.githubusercontent.com/erblast/parcats/master/man/figures/demo1.gif) +
+ + +
-- **[Live - Widget](https://erblast.github.io/parcats/articles/parcats.html)** +- **[Live + Widget](https://erblast.github.io/parcats/articles/parcats.html)** ### Partial Dependence Alluvial Plots @@ -190,14 +198,15 @@ in the end. Each of the possible combinations is plotted as a flow which is coloured by the bin corresponding to the average model response generated by that particular combination. -- [more on partial dependence plots - (ebook)](https://christophm.github.io/interpretable-ml-book/) -- [Tutorial](https://www.datisticsblog.com/2019/04/visualising-model-response-with-easyalluvial/) +- [more on partial dependence plots + (ebook)](https://christophm.github.io/interpretable-ml-book/) +- [Tutorial](https://www.datisticsblog.com/2019/04/visualising-model-response-with-easyalluvial/) `easyalluvial` contains wrappers for `parsnip` and `caret` models. Custom Wrappers for other models can easily be created. ``` r + df = select(mtcars2, -ids) m = parsnip::rand_forest(mode = "regression") %>% @@ -216,11 +225,12 @@ p_grid = add_marginal_histograms(p, df, plot = F) %>% ### Interactive Partial Dependence Plot ``` r + parcats(p, marginal_histograms = TRUE, imp = TRUE, data_input = df) ``` -![demo](https://raw.githubusercontent.com/erblast/parcats/master/man/figures/demo2.gif) -- **[Live +![demo](https://raw.githubusercontent.com/erblast/parcats/master/man/figures/demo2.gif) - +**[Live Widget](https://erblast.github.io/parcats/articles/parcats.html)** # ClinicoPath {jamovi} Module @@ -232,7 +242,7 @@ interface for doing statistics with `R`. # Similar Packages -- [`ggalluvial`](https://github.com/corybrunson/ggalluvial/) -- [`alluvial`](https://github.com/mbojan/alluvial) -- [`networkD3`](https://github.com/christophergandrud/networkD3) -- [`ggbump`](https://github.com/davidsjoberg/ggbump) +- [`ggalluvial`](https://github.com/corybrunson/ggalluvial/) +- [`alluvial`](https://github.com/mbojan/alluvial) +- [`networkD3`](https://github.com/christophergandrud/networkD3) +- [`ggbump`](https://github.com/davidsjoberg/ggbump) diff --git a/appveyor.yml b/appveyor.yml deleted file mode 100644 index c6c1438..0000000 --- a/appveyor.yml +++ /dev/null @@ -1,45 +0,0 @@ -# DO NOT CHANGE the "init" and "install" sections below - -# Download script file from GitHub -init: - ps: | - $ErrorActionPreference = "Stop" - Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1" - Import-Module '..\appveyor-tool.ps1' - -install: - ps: Bootstrap - -cache: - - C:\RLibrary - -# Adapt as necessary starting from here - -build_script: - - travis-tool.sh install_deps - -test_script: - - travis-tool.sh run_tests - -on_failure: - - 7z a failure.zip *.Rcheck\* - - appveyor PushArtifact failure.zip - -artifacts: - - path: '*.Rcheck\**\*.log' - name: Logs - - - path: '*.Rcheck\**\*.out' - name: Logs - - - path: '*.Rcheck\**\*.fail' - name: Logs - - - path: '*.Rcheck\**\*.Rout' - name: Logs - - - path: '\*_*.tar.gz' - name: Bits - - - path: '\*_*.zip' - name: Bits diff --git a/cran-comments.md b/cran-comments.md index 17d0f5b..c13916a 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,12 +1,19 @@ # Resubmission after being archived on CRAN -clean up package dependencies +All suggested dependencies were already controlled for, meaning there was a +check in place that would raise an error with a message to install the missing +package. Those are limited to functions most users will not use. + +All unit tests would skip if suggested packages were missing. + +One example missed a check for a suggested package installation which was added: + +- check for vip pkg installation before executing example of alluvial_model_response_parsnip ## Test Environments -* local macOS M1 R 4.2.1 -* Appveyor x86_64-w64-mingw32/x64 (64-bit) R 4.2.1 -* github actions macos-latest R 4.2.1 -* WinBuilder R 4.2.1 +* local macOS M1 R 4.3.2 +* github actions macos-latest R 4.3.2 +* WinBuilder R 4.3.2 * WinBuilder R devel coverage -> 96 % diff --git a/man/figures/README-plot_long-1.png b/man/figures/README-plot_long-1.png index 5983a51..c343c89 100644 Binary files a/man/figures/README-plot_long-1.png and b/man/figures/README-plot_long-1.png differ diff --git a/man/figures/README-unnamed-chunk-3-1.png b/man/figures/README-unnamed-chunk-3-1.png index 041c35f..c81f208 100644 Binary files a/man/figures/README-unnamed-chunk-3-1.png and b/man/figures/README-unnamed-chunk-3-1.png differ diff --git a/man/figures/README-unnamed-chunk-5-1.png b/man/figures/README-unnamed-chunk-5-1.png index e9bea3f..6cc3ba0 100644 Binary files a/man/figures/README-unnamed-chunk-5-1.png and b/man/figures/README-unnamed-chunk-5-1.png differ diff --git a/man/figures/README-wide_plot-1.png b/man/figures/README-wide_plot-1.png index 2b60bf4..c69e2a3 100644 Binary files a/man/figures/README-wide_plot-1.png and b/man/figures/README-wide_plot-1.png differ diff --git a/man/get_data_space.Rd b/man/get_data_space.Rd index 6d132ce..54108b5 100644 --- a/man/get_data_space.Rd +++ b/man/get_data_space.Rd @@ -41,8 +41,8 @@ It selects a the top most important variables based on the degree \code{\link[easyalluvial]{manip_bin_numerics}}, while leaving categoric variables unchanged. 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