Merge pull request #373 from tlverse/devel

Author: nhejazi

.Rbuildignore

@@ -6,6 +6,7 @@
 ^README\.md
 
 # Automated testing files.
+^\.github$
 ^\.travis\.yml$
 ^appveyor\.yml$
 ^codecov\.yml$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/R-CMD-check.yml

@@ -0,0 +1,68 @@
+on:
+  push:
+    branches:
+      - master
+      - devel
+  pull_request:
+    branches:
+      - master
+      - devel
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: ubuntu-latest, r: 'release'}
+          - {os: macOS-latest, r: 'release'}
+          - {os: windows-latest, r: 'release'}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - name: Install pandoc
+        uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Install tinyTeX
+        uses: r-lib/actions/setup-tinytex@v1
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt install -y curl libcurl4-doc libcurl4-openssl-dev
+          sudo $(which R) CMD javareconf
+
+      - name: Install package dependencies
+        run: |
+          install.packages(c("remotes", "rcmdcheck", "covr", "sessioninfo"))
+          if(Sys.info()["sysname"] == "Windows") install.packages("igraph", type = "binary")
+          remotes::install_deps(dependencies = TRUE)
+        shell: Rscript {0}
+
+      - name: Check package
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
+        shell: Rscript {0}
+
+      - name: Upload code coverage
+        if: runner.os == 'Linux'
+        run: |
+          covr::codecov()
+        shell: Rscript {0}

.travis.yml

@@ -1,6 +1,6 @@
 Package: sl3
 Title: Pipelines for Machine Learning and Super Learning
-Version: 1.4.2
+Version: 1.4.4
 Authors@R: c(
     person("Jeremy", "Coyle", email = "[email protected]",
            role = c("aut", "cre", "cph"),
@@ -43,9 +43,11 @@ Imports:
     methods,
     ggplot2,
     digest,
+    Rdpack,
     imputeMissings,
     dplyr,
-    caret
+    caret,
+    ROCR
 Suggests:
     testthat,
     rmarkdown,
@@ -57,6 +59,7 @@ Suggests:
     reticulate,
     rgl,
     rJava,
+    arm,
     bartMachine,
     cvAUC,
     e1071,
@@ -66,7 +69,7 @@ Suggests:
     glmnet,
     grf,
     gbm,
-    hal9001 (>= 0.2.5),
+    hal9001 (>= 0.4.0),
     h2o,
     keras,
     kerasR,
@@ -81,12 +84,19 @@ Suggests:
     SuperLearner,
     tsDyn,
     xgboost,
+    lightgbm,
     dbarts,
     gam (>= 1.15.0),
-    haldensify,
+    haldensify (>= 0.1.5),
     mgcv,
-    hts
+    hts,
+    GA
+Remotes:
+    github::tlverse/origami,
+    github::tlverse/hal9001@devel,
+    github::nhejazi/haldensify
 License: GPL-3
+Language: en-US
 URL: https://tlverse.org/sl3
 BugReports: https://github.com/tlverse/sl3/issues
 Encoding: UTF-8
@@ -95,5 +105,6 @@ LazyLoad: yes
 VignetteBuilder:
     knitr,
     R.rsp
-RoxygenNote: 7.1.1.9000
 Roxygen: list(markdown = TRUE, old_usage = TRUE, r6 = FALSE)
+RoxygenNote: 7.1.2
+RdMacros: Rdpack

DESCRIPTION

@@ -2,6 +2,7 @@ md:
 	Rscript -e "rmarkdown::render('README.Rmd', output_file = 'README.md')"
 
 site:
+	Rscript -e "rmarkdown::render('README.Rmd', output_file = 'README.md')"
 	Rscript -e "pkgdown::build_site()"
 
 check:
@@ -31,5 +32,5 @@ coverage:
 style:
 	Rscript -e "styler::style_pkg()"
 
-pr: style check md site
+pr: style check site
 	echo "If all checks have passed, you are ready to submit PR"

Makefile

@@ -7,6 +7,7 @@ export(Lrnr_HarmonicReg)
 export(Lrnr_arima)
 export(Lrnr_bartMachine)
 export(Lrnr_base)
+export(Lrnr_bayesglm)
 export(Lrnr_bilstm)
 export(Lrnr_bound)
 export(Lrnr_caret)
@@ -19,6 +20,7 @@ export(Lrnr_density_hse)
 export(Lrnr_density_semiparametric)
 export(Lrnr_earth)
 export(Lrnr_expSmooth)
+export(Lrnr_ga)
 export(Lrnr_gam)
 export(Lrnr_gbm)
 export(Lrnr_glm)
@@ -35,7 +37,7 @@ export(Lrnr_hal9001)
 export(Lrnr_haldensify)
 export(Lrnr_hts)
 export(Lrnr_independent_binomial)
-export(Lrnr_lstm)
+export(Lrnr_lightgbm)
 export(Lrnr_lstm_keras)
 export(Lrnr_mean)
 export(Lrnr_multiple_ts)
@@ -72,6 +74,7 @@ export(Shared_Data)
 export(Stack)
 export(Variable_Type)
 export(args_to_list)
+export(custom_ROCR_risk)
 export(customize_chain)
 export(debug_predict)
 export(debug_train)
@@ -80,6 +83,7 @@ export(debugonce_train)
 export(define_h2o_X)
 export(delayed_learner_fit_chain)
 export(delayed_learner_fit_predict)
+export(delayed_learner_process_formula)
 export(delayed_learner_subset_covariates)
 export(delayed_learner_train)
 export(delayed_make_learner)
@@ -90,6 +94,7 @@ export(importance_plot)
 export(inverse_sample)
 export(learner_fit_chain)
 export(learner_fit_predict)
+export(learner_process_formula)
 export(learner_subset_covariates)
 export(learner_train)
 export(loss_loglik_binomial)
@@ -129,6 +134,9 @@ import(delayed)
 import(ggplot2)
 importFrom(BBmisc,requirePackages)
 importFrom(R6,R6Class)
+importFrom(ROCR,performance)
+importFrom(ROCR,prediction)
+importFrom(Rdpack,reprompt)
 importFrom(assertthat,assert_that)
 importFrom(assertthat,is.count)
 importFrom(assertthat,is.flag)
@@ -144,14 +152,19 @@ importFrom(dplyr,"%>%")
 importFrom(dplyr,group_by)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise_all)
+importFrom(ggplot2,coord_flip)
 importFrom(ggplot2,cut_interval)
 importFrom(ggplot2,cut_number)
-importFrom(graphics,dotchart)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,scale_x_discrete)
 importFrom(imputeMissings,impute)
 importFrom(methods,is)
 importFrom(origami,combiner_c)
 importFrom(origami,cross_validate)
 importFrom(origami,fold_index)
+importFrom(origami,folds2foldvec)
 importFrom(origami,id_folds_to_folds)
 importFrom(origami,make_folds)
 importFrom(origami,training)
@@ -166,6 +179,7 @@ importFrom(stats,median)
 importFrom(stats,plogis)
 importFrom(stats,predict)
 importFrom(stats,qlogis)
+importFrom(stats,quasibinomial)
 importFrom(stats,runif)
 importFrom(stats,sd)
 importFrom(stats,weighted.mean)