Merge branch 'master' into EmilHvitfeldt-survnip-integration

Author: topepo

.github/workflows/check-pak.yaml

@@ -0,0 +1,114 @@
+# NOTE: This workflow is overkill for most R packages
+# check-standard.yaml is likely a better choice
+# usethis::use_github_action("check-standard") will install it.
+#
+# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
+# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
+
+name: R-CMD-check-pak
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: windows-latest, r: '3.6'}
+          - {os: ubuntu-16.04,   r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest", http-user-agent: "R/4.0.0 (ubuntu-16.04) R (4.0.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+          - {os: ubuntu-16.04,   r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: 'oldrel',  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: '3.5',     rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        id: install-r
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Install pak and query dependencies
+        run: |
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/dev/")
+          saveRDS(pak::pkg_deps_tree("local::.", dependencies = TRUE), ".github/r-depends.rds")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-${{ hashFiles('.github/r-depends.rds') }}
+          restore-keys: ${{ runner.os }}-${{ steps.install-r.outputs.installed-r-version }}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: Rscript -e 'pak::local_system_requirements(execute = TRUE)'
+
+      - name: Install dependencies
+        run: |
+          pak::local_install_dev_deps(upgrade = TRUE)
+          pak::pkg_install("rcmdcheck")
+        shell: Rscript {0}
+
+      - name: Install Miniconda
+        run: |
+          Rscript -e "pak::pkg_install('rstudio/reticulate')"
+          Rscript -e "reticulate::install_miniconda()"
+
+      - name: Find Miniconda on macOS
+        if: runner.os == 'macOS'
+        run: echo "options(reticulate.conda_binary = reticulate:::miniconda_conda())" >> .Rprofile
+
+      - name: Install TensorFlow
+        run: |
+          reticulate::conda_create('r-reticulate', packages = c('python==3.6.9'))
+          tensorflow::install_tensorflow(version='1.14.0')
+        shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check

.github/workflows/pkgdown.yaml

@@ -1,6 +1,12 @@
 on:
   push:
-    branches: master
+    branches:
+      - master
+      - main
+  pull_request:
+    branches:
+      - master
+      - main
 
 name: pkgdown
 
@@ -12,9 +18,12 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v1
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: System dependencies
+        run: brew install harfbuzz fribidi
 
       - name: Query dependencies
         run: |
@@ -24,7 +33,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Cache R packages
-        uses: actions/cache@v1
+        uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
@@ -36,13 +45,19 @@ jobs:
           remotes::install_github("tidyverse/tidytemplate")
           remotes::install_cran("tidymodels")
           remotes::install_cran("C50")
-          install.packages("pkgdown")
+          install.packages("pkgdown", type = "binary")
         shell: Rscript {0}
 
       - name: Install package
         run: R CMD INSTALL .
 
+      - name: Build site
+        if: github.event_name == 'pull_request'
+        run: |
+          Rscript -e 'pkgdown::build_site()'
+
       - name: Deploy package
+        if: github.event_name == 'push'
         run: |
           git config --local user.email "[email protected]"
           git config --local user.name "GitHub Actions"

.gitignore

@@ -8,3 +8,4 @@ tests/testthat/logs/
 derby.log
 logs/*
 revdep/*
+docs*

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: parsnip
-Version: 0.1.4.9000
+Version: 0.1.5.9000
 Title: A Common API to Modeling and Analysis Functions
 Description: A common interface is provided to allow users to specify a model without having to remember the different argument names across different functions or computational engines (e.g. 'R', 'Spark', 'Stan', etc). 
 Authors@R: c(
@@ -22,8 +22,9 @@ Imports:
     purrr,
     utils,
     tibble (>= 2.1.1),
-    generics,
+    generics (>= 0.1.0),
     glue,
+    lifecycle,
     magrittr,
     stats,
     tidyr (>= 1.0.0),
@@ -51,5 +52,5 @@ Suggests:
     MASS,
     nlme,
     modeldata,
-    liquidSVM,
+    LiblineaR,
     Matrix

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(augment,model_fit)
 S3method(fit,model_spec)
 S3method(fit_xy,model_spec)
 S3method(glance,model_fit)
@@ -56,6 +57,7 @@ S3method(print,nearest_neighbor)
 S3method(print,nullmodel)
 S3method(print,rand_forest)
 S3method(print,surv_reg)
+S3method(print,svm_linear)
 S3method(print,svm_poly)
 S3method(print,svm_rbf)
 S3method(req_pkgs,model_fit)
@@ -77,6 +79,7 @@ S3method(translate,multinom_reg)
 S3method(translate,nearest_neighbor)
 S3method(translate,rand_forest)
 S3method(translate,surv_reg)
+S3method(translate,svm_linear)
 S3method(translate,svm_poly)
 S3method(translate,svm_rbf)
 S3method(type_sum,model_fit)
@@ -91,6 +94,7 @@ S3method(update,multinom_reg)
 S3method(update,nearest_neighbor)
 S3method(update,rand_forest)
 S3method(update,surv_reg)
+S3method(update,svm_linear)
 S3method(update,svm_poly)
 S3method(update,svm_rbf)
 S3method(varying_args,model_spec)
@@ -107,6 +111,7 @@ export(.x)
 export(.y)
 export(C5.0_train)
 export(add_rowindex)
+export(augment)
 export(boost_tree)
 export(check_empty_ellipse)
 export(check_final_param)
@@ -149,6 +154,7 @@ export(new_model_spec)
 export(null_model)
 export(null_value)
 export(nullmodel)
+export(parsnip_addin)
 export(pred_value_template)
 export(predict.model_fit)
 export(predict_class.model_fit)
@@ -187,7 +193,9 @@ export(show_call)
 export(show_engines)
 export(show_fit)
 export(show_model_info)
+export(stan_conf_int)
 export(surv_reg)
+export(svm_linear)
 export(svm_poly)
 export(svm_rbf)
 export(tidy)
@@ -216,6 +224,7 @@ importFrom(dplyr,starts_with)
 importFrom(dplyr,summarise)
 importFrom(dplyr,tally)
 importFrom(dplyr,vars)
+importFrom(generics,augment)
 importFrom(generics,fit)
 importFrom(generics,fit_xy)
 importFrom(generics,glance)
@@ -284,4 +293,5 @@ importFrom(utils,getFromNamespace)
 importFrom(utils,globalVariables)
 importFrom(utils,head)
 importFrom(utils,methods)
+importFrom(vctrs,vec_size)
 importFrom(vctrs,vec_unique)

NEWS.md

@@ -1,5 +1,22 @@
 # parsnip (development version)
 
+* The `liquidSVM` engine for `svm_rbf()` was deprecated due to that package's removal from CRAN. (#425)
+
+* A new linear SVM model `svm_linear()` is now available with the `LiblineaR` engine. (#424)
+
+# parsnip 0.1.5
+
+* An RStudio add-in is available that makes writing multiple `parsnip` model specifications to the source window. It can be accessed via the IDE addin menus or by calling `parsnip_addin()`.
+
+* For `xgboost` models, users can now pass `objective` to `set_engine("xgboost")`. (#403)
+
+* Changes to test for cases when CRAN cannot get `xgboost` to work on their Solaris configuration.
+
+* There is now an `augument()` method for fitted models. See `augment.model_fit`. (#401)
+
+* Column names for `x` are now required when `fit_xy()` is used. (#398)
+
+
 # parsnip 0.1.4
 
 * `show_engines()` will provide information on the current set for a model. 

R/aaa_models.R

@@ -353,7 +353,7 @@ check_interface_val <- function(x) {
 #'  a formula interface, typically some predictor preprocessing must
 #'  be conducted. `glmnet` is a good example of this.
 #'
-#'   There are three options that can be used for the encodings:
+#'   There are four options that can be used for the encodings:
 #'
 #'  `predictor_indicators` describes whether and how to create indicator/dummy
 #'  variables from factor predictors. There are three options: `"none"` (do not
@@ -370,10 +370,15 @@ check_interface_val <- function(x) {
 #'  intercept, `model.matrix()` computes a full set of indicators for the
 #'  _first_ factor variable, but an incomplete set for the remainder.
 #'
-#'  Finally, the option `remove_intercept` will remove the intercept column
+#'  Next, the option `remove_intercept` will remove the intercept column
 #'  _after_ `model.matrix()` is finished. This can be useful if the model
 #'  function (e.g. `lm()`) automatically generates an intercept.
 #'
+#' Finally, `allow_sparse_x` specifies whether the model function can natively
+#'  accommodate a sparse matrix representation for predictors during fitting
+#'  and tuning.
+#'
+#'
 #' @references "How to build a parsnip model"
 #'  \url{https://www.tidymodels.org/learn/develop/models/}
 #' @examples

R/add_in.R

@@ -0,0 +1,15 @@
+#' Start an RStudio Addin that can write model specifications
+#'
+#' `parsnip_addin()` starts a process in the RStudio IDE Viewer window
+#' that allows users to write code for `parsnip` model specifications from
+#' various R packages. The new code is written to the current document at the
+#' location of the cursor.
+#'
+#' @export
+parsnip_addin <- function() {
+  sys.source(
+    system.file("add-in", "gadget.R", package = "parsnip", mustWork = TRUE),
+    envir = rlang::new_environment(parent = rlang::global_env()),
+    keep.source = FALSE
+  )
+}