tidymodels · topepo · Oct 30, 2023 · Oct 30, 2023 · Oct 30, 2023 · Oct 30, 2023
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -12,3 +12,4 @@
 ^CODE_OF_CONDUCT\.md$
 ^\.github$
 ^codecov\.yml$
+^README\.Rmd$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -33,6 +33,9 @@ jobs:
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-latest,   r: 'oldrel-2'}
+          - {os: ubuntu-latest,   r: 'oldrel-3'}
+          - {os: ubuntu-latest,   r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -19,6 +19,8 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
       - uses: actions/checkout@v3
 

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -31,7 +31,7 @@ jobs:
           covr::codecov(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
         shell: Rscript {0}
 

diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,4 @@
 .Rproj.user
 .DS_Store
 inst/doc
+docs
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -4,7 +4,7 @@ Version: 0.0.1.1
 Authors@R: c(
     person("Marly", "Gotti", , "[email protected]", role = c("aut", "cre")),
     person("Max", "Kuhn", , "[email protected]", role = "aut"),
-    person(given = "Posit Software, PBC", role = c("cph", "fnd"))
+    person("Posit Software, PBC", role = c("cph", "fnd"))
   )
 Description: A modeling package compiling applicability domain methods in
     R.  It combines different methods to measure the amount of
@@ -17,15 +17,15 @@ URL: https://github.com/tidymodels/applicable,
 BugReports: https://github.com/tidymodels/applicable/issues
 Depends: 
     ggplot2,
-    R (>= 3.4)
+    R (>= 3.6)
 Imports: 
     dplyr,
     glue,
-    hardhat (>= 0.1.2),
+    hardhat (>= 1.3.0),
     Matrix,
     proxyC,
     purrr,
-    rlang,
+    rlang (>= 1.1.1),
     stats,
     tibble,
     tidyr,
@@ -35,17 +35,17 @@ Suggests:
     covr,
     knitr,
     modeldata,
-    recipes (>= 0.1.7),
+    recipes (>= 1.0.8),
     rmarkdown,
     spelling,
-    testthat (>= 3.0.0),
+    testthat (>= 3.2.0),
     xml2
 VignetteBuilder: 
     knitr
+Config/Needs/website: tidyverse/tidytemplate
+Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Config/Needs/website: tidyverse/tidytemplate
-Config/testthat/edition: 3
diff --git a/NAMESPACE b/NAMESPACE
@@ -31,6 +31,7 @@ export(autoplot.apd_pca)
 export(autoplot.apd_similarity)
 export(score)
 export(score.default)
+import(rlang)
 importFrom(Matrix,Matrix)
 importFrom(Matrix,colSums)
 importFrom(dplyr,"%>%")
@@ -59,9 +60,6 @@ importFrom(hardhat,validate_prediction_size)
 importFrom(proxyC,simil)
 importFrom(purrr,map2_dfc)
 importFrom(purrr,map_dfc)
-importFrom(rlang,abort)
-importFrom(rlang,arg_match)
-importFrom(rlang,enquos)
 importFrom(stats,approx)
 importFrom(stats,ecdf)
 importFrom(stats,prcomp)

diff --git a/R/0.R b/R/0.R
diff --git a/R/applicable-package.R b/R/applicable-package.R
@@ -1,8 +1,50 @@
 #' @keywords internal
 "_PACKAGE"
 
-# The following block is used by usethis to automatically manage
-# roxygen namespace tags. Modify with care!
 ## usethis namespace: start
+
+#' @import rlang
+#' @importFrom dplyr %>%
+#' @importFrom dplyr count
+#' @importFrom dplyr group_by
+#' @importFrom dplyr matches
+#' @importFrom dplyr mutate
+#' @importFrom dplyr mutate_all
+#' @importFrom dplyr rename_all
+#' @importFrom dplyr sample_n
+#' @importFrom dplyr select
+#' @importFrom dplyr slice
+#' @importFrom dplyr starts_with
+#' @importFrom dplyr ungroup
+#' @importFrom ggplot2 ggplot geom_step xlab ylab aes autoplot
+#' @importFrom glue glue
+#' @importFrom hardhat forge
+#' @importFrom hardhat mold
+#' @importFrom hardhat new_model
+#' @importFrom hardhat validate_prediction_size
+#' @importFrom Matrix Matrix colSums
+#' @importFrom proxyC simil
+#' @importFrom purrr map_dfc
+#' @importFrom purrr map2_dfc
+#' @importFrom stats approx
+#' @importFrom stats ecdf
+#' @importFrom stats prcomp
+#' @importFrom stats predict
+#' @importFrom stats quantile
+#' @importFrom stats setNames
+#' @importFrom tibble as_tibble
+#' @importFrom tibble tibble
+#' @importFrom tidyr gather
+#' @importFrom tidyselect vars_select
+#' @importFrom utils globalVariables
 ## usethis namespace: end
+
+# ------------------------------------------------------------------------------
+# global variable" check
+# nocov
+# nocov end
+# Reduce false positives when R CMD check runs its "no visible binding for
+utils::globalVariables(
+  c("cumulative", "n", "sim", "percentile", "component", "value")
+)
 NULL
diff --git a/R/data.R b/R/data.R
@@ -30,7 +30,7 @@ NULL
 #' @return \item{okc_binary_train,okc_binary_test}{data frame frames with 61 columns}
 #'
 #' @source
-#' Kim (2015), "OkCupid Data for Introductory Statistics and Data Science Courses", _Journal of Statistics Education_, Volume 23, Number 2. \url{https://www.tandfonline.com/doi/abs/10.1080/10691898.2015.11889737}
+#' Kim (2015), "OkCupid Data for Introductory Statistics and Data Science Courses", _Journal of Statistics Education_, Volume 23, Number 2. \doi{10.1080/10691898.2015.11889737}
 #'
 #' Kuhn and Johnson (2020), _Feature Engineering and Selection_, Chapman and Hall/CRC . \url{https://bookdown.org/max/FES/} and \url{https://github.com/topepo/FES}
 #'
@@ -60,7 +60,7 @@ NULL
 #' Data as an End of Semester Regression Project," \emph{Journal of Statistics
 #' Education},  Volume 19, Number 3.
 #'
-#' \url{https://www.cityofames.org/government/departments-divisions-a-h/city-assessor}
+#' `https://www.cityofames.org/government/departments-divisions-a-h/city-assessor`
 #'
 #' \url{http://jse.amstat.org/v19n3/decock/DataDocumentation.txt}
 #'

diff --git a/R/print.R b/R/print.R
@@ -74,7 +74,7 @@ print.apd_hat_values <- function(x, ...) {
 #' tr_x <- matrix(
 #'   sample(0:1, size = 20 * 50, prob = rep(.5, 2), replace = TRUE),
 #'   ncol = 20
-#'  )
+#' )
 #' model <- apd_similarity(tr_x)
 #' print(model)
 #' @export

diff --git a/README.Rmd b/README.Rmd
@@ -15,7 +15,6 @@ knitr::opts_chunk$set(
 )
 
 options(rlang__backtrace_on_error = "reminder")
-
 ```
 
 # applicable <img src="man/figures/logo.png" align="right"/>
@@ -58,7 +57,7 @@ To learn about how to use applicable, check out the vignettes:
 
 This project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
 
-- For questions and discussions about tidymodels packages, modeling, and machine learning, please [post on RStudio Community](https://community.rstudio.com/new-topic?category_id=15&tags=tidymodels,question).
+- For questions and discussions about tidymodels packages, modeling, and machine learning, please [post on Posit Community](https://community.rstudio.com/new-topic?category_id=15&tags=tidymodels,question).
 
 - If you think you have encountered a bug, please [submit an issue](https://github.com/tidymodels/applicable/issues).
 

diff --git a/README.md b/README.md
@@ -57,7 +57,7 @@ Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).
 By contributing to this project, you agree to abide by its terms.
 
 - For questions and discussions about tidymodels packages, modeling, and
-  machine learning, please [post on RStudio
+  machine learning, please [post on Posit
   Community](https://community.rstudio.com/new-topic?category_id=15&tags=tidymodels,question).
 
 - If you think you have encountered a bug, please [submit an

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -1,21 +1,15 @@
-url: https://applicable.tidymodels.org
-
+url: https://applicable.tidymodels.org/
 template:
   package: tidytemplate
   bootstrap: 5
   bslib:
-    primary: "#CA225E"
-
+    primary: '#CA225E'
   includes:
-      in_header: |
-        <script defer data-domain="applicable.tidymodels.org,all.tidymodels.org" src="https://plausible.io/js/plausible.js"></script>
-
-# https://github.com/tidyverse/tidytemplate for css
-
+    in_header: |
+      <script defer data-domain="applicable.tidymodels.org,all.tidymodels.org" src="https://plausible.io/js/plausible.js"></script>
 development:
   mode: auto
-
-
 figures:
   fig.width: 8
   fig.height: 5.75
+
diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -1,24 +1,27 @@
-al
 Ames
-Chemoinformatics
+CMD
 CRC
+Chemoinformatics
+Codecov
 De
-doi
-et
-extensibility
 Gillet
 Jaccard
 Lifecycle
 Netzeva
 OkCupid
-pca
-pcas
-pre
+PBC
 QSAR
 Springer
-tibble
 X'X
+al
+doi
+et
+extensibility
+funder
 intercal
-CMD
+pca
+pcas
+pre
 reprex
+tibble
 tidymodels
diff --git a/man/ames_new.Rd b/man/ames_new.Rd
diff --git a/man/okc_binary.Rd b/man/okc_binary.Rd
diff --git a/man/print.apd_similarity.Rd b/man/print.apd_similarity.Rd
diff --git a/tests/testthat/_snaps/hat_values-fit.md b/tests/testthat/_snaps/hat_values-fit.md
@@ -2,29 +2,33 @@
 
     Code
       new_apd_hat_values(blueprint = hardhat::default_xy_blueprint())
-    Error <simpleError>
-      argument "XtX_inv" is missing, with no default
+    Condition
+      Error in `new_apd_hat_values()`:
+      ! argument "XtX_inv" is missing, with no default
 
 # `new_apd_hat_values` fails when blueprint is numeric
 
     Code
       new_apd_hat_values(XtX_inv = 1, blueprint = 1)
-    Error <rlang_error>
-      blueprint should be a blueprint, not a numeric.
+    Condition
+      Error in `hardhat::new_model()`:
+      ! `blueprint` must be a <hardhat_blueprint>, not the number 1.
 
 # `apd_hat_values` fails when matrix has more predictors than samples
 
     Code
       apd_hat_values(bad_data)
-    Error <rlang_error>
-      The number of columns must be less than the number of rows.
+    Condition
+      Error in `apd_hat_values_bridge()`:
+      ! The number of columns must be less than the number of rows.
 
 # `apd_hat_values` fails when the matrix X^tX is singular
 
     Code
       apd_hat_values(bad_data)
-    Error <rlang_error>
-      Unable to compute the hat values of the matrix X of
+    Condition
+      Error in `get_inv()`:
+      ! Unable to compute the hat values of the matrix X of
       predictors because the matrix resulting from multiplying
       the transpose of X by X is singular.