From cb08c516f5477f6b9da839eb9ee39f0ee928c7e3 Mon Sep 17 00:00:00 2001 From: topepo Date: Wed, 30 Jul 2025 11:28:12 -0400 Subject: [PATCH] prep for submission --- DESCRIPTION | 2 +- NEWS.md | 2 +- man/int_conformal_full.Rd | 71 --------------------- revdep/README.md | 126 +++++++++++++++++++++++++++----------- revdep/cran.md | 2 +- 5 files changed, 94 insertions(+), 109 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 44f54380..55cb3b91 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: probably Title: Tools for Post-Processing Predicted Values -Version: 1.1.0.9000 +Version: 1.1.1 Authors@R: c( person("Max", "Kuhn", , "max@posit.co", role = c("aut", "cre")), person("Davis", "Vaughan", , "davis@posit.co", role = "aut"), diff --git a/NEWS.md b/NEWS.md index 15848925..b2439fe4 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# probably (development version) +# probably 1.1.1 * Updated unit tests for new ggplot2 release (#180). diff --git a/man/int_conformal_full.Rd b/man/int_conformal_full.Rd index e950fe7e..09faf208 100644 --- a/man/int_conformal_full.Rd +++ b/man/int_conformal_full.Rd @@ -68,77 +68,6 @@ the initial set of training set residuals are modeled using a Gamma generalized linear model with a log link (see the reference by Aitkin below). For a new sample, the absolute size of the residual is estimated and a multiple of this value is computed as an initial guess of the search boundaries. - -\subsection{Speed}{ - -The time it takes to compute the intervals depends on the training set -size, search parameters (i.e., convergence criterion, number of -iterations), the grid size, and the number of worker processes that are -used. For the last item, the computations can be parallelized using the -future and furrr packages. - -To use parallelism, the \code{\link[future:plan]{future::plan()}} function can -be invoked to create a parallel backend. For example, let’s make an -initial workflow: - -\if{html}{\out{
}}\preformatted{library(tidymodels) -library(probably) -library(future) - -tidymodels_prefer() - -## Make a fitted workflow from some simulated data: -set.seed(121) -train_dat <- sim_regression(200) -new_dat <- sim_regression( 5) |> select(-outcome) - -lm_fit <- - workflow() |> - add_model(linear_reg()) |> - add_formula(outcome ~ .) |> - fit(data = train_dat) - -# Create the object to be used to make prediction intervals -lm_conform <- int_conformal_full(lm_fit, train_dat) -}\if{html}{\out{
}} - -We’ll use a \code{"multisession"} parallel processing plan to compute the -intervals for the five new samples in parallel: - -\if{html}{\out{
}}\preformatted{plan("multisession") - -# This is run in parallel: -predict(lm_conform, new_dat) -}\if{html}{\out{
}} - -\if{html}{\out{
}}\preformatted{## # A tibble: 5 x 2 -## .pred_lower .pred_upper -## -## 1 -17.9 59.6 -## 2 -33.7 51.1 -## 3 -30.6 48.2 -## 4 -17.3 59.6 -## 5 -23.3 55.2 -}\if{html}{\out{
}} - -Using simulations, there are slightly sub-linear speed-ups when using -parallel processing to compute the row-wise intervals. - -In comparison with parametric intervals: - -\if{html}{\out{
}}\preformatted{predict(lm_fit, new_dat, type = "pred_int") -}\if{html}{\out{
}} - -\if{html}{\out{
}}\preformatted{## # A tibble: 5 x 2 -## .pred_lower .pred_upper -## -## 1 -19.2 59.1 -## 2 -31.8 49.7 -## 3 -31.0 47.6 -## 4 -17.8 60.1 -## 5 -23.6 54.3 -}\if{html}{\out{
}} -} } \references{ Jing Lei, Max G'Sell, Alessandro Rinaldo, Ryan J. Tibshirani and Larry diff --git a/revdep/README.md b/revdep/README.md index 1112f1d9..543a3270 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,43 +1,99 @@ # Platform -|field |value | -|:--------|:---------------------------------------------------------------------------------| -|version |R version 4.1.3 (2022-03-10) | -|os |macOS Monterey 12.5.1 | -|system |x86_64, darwin17.0 | -|ui |RStudio | -|language |(EN) | -|collate |en_US.UTF-8 | -|ctype |en_US.UTF-8 | -|tz |America/New_York | -|date |2022-08-29 | -|rstudio |2022.07.1+554 Spotted Wakerobin (desktop) | -|pandoc |2.18 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown) | +|field |value | +|:--------|:------------------------------------------------------------------------------------------------| +|version |R version 4.5.1 (2025-06-13) | +|os |macOS Sequoia 15.5 | +|system |aarch64, darwin20 | +|ui |RStudio | +|language |(EN) | +|collate |en_US.UTF-8 | +|ctype |en_US.UTF-8 | +|tz |America/New_York | +|date |2025-07-30 | +|rstudio |2025.05.1+513 Mariposa Orchid (desktop) | +|pandoc |3.4 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown) | +|quarto |1.7.31 @ /usr/local/bin/quarto | # Dependencies -|package |old |new |Δ | -|:----------|:-----|:----------|:--| -|probably |0.0.6 |0.0.6.9000 |* | -|cli |3.3.0 |3.3.0 | | -|dplyr |1.0.9 |1.0.9 | | -|ellipsis |0.3.2 |0.3.2 | | -|fansi |1.0.3 |1.0.3 | | -|generics |0.1.3 |0.1.3 | | -|glue |1.6.2 |1.6.2 | | -|hardhat |1.2.0 |1.2.0 | | -|lifecycle |1.0.1 |1.0.1 | | -|magrittr |2.0.3 |2.0.3 | | -|pillar |1.8.1 |1.8.1 | | -|pkgconfig |2.0.3 |2.0.3 | | -|purrr |0.3.4 |0.3.4 | | -|R6 |2.5.1 |2.5.1 | | -|rlang |1.0.4 |1.0.4 | | -|tibble |3.1.8 |3.1.8 | | -|tidyselect |1.1.2 |1.1.2 | | -|utf8 |1.2.2 |1.2.2 | | -|vctrs |0.4.1 |0.4.1 | | -|yardstick |1.0.0 |1.0.0 | | +|package |old |new |Δ | +|:------------|:----------|:----------|:--| +|probably |1.1.0 |1.1.1 |* | +|butcher |0.3.5 |0.3.5 | | +|cli |3.6.5 |3.6.5 | | +|clock |0.7.3 |0.7.3 | | +|cpp11 |0.5.2 |0.5.2 | | +|crayon |1.5.3 |1.5.3 | | +|data.table |1.17.8 |1.17.8 | | +|diagram |1.6.5 |1.6.5 | | +|dials |1.4.1 |1.4.1 | | +|DiceDesign |1.10 |1.10 | | +|digest |0.6.37 |0.6.37 | | +|doFuture |1.1.2 |1.1.2 | | +|dplyr |1.1.4 |1.1.4 | | +|farver |2.1.2 |2.1.2 | | +|foreach |1.5.2 |1.5.2 | | +|furrr |0.3.1 |0.3.1 | | +|future |1.67.0 |1.67.0 | | +|future.apply |1.20.0 |1.20.0 | | +|generics |0.1.4 |0.1.4 | | +|ggplot2 |3.5.2 |3.5.2 | | +|globals |0.18.0 |0.18.0 | | +|glue |1.8.0 |1.8.0 | | +|gower |1.0.2 |1.0.2 | | +|GPfit |1.0-9 |1.0-9 | | +|gtable |0.3.6 |0.3.6 | | +|hardhat |1.4.1 |1.4.1 | | +|ipred |0.9-15 |0.9-15 | | +|isoband |0.2.7 |0.2.7 | | +|iterators |1.0.14 |1.0.14 | | +|labeling |0.4.3 |0.4.3 | | +|lava |1.8.1 |1.8.1 | | +|lhs |1.2.0 |1.2.0 | | +|lifecycle |1.0.4 |1.0.4 | | +|listenv |0.9.1 |0.9.1 | | +|lobstr |1.1.2 |1.1.2 | | +|lubridate |1.9.4 |1.9.4 | | +|magrittr |2.0.3 |2.0.3 | | +|modelenv |0.2.0 |0.2.0 | | +|numDeriv |2016.8-1.1 |2016.8-1.1 | | +|parallelly |1.45.1 |1.45.1 | | +|parsnip |1.3.2 |1.3.2 | | +|pillar |1.11.0 |1.11.0 | | +|pkgconfig |2.0.3 |2.0.3 | | +|prettyunits |1.2.0 |1.2.0 | | +|prodlim |2025.04.28 |2025.04.28 | | +|progressr |0.15.1 |0.15.1 | | +|purrr |1.1.0 |1.1.0 | | +|R6 |2.6.1 |2.6.1 | | +|RColorBrewer |1.1-3 |1.1-3 | | +|Rcpp |1.1.0 |1.1.0 | | +|recipes |1.3.1 |1.3.1 | | +|rlang |1.1.6 |1.1.6 | | +|rsample |1.3.1 |1.3.1 | | +|scales |1.4.0 |1.4.0 | | +|sfd |0.1.0 |0.1.0 | | +|shape |1.4.6.1 |1.4.6.1 | | +|slider |0.3.2 |0.3.2 | | +|sparsevctrs |0.3.4 |0.3.4 | | +|SQUAREM |2021.1 |2021.1 | | +|stringi |1.8.7 |1.8.7 | | +|stringr |1.5.1 |1.5.1 | | +|tibble |3.3.0 |3.3.0 | | +|tidyr |1.3.1 |1.3.1 | | +|tidyselect |1.2.1 |1.2.1 | | +|timechange |0.3.0 |0.3.0 | | +|timeDate |4041.110 |4041.110 | | +|tune |1.3.0 |1.3.0 | | +|tzdb |0.5.0 |0.5.0 | | +|utf8 |1.2.6 |1.2.6 | | +|vctrs |0.6.5 |0.6.5 | | +|viridisLite |0.4.2 |0.4.2 | | +|warp |0.2.1 |0.2.1 | | +|withr |3.0.2 |3.0.2 | | +|workflows |1.2.0 |1.2.0 | | +|yardstick |1.3.2 |1.3.2 | | # Revdeps diff --git a/revdep/cran.md b/revdep/cran.md index 782ef684..29c19611 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,6 +1,6 @@ ## revdepcheck results -We checked 1 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. +We checked 3 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. * We saw 0 new problems * We failed to check 0 packages