CVS commit: pkgsrc/math/R-insight

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Sat May 21 15:27:28 UTC 2022

Modified Files:
        pkgsrc/math/R-insight: Makefile distinfo

Log Message:
(math/R-insight) Updated 0.14.4 to 0.17.1

# Insight 0.17.1

## New supported model classes

* `deltaMethod` (*car*), `marginaleffects`, `marginaleffects.summary`
  (*marginaleffects*)

## General

* `get_predicted()` now supports models of class `iv_robust` and `ivreg`.

* For `get_predicted()`, when both `type` and `predict` are given, `type`
  will overwrite `predict`. Note that this will print a message, because
  `predict` is the preferred argument.

* `get_varcov()` gains `vcov` and `vcov_args` arguments, to specify the
  variance-covariance matrix used to compute uncertainty estimates (e.g., for
  robust standard errors).

* `get_loglikehood()` improved handling of models from package *estimator*.

## Bug fixes

* Fixed bug in `get_data()` for model objects whose data needs to be recovered
  from the environment, and where the data name was a reserved word (e.g., named
  like an R function).

* The matrix returned by `get_varcov()` for models of class *bife* now returns
  row and column names.

* `find_offset()` did not find offset-terms for `merMod` objects when the
  offset was specified as `offset` argument in the function call.

# insight 0.17.0

## Breaking changes

* Arguments `vcov_estimation` and `vcov_type` in `get_predicted()`,
  `get_predicted_se()` and `get_predicted_ci()` are replaced by `vcov` and
  `vcov_args`, to have a more simplified and common interface to control
  robust covariance matrix estimation.

## General

* Improved performance for various functions, in particular `get_data()` and
  `model_info()`.

## New functions

* To check for names: `object_has_names()` and `object_has_rownames()`

* To work with lists: `is_empty_object()` and `compact_list()`

* To work with strings: `compact_character()`

* Further utility functions are `safe_deparse()`, `trim_ws()` and `n_unique()`.

## Changes to functions

* `export_table()` now better checks for invalid values of caption and footer
  for tables in HTML format, and silently removes, e.g., ansi-colour codes that
  only work for text-format.

* `get_data.coxph()` returns the original data frame instead of data with type
   coercion.

* `get_loglikelihood()` gets a `check_response` argument, to check if a model
  has a transformed response variable (like `log()` or `sqrt()` transformation),
  and if so, returns a corrected log-likelihood.

* `get_modelmatrix()` now supports *BayesFactor* models.

* `get_loglikelihood()` and `get_df()` now support more model classes.

* `get_predicted()` was improved for multinomial models from *brms*.

* `get_variance()` was improved to cover more edge cases of (more complex)
  random effect structures.

* `get_data()` now includes variables in the returned data frame that were
  used in the `subset` argument of regression functions (like `lm()`).

* In some edge cases, where `get_data()` is unable to retrieve the data that
  was used to fit the model, now a more informative error is printed.

* `ellipses_info()` now also accepts a list of model objects, is more stable
  and returns more information about the provided models (like if all fixed
  or random effects are the same across models, if all models are mixed models
  or null-models, etc.)

* `check_if_installed()` now works interactively and lets the user prompt
  whether to automatically update or install packages.

## Bug fixes

* Fixed incorrect column name conversion in `standardize_names()` for certain
  columns returned by `broom::glance()`.

* Fixed issue with correctly detecting Tweedie-models in `model_info()`.

* Fixed issue with `get_datagrid()` for *brms* models with monotonic factors.

* Fixed issue in `find_formula()` when argument `correlation` was defined
  outside of `lme()` and `gls()` (@etiennebacher, #525).

* Fixed issue with `get_data()` when back-transforming data from predictors
  that used `cos()`, `sin()` or `tan()` transformations.

# insight 0.16.0

## New functions

* `get_datagrid()`, to generate a reference grid, usually used when computing
  adjusted predictions or marginal means from regression models.

## Changes to functions

### `get_predicted()`

* `get_predicted()` was revised. Beside the four core options for the `predict`
  argument, it is now also possible to use any value that is valid for the
  model's `predict()` method's `type` argument.

* `get_predicted()` now supports more models (e.g., from packages like
  _GLMMadaptive_ or _survival_).

* `get_predicted()` is now more robust when calculating standard errors of
  predictions.

### Other functions

* `get_statistic()` and `find_statistic()` now support *htest* objects.

## General

* Various minor improvements.

# insight 0.15.1

## General

* Improved speed performance, especially for `get_data()`.

## Changes to functions

* `get_data()` for `coxph` models now returns the original factor levels for
  variables transformed with `strata()` inside formulas.

# insight 0.15.0

## Breaking changes

* Data management functions (like `reshape_longer()`, or `data_match()`) have
  been moved to the *datawizard* package.

* `get_data()` no longer returns factor types for numeric variables that have
  been converted to factors on-the-fly within formulas (like `y ~ as.factor(x)`).
  Instead, for each numeric variable that was coerced to factor within a formula
  gets a `factor` attribute (set to `TRUE`), and the returned data frame gets
  a `factors` attribute including all names of affected variables.

## New supported model classes

* Support for `bfsl` (*bfsl*)

## New functions

* New `standardize_column_order()` function can be used to standardize the
  column order in output dataframes.

## General

* Improved speed performance for some functions.

* Improved handling of table captions and footers in `export_table()`. See also
  the new vignette on exporting data frames into human readable tables here:
  https://easystats.github.io/insight/articles/export.html

* Revised `width` argument in `export_table()`, which now allows to set
  different column widths across table columns. See examples in
  `?export_table`.

* `export_table()` gets a `table_width` argument to split wide tables into
  two parts.

* `get_varcov()` for `MixMod` (package *GLMMadaptive*) was revised, and now
  allows to return a robust variance-covariance matrix.

* Added more `get_df()` methods.

## Bug fixes

* Fixed issues with manual sigma computation to handle dispersion models in
  `get_sigma()`.

* Fixed issue in `find_formula()` for `BayesFactor::lmBF()` with multiple random
  effects.

* Fixed issue in `get_parameters.BFBayesFactor()` with wrong sign of difference
  estimate for t-tests.

* Argument `width` in `format_value()` was ignored when formatting integer
  values and `protect_integers` was set to `TRUE`.

# insight 0.14.5

## New functions

* `find_transformation()` and `get_transformation()` to find or get any function
  that was used to transform the response variable in a regression model.

## General

* Improved support for models of class `sampleSelection`.

* Improved documentation.

* `get_modelmatrix()` now supports: `rms::lrm`

* `get_predicted()` supports: `MASS::polr`, `MASS::rlm`, `rms::lrm`, `fixest`,
  `bife::bife`, `ordinal::clm`.

* `get_predicted()` standard errors are often much faster to compute.

* `get_predicted()` supports models with "grouped" or "level" outcomes (e.g.,
  multinomial logit).

* `get_predicted()` handles factors better.

* Improved documentation

## Changes to functions

* `check_if_installed()` gains a `quietly` argument, if neither stopping nor a
  warning message for non-installed packages is requested.

* `get_predicted()`'s `predict` argument now accepts these values: "link",
  "expectation", "prediction", "classification", or NULL.

* `get_predicted()` accepts `predict=NULL`, which allows users to push a `type`
  argument through the `...` ellipsis, forward to the `predict()` method of the
  modelling package.

## Bug fixes

* Fixed issue with parameter names from *emmeans* objects in
  `get_parameters()`.

* Fixed issues with unknown arguments in `get_predicted()`.


To generate a diff of this commit:
cvs rdiff -u -r1.1 -r1.2 pkgsrc/math/R-insight/Makefile
cvs rdiff -u -r1.3 -r1.4 pkgsrc/math/R-insight/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/math/R-insight/Makefile
diff -u pkgsrc/math/R-insight/Makefile:1.1 pkgsrc/math/R-insight/Makefile:1.2
--- pkgsrc/math/R-insight/Makefile:1.1  Mon Sep 20 02:48:37 2021
+++ pkgsrc/math/R-insight/Makefile      Sat May 21 15:27:28 2022
@@ -1,23 +1,25 @@
-# $NetBSD: Makefile,v 1.1 2021/09/20 02:48:37 mef Exp $
+# $NetBSD: Makefile,v 1.2 2022/05/21 15:27:28 mef Exp $
 
 R_PKGNAME=     insight
-R_PKGVER=      0.14.4
+R_PKGVER=      0.17.1
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
 COMMENT=       Easy Access to Model Information for Various Model Objects
 LICENSE=       gnu-gpl-v3
 
 # Packages suggested but not available:
-#   'AER', 'afex', 'aod', 'BayesFactor', 'bayestestR', 'bdsmatrix',
-#   'betareg', 'biglm', 'blavaan', 'blme', 'brms', 'censReg', 'cgam',
-#   'clubSandwich', 'coxme', 'cplm', 'crch', 'effectsize', 'emmeans',
-#   'epiR', 'estimatr', 'feisr', 'fixest', 'fungible', 'gam', 'gamlss',
-#   'gamm4', 'gbm', 'gee', 'geepack', 'GLMMadaptive', 'glmmTMB', 'gmnl',
-#   'gt', 'ivreg', 'JM', 'lavaan', 'lfe', 'logistf', 'mclust',
-#   'MCMCglmm', 'merTools', 'metaBMA', 'mice', 'mlogit', 'multgee',
-#   'nonnest2', 'ordinal', 'panelr', 'parameters', 'parsnip',
-#   'performance', 'plm', 'pscl', 'rms', 'robustlmm', 'rstanarm',
-#   'rstantools', 'speedglm', 'tripack', 'truncreg'
+#   'AER', 'afex', 'aod', 'BayesFactor', 'bayestestR', 'betareg', 'bife',
+#   'biglm', 'blavaan', 'blme', 'brms', 'censReg', 'cgam',
+#   'clubSandwich', 'coxme', 'cplm', 'crch', 'datawizard', 'effectsize',
+#   'emmeans', 'epiR', 'estimatr', 'feisr', 'fixest', 'fungible', 'gam',
+#   'gamlss', 'gamm4', 'gbm', 'gee', 'geepack', 'GLMMadaptive',
+#   'glmmTMB', 'gmnl', 'gt', 'ivreg', 'JM', 'lavaan', 'lfe', 'lmerTest',
+#   'logistf', 'marginaleffects', 'mclust', 'MCMCglmm', 'merTools',
+#   'metaBMA', 'mice', 'mlogit', 'mhurdle', 'multgee', 'nonnest2',
+#   'ordinal', 'panelr', 'parameters', 'parsnip', 'pbkrtest',
+#   'performance', 'plm', 'poorman', 'pscl', 'rms', 'robustlmm',
+#   'rstanarm', 'rstantools', 'speedglm', 'tripack', 'truncreg',
+#   'tweedie'
 
 
 TEST_DEPENDS+= R-VGAM-[0-9]*:../../math/R-VGAM

Index: pkgsrc/math/R-insight/distinfo
diff -u pkgsrc/math/R-insight/distinfo:1.3 pkgsrc/math/R-insight/distinfo:1.4
--- pkgsrc/math/R-insight/distinfo:1.3  Tue Oct 26 10:55:28 2021
+++ pkgsrc/math/R-insight/distinfo      Sat May 21 15:27:28 2022
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.3 2021/10/26 10:55:28 nia Exp $
+$NetBSD: distinfo,v 1.4 2022/05/21 15:27:28 mef Exp $
 
-BLAKE2s (R/insight_0.14.4.tar.gz) = db98fdc0fd6399021f598976054256ca89bdfa7ce2034c765ba5a7896f647ab5
-SHA512 (R/insight_0.14.4.tar.gz) = 1ab27e6d96ef557df5c20aff8e737e9f82a81bfb0088a785b7f51185fe9325b574a3bb06e26b77507b97dd4a400a44982a52ca20ac752ebc81c5df618a82355f
-Size (R/insight_0.14.4.tar.gz) = 841657 bytes
+BLAKE2s (R/insight_0.17.1.tar.gz) = c2f481d336101c002e26a4f8b9b416ea6f630ce9091c1214fbfbfb26d7ebed5f
+SHA512 (R/insight_0.17.1.tar.gz) = 1d0998a7094c5aae1087b4f843b57515e80f4f57b15ba8c420e66939ed5dfd8274f520c69fc2e47c70a949d1347c880de2c9605b98a80e22925db212c33bbccb
+Size (R/insight_0.17.1.tar.gz) = 863795 bytes