CVS commit: pkgsrc/math/R-insight

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

Module Name:    pkgsrc
Committed By:   mef
Date:           Sun Nov  3 13:25:17 UTC 2024

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

Log Message:
(math/R-insight) Updated 0.19.7 to 0.20.5

# insight 0.20.5

## General

* `get_datagrid()` can now be used to extract the "grid" information from
  `{emmeans}` and `{marginaleffects}` outputs.

* Arguments `na.rm` and `na_rm` are deprecated throughout the package's functions.
  Instead, use `remove_na`.

## Bug fixes

* Fixed rendering issue of the example in `?insight::display`.

* Fixed issues due to recent changes in the *glmmTMB* package.

# insight 0.20.4

## New supported models

* Support for models of classes `glm_weighit`, `multinom_weightit` and
  `ordinal_weightit` (package *WeightIt*).

## Changes

* `null_model()` and `formula_ok()` now warn when indexed data frames, such as
  `df[, 5]`, are used as response variable in the formula, as this can lead to
  unexpected results.

* Minor improvements to `link_function()` and `link_inverse()`.

## Bug fixes

* Fixed regression from latest fix related to `get_variance()` for *brms* models.

* Fixed issue in `link_function()` and `link_inverse()` for models of class
  *cglm* with `"identity"` link, which was not correctly recognized due to a
  typo.

# insight 0.20.3

## Changes

* `get_df()` now supports more model classes.

* `get_variance()` gives an informative error if no mixed model is provided.

## Bug fixes

* Fixed issue in `find_formula()`, `find_predictors()` and `find_variables()`
  for models from package *brms* with custom formulas.

* Fixed issues in `find_response()` for *brms* models with `mi()` function in
  the response variable.

* Fixed issue in `get_variance()` that could lead to recursive calls for
  *brms* models, resulting in "infinite" resampling of the model.

* Fixed issue in `check_if_installed()` that erroneously tried to guess the
  minimum required package version based on the SUGGEST field of the _insight_
  package, instead of the package that was calling the function.

* Fixed issue in `get_modelmatrix()` for models from package *brms* with
  special functions in the formula (like `mo()`).

* Fixed issue in `ellipses_info()` when this function was called from `do.call()`.

* Fixed issue with formatting unicode-symbols, where a wrong unicode-character
  was used for "Omega". Furthermore, Omega2 and Eta2 are now correctly converted.

# insight 0.20.2

## New supported models

* Support for models of class `glmgee` (package *glmtoolbox*).

* Support for models of class `svy2lme` (package *svylme*).

## General

* Massive overhaul of `get_variance()`. The function should be now more
  accurate for different distributional families, in particular for
  mixed regression models with Beta family.

* Improved accuracy of singularity-checks in `get_variance()`.

* `get_variance()` gets a few new arguments:

  * `null_model`, to provide a null-model to be used for the calculation of
    random effect variances. If `NULL`, the null-model is computed internally.
    This argument is optional, but may be useful to save time, or when the
    null-model cannot be calculated internally.

  * `approximation`, indicating the approximation method for the
    distribution-specific (observation level, or residual) variance.

  * `model_component`, for models that can have a zero-inflation component,
    specify for which component variances should be returned. By default, both
    the conditional and the zero-inflation component are taken into account.

* `format_alert()` and `format_warning()` get an `immediate` argument, to output
  warnings immediately.

* `find_terms()` and `find_transformation()` now better cope with inverse
  transformations of the response value, such as `1/y`.

* `get_transformation()` now returns more transformations for power-transformed
  response variables.

* `model_info()` for `MixMod` objects from package *GLMMadaptive* now recognize
  zero-inflation and hurdle models for custom families.

## Bug fixes

* `null_model()` now correctly handles zero-inflated models from package
  *glmmTMB*.

* Fixed issue in `null_model()` for models from package *GLMMadaptive*.

* Fixed issues in `link_inverse()` and `link_function()` for models of class
  `gamlss` from `LOGNO()` family.

# insight 0.20.1

## Bug fixes

* Fixed possible memory allocation issues when the deprecated argument `at` was
  used in `get_datagrid()`.

# insight 0.20.0

## Breaking

* Arguments named `group`, `at`, `group_by` and `split_by` will be deprecated
  in future releases of _easystats_ packages. Please use `by` instead. This
  affects following functions in *insight*:

  * `export_table()`
  * `get_datagrid()`
  * `print_parameters()`

## Bug fixes

* Fixed errors in CRAN checks.

# insight 0.19.11

## General

* More informative error message for `get_varcov()` when the requested
  `vcov`-function failed.

## Bug fixes

* Fixed issue with `get_data()` for `coxme` models when `source` was set to
  `"modelframe"`.

# insight 0.19.10

## Bug fixes

* Functions like `find_variables()` or `clean_names()` now support multi-membership
  formulas for models from *brms*.

* Updated tests to work with the latest changes in *glmmTMB 1.1.9*.

# insight 0.19.9

## New supported models

* Support for models of class `serp` (package *serp*).

## General

* `standardize_names()` now also recognizes column `s.value` from objects of
  package *marginaleffects*.

## Bug fixes

* Fixed issue in `find_predictors()` for models with splines (`s()`), where
  number of dimensions was indicated with a variable, not a number.

* `format_ci()` now works for factors and character vectors again.

* Fixed issues with latest release of _tinytable_.

* Fixed issues with latest release of _PROreg_.

# insight 0.19.8

## General

* Removed deprecated arguments in `get_data.mmrm()`.

* Improved support for models of class `rqs` (package *quantreg*).

* Revised test to address forthcoming changes in the *pscl* package.

## Bug fixes

* Fixed issue in `get_loglikelihood()` for glm-models with binary outcome, where
  levels were defined in reversed order.

* Fixed issue in `find_formula()` for models of class `glmmPQL` (package *MASS*).

* Fixed issue in `find_formula()` for models of class `gam` (package *mgcv*) for
  the `"gaulss"` family.

* Fixed issue in `get_variance()` for *glmmTMB* models with `family = "ordbeta"`.

* Fixed issue in `model_info()` with correctly detecting multivariate vgam/vglm
  models.


To generate a diff of this commit:
cvs rdiff -u -r1.5 -r1.6 pkgsrc/math/R-insight/Makefile
cvs rdiff -u -r1.7 -r1.8 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:1.5 pkgsrc/math/R-insight/Makefile:1.6
--- pkgsrc/math/R-insight/Makefile:1.5  Fri Jan 26 22:06:19 2024
+++ pkgsrc/math/R-insight/Makefile      Sun Nov  3 13:25:17 2024
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.5 2024/01/26 22:06:19 mef Exp $
+# $NetBSD: Makefile,v 1.6 2024/11/03 13:25:17 mef Exp $
 
 R_PKGNAME=     insight
-R_PKGVER=      0.19.7
+R_PKGVER=      0.20.5
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
 COMMENT=       Easy Access to Model Information for Various Model Objects
@@ -9,26 +9,34 @@ LICENSE=      gnu-gpl-v3
 
 # Packages suggested but not available:
 #   'AER', 'afex', 'aod', 'BayesFactor', 'bayestestR', 'betareg', 'bife',
-#   'biglm', 'blavaan', 'blme', 'brms', 'broom', 'car', 'carData',
-#   'censReg', 'cgam', 'clubSandwich', 'coxme', 'cplm', 'crch',
-#   'datawizard', 'effectsize', 'emmeans', 'epiR', 'estimatr', 'feisr',
-#   'fixest', 'fungible', 'gam', 'gamlss', 'gamlss.data', 'gamm4', 'gbm',
-#   'gee', 'geepack', 'geoR', 'GLMMadaptive', 'glmmTMB', 'gmnl', 'gt',
-#   'interp', 'ivreg', 'JM', 'lavaan', 'lavaSearch2', 'lfe', 'lmerTest',
+#   'blavaan', 'blme', 'brms', 'censReg', 'cgam', 'clubSandwich',
+#   'cobalt', 'coxme', 'cplm', 'crch', 'datawizard', 'effectsize',
+#   'emmeans', 'epiR', 'estimatr', 'feisr', 'fixest', 'fungible', 'fwb',
+#   'gam', 'gamlss', 'gamlss.data', 'gamm4', 'gbm', 'gee', 'geepack',
+#   'ggeffects', 'GLMMadaptive', 'glmmTMB', 'glmtoolbox', 'gmnl', 'gt',
+#   'httptest2', 'httr2', 'ivreg', 'JM', 'lavaan', 'lavaSearch2', 'lfe',
+#   'lmerTest', 'logistf', 'logitr', 'marginaleffects', 'mclogit',
 #   'MCMCglmm', 'merTools', 'metaBMA', 'metadat', 'metafor', 'metaplus',
-#   'mice', 'mlogit', 'mhurdle', 'mmrm', 'multgee', 'nestedLogit',
-#   'nonnest2', 'ordinal', 'parameters', 'parsnip', 'pbkrtest',
-#   'performance', 'plm', 'poorman', 'pscl', 'rms', 'robustlmm',
-#   'rstanarm', 'rstantools', 'speedglm', 'truncreg', 'tweedie', 'TMB'
-
+#   'mice', 'mlogit', 'mmrm', 'modelbased', 'multgee', 'MuMIn',
+#   'nestedLogit', 'nonnest2', 'ordinal', 'panelr', 'parameters',
+#   'parsnip', 'performance', 'plm', 'poorman', 'PROreg', 'pscl', 'rms',
+#   'robustlmm', 'rstanarm', 'rstantools', 'serp', 'speedglm', 'svylme',
+#   'tinytable', 'TMB', 'truncreg', 'tweedie', 'WeightIt'
 
 TEST_DEPENDS+= R-VGAM-[0-9]*:../../math/R-VGAM
-TEST_DEPENDS+= R-bbmle-[0-9]*:../../math/R-bbmle
+TEST_DEPENDS+= R-biglm-[0-9]*:../../sysutils/R-biglm
+TEST_DEPENDS+= R-broom-[0-9]*:../../math/R-broom
+TEST_DEPENDS+= R-car-[0-9]*:../../math/R-car
+TEST_DEPENDS+= R-carData-[0-9]*:../../math/R-carData
 TEST_DEPENDS+= R-dplyr-[0-9]*:../../math/R-dplyr
+TEST_DEPENDS+= R-geoR-[0-9]*:../../math/R-geoR
 TEST_DEPENDS+= R-httr-[0-9]*:../../www/R-httr
+TEST_DEPENDS+= R-interp-[0-9]*:../../graphics/R-interp
 TEST_DEPENDS+= R-knitr-[0-9]*:../../print/R-knitr
 TEST_DEPENDS+= R-lme4-[0-9]*:../../math/R-lme4
 TEST_DEPENDS+= R-lmtest-[0-9]*:../../math/R-lmtest
+TEST_DEPENDS+= R-mclust-[0-9]*:../../math/R-mclust
+TEST_DEPENDS+= R-pbkrtest-[0-9]*:../../math/R-pbkrtest
 TEST_DEPENDS+= R-psych-[0-9]*:../../math/R-psych
 TEST_DEPENDS+= R-quantreg-[0-9]*:../../math/R-quantreg
 TEST_DEPENDS+= R-rmarkdown-[0-9]*:../../textproc/R-rmarkdown

Index: pkgsrc/math/R-insight/distinfo
diff -u pkgsrc/math/R-insight/distinfo:1.7 pkgsrc/math/R-insight/distinfo:1.8
--- pkgsrc/math/R-insight/distinfo:1.7  Fri Jan 26 22:06:19 2024
+++ pkgsrc/math/R-insight/distinfo      Sun Nov  3 13:25:17 2024
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.7 2024/01/26 22:06:19 mef Exp $
+$NetBSD: distinfo,v 1.8 2024/11/03 13:25:17 mef Exp $
 
-BLAKE2s (R/insight_0.19.7.tar.gz) = 36597783133b567f4a6b45a5f896727a97475e29fd698e54aa6ca7dfdcc9bc4b
-SHA512 (R/insight_0.19.7.tar.gz) = 0575887aaa15ebe983fd0bd11bedf392f0a5047e89df9d823c49537cc4e406ecb18c935d6a5f144b0248f7536fbdcdd69dc9b3910202954c4105879fdd6ce91f
-Size (R/insight_0.19.7.tar.gz) = 942564 bytes
+BLAKE2s (R/insight_0.20.5.tar.gz) = ce749814b0a55c61217713bbcb5a39d9bfeb6a2e975461e3e420dfa94897920d
+SHA512 (R/insight_0.20.5.tar.gz) = 6c0b168badfc4332428a38c60786eba413825d2e2a454a69baad5e9b3e3460ba0b40c1bf4c9ebee0594ad6d7f3e1c0564060f5ae5bb48bdbaf30450001a1764f
+Size (R/insight_0.20.5.tar.gz) = 984181 bytes