CVS commit: pkgsrc/math/R-insight

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

Module Name:    pkgsrc
Committed By:   mef
Date:           Thu Jun 15 12:53:56 UTC 2023

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

Log Message:
(math/R-insight) Updated 0.17.1 to 0.19.2

# insight 0.19.2

## Breaking changes

* The minimum needed R version has been bumped to `3.6`.

* `download_model()` no longer errors when a model object could not be downloaded,
  but instead returns `NULL`. This prevents test failures, and allows to skip
  tests when the return value of `download_model()` is `NULL`.

## General

* Improved support for `mclogit` models (package *mclogit*) and `mipo` objects
  (package *mice*) for models with ordinal or categorical response.

## New supported models

* `phylolm` and `phyloglm` (package *phylolm*), `nestedLogit` (package *nestedLogit*).

## Bug fixes

* Fixed issue in `get_variance()` for *glmmTMB* models with rank deficient
  coefficients.

* Fixed issues in `get_weights()` for `glm` models without weights and `na.action`
  not set to default in the model call.

* `clean_names()` now also removes the `relevel()` pattern.

* Fixed issue in `model_info()` for models of class `gamlss`.

* Fixed problems preventing `get_data()` from locating data defined in
  non-global environments.

* Fixed issue in `get_predicted()` for variables of class numeric matrix created
  by `scale()`, which were correctly handled only when `get_data()` failed to
  find the data in the appropriate environment.

* Fixed issue in `model_info()` for `gee` models from `binomial` families.

# insight 0.19.1

## New supported models

* `hglm` (package *hglm*).

## Changes to functions

* Minor improvements to `get_data()` for `t.test()`.

* `format_value()` gets a `lead_zero` argument, to keep or drop the leading
  zero of a formatted value, as well as arguments `style_positive` and
  `style_negative` to style positive or negative numbers.

* `format_table()` now also formats columns named `SGPV` (second generation
  p-values) as p-values.

* Functions for models of class `clm` (like `find_formula()`, `find_variables()`,
  `get_data()` etc.) now also include variables that were defined as `scale` or
  `nominal` component.

## Bug fixes

* Fixed issue in `get_data()` for results from `kruskal.test()`.

* Fixed issue in `find_weights()` for models of class `lme` and `gls`.

* Fixed issue in `get_datagrid()` for models with multiple weight variables.

# insight 0.19.0

## New supported models

* `mmrm` (package *mmrm*), `flac` and `flic` (*logistf*)

## Breaking changes

* `get_data()` was revised and now always tries to recover the data that was
  used to fit a model from the environment. If this fails, it falls back to
  recovering data from the model frame (the former default behaviour).
  Futrhermore, the `source` argument can be used to explicitly force the old
  behaviour: `source = "mf"` will try to recover data from the model frame first,
  then possibly falling back to look in the environment.

## New functions

* `n_grouplevels()`, to return random effect groups and number of group levels
  for mixed models.

## Changes to functions

* `get_datagrid()` preserves all factor levels for factors that are hold constant
  at their reference level. This is required to work together with
  `get_modelmatrix()` when calculating standard errors for `get_predicted()`.

## Bug fixes

* Fixed but in `get_modelmatrix()` handling of incomplete factors which
  sometimes had downstream implications for numerical results in the uncertainty
  estimates produced by `get_predicted()`.

* Fixed minor issues for HTML tables in `export_table()` when model parameters
  were grouped.

* Fixed issue with incorrect back-transforming in `get_data()` for models with
  log-transformed variables.

* Fixes issue in `compact_list()`.

* `has_single_value()` now returns `FALSE` when the object only has `NA` and
  `na.rm = TRUE`.

* Fixed issue in `get_parameters()` for gam-models without smooth terms, or with
  only smooth terms and removed intercept.

# insight 0.18.8

## Bug fixes

* Fixed test due to changes in the _performance_ package.

# insight 0.18.7

## General

* Minor revisions to `get_predicted.glmmTMB()` due to changes in behaviour
  of `predict.glmmTMB()` for truncated-family models since _glmmTMB_ 1.1.5.

* New function `has_single_value()` that is equivalent to `length(unique()) == 1`
  (or `n_unique() == 1`) but faster.

## Changes to functions

* `ellipses_info()` now includes an attribute `$is_binomial`, which is `TRUE`
  for each model from binomial family.

## Bug fixes

* Fixed behaviour of the `at` argument in `get_datagrid()`.

* Fixed issue for accessing model data in `get_datagrid()` for some edge cases.

# insight 0.18.6

## New supported models

* Support the *logitr* package: `get_data()`, `find_variables()` and more.

## Bug fixes

* Better detection of unicode-support, to avoid failures when building
  vignettes.

* `get_predicted()` now correctly handles variables of class numeric matrix
  created by `scale()`, which fixes a bug in `performance::check_model()`
  (easystats/performance#432).

* Fixed issue with `iterations` argument in `get_predicted()` with _brms_
  models.

# insight 0.18.5

## Breaking

* `get_df(type = "satterthwaite")` for `lmerMod` objects now return degrees of
  freedom per parameter, and no longer per observation. Use `df_per_obs TRUE`
  to return degrees of freedom per observation.

## New functions

* `safe_deparse_symbol()` to only deparses a substituted expressions when
  possible,which increases performance in case many calls to
  `deparse(substitute())`.

## Changes to functions

* `format_table()` gets a `use_symbols` argument. If `TRUE`, column names that
  refer to particular effectsizes (like Phi, Omega or Epsilon) include the related unicode-character instead of the written name. This only works on Windows for
  R >= 4.2, and on OS X or Linux for R >= 4.0.

* The `stars` argument in `format_table()` can now also be a character vector,
  naming the columns that should include stars for significant values. This is
  especially useful for Bayesian models, where we might have multiple columns
  with significant values, e.g. `"BF"` for the Bayes factor or `"pd"` for the
  probability of direction.

* `get_df()` gets more `type` options to return different type of degrees of
  freedom (namely, `"wald"` and `"normal"`, and for mixed models, `"ml1"`,
  `"betwithin"`, `"satterthwaite"` and `"kenward-roger"`).

* `standardize_names()` now recognized more classes from package _marginaleffects_.

* Minor improvements to `find_parameters()` for models with nonlinear formula.

* Minor speed improvements.

## Bug fixes

* Fixed issue in `get_data()` for models of class `plm`, which accidentally
  converted factors into character vectors.

* Fixed issue with column alignment in `export_table()` when the data frame
  to print contained unicode-characters longer than 1 byte.

* Correctly extract predictors for `fixest::i(f1, i.f2)` interactions (#649 by
  @grantmcdermott).

# insight 0.18.4

## Changes to functions

* `model_info()` now includes information for `htest` objects from
  `shapiro.test()` and `bartlett.test()` (will return `$is_variancetest = TRUE`).

## Bug fixes

* Fixed issue in `get_data()` which did not correctly backtransform to original
  data when terms had log-transformations such as `log(1 + x)` or `log(x + 1)`.

* Fixed CRAN check issues.

# insight 0.18.3

## New functions

* `format_alert()`, `format_warning()` and `format_error()`, as convenient
  wrappers around `message()`, `warning()` or `stop()` in combination with
  `format_message()`. You can use these funcionts to format messages, warnings
  or errors.

## Changes to functions

* `get_predicted()` for models of class `clm` now includes confidence intervals
  of predictions.

* `format_message()` gets some additional formatting features. See 'Details'
  in `?format_message` for more information and some current limitations.

* `format_message()` gets an `indent` argument, to specify indention string
  for subsequent lines.

* `format_table()` now merges IC and IC weights columns into one column (e.g.,
  former columns `"AIC"` and `"AIC_wt"` will now be printed as one column, named
  `"AIC (weights)"`). Furthermore, an `ic_digits` argument was added to control
  the number of significant digits for the IC values.

* `print_color()` and `color_text()` now support bright variants of colors and
  background colors.

* `get_datagrid()` gets more options for `at` and `range`, to provide more
  control how to generate the reference grid.

* `get_data()` for models of class `geeglm` and `fixest`now more reliably
  retrieves the model data.

## New supported models

* Support for models of class `mblogit` and `mclogit`.

## Bug fixes

* Fixed issues with wrong attribute `adjusted_for` in `insight::get_datagrid()`.

* Fixed issue (resp. implemented workaround) in `get_data.iv_robust()`, which
  failed due to a bug in the _estimatr_ package.

* Fixed issue where `get_predicted()` failed when data contains factors with
  only one or incomplete levels.

* Fixed issue in `get_predicted()` for models of class `mlm`.

* Fixed issue where `get_predicted()` failed to compute confidence intervals
  of predictions when model contained matrix-alike response columns, e.g. a
  response variable created with `cbind()`.

# insight 0.18.2

## New functions

* `format_percent()` as short-cut for `format_value(as_percent = TRUE)`.

* `is_converged()`, to check whether a mixed model has converged or not.

## Changes to functions

* `format_table()` gains an `exact` argument, to either report exact or rounded
  Bayes factors.

* `get_predicted()` gets a method for models of class `gamlss` (and thereby,
  `get_loglikelihood()` now also works for those model classes).

* `get_predicted()` now better handles models of class `polr`, `multinom` and
  `rlm`.

## Bug fixes

* Fixed test failures.

* Minor fixes to address changes in other packages.

# insight 0.18.0

## Breaking changes

* The `ci` argument in `get_predicted()` now defaults to `NULL`. One reason was
  to make the function faster if confidence intervals are not required, which
  was the case for many downstream usages of that function. Please set `ci`
  explicitly to compute confidence intervals for predictions.

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

* `parameters_table()`, the alias for `format_table()`, was removed.

## Changes to functions

* `find_transformation()` and `get_transformation()` now also work for models
  where the response was transformed using `log2()` or `log10()`.

## Bug fixes

* `get_sigma()` for models from package _VGAM_ returned wrong sigma-parameter.

* `find_predictors()` for models from package _fixest_ that contained
  interaction terms in the endogenous formula part did not correctly return
  all instruments.

* Fixed formatting of HTML table footers in `export_table()`.

* Several fixes to `get_predicted()` for models from `mgcv::gam()`.

* The `component` argument in `find_parameters()` for `stanmvreg` models did
  not accept the `"location"` value.

* `null_model()` did not consider offset-terms if these were specified inside
  formulas.

* Argument `allow.new.levels` was not passed to `predict()` for
  `get_predicted.glmmTMB()`.

* `clean_names()` now works correctly when several variables are specified in
  `s()` (#573, @etiennebacher).


To generate a diff of this commit:
cvs rdiff -u -r1.2 -r1.3 pkgsrc/math/R-insight/Makefile
cvs rdiff -u -r1.4 -r1.5 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:1.2 pkgsrc/math/R-insight/Makefile:1.3
--- pkgsrc/math/R-insight/Makefile:1.2  Sat May 21 15:27:28 2022
+++ pkgsrc/math/R-insight/Makefile      Thu Jun 15 12:53:56 2023
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.2 2022/05/21 15:27:28 mef Exp $
+# $NetBSD: Makefile,v 1.3 2023/06/15 12:53:56 mef Exp $
 
 R_PKGNAME=     insight
-R_PKGVER=      0.17.1
+R_PKGVER=      0.19.2
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
 COMMENT=       Easy Access to Model Information for Various Model Objects

Index: pkgsrc/math/R-insight/distinfo
diff -u pkgsrc/math/R-insight/distinfo:1.4 pkgsrc/math/R-insight/distinfo:1.5
--- pkgsrc/math/R-insight/distinfo:1.4  Sat May 21 15:27:28 2022
+++ pkgsrc/math/R-insight/distinfo      Thu Jun 15 12:53:56 2023
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.4 2022/05/21 15:27:28 mef Exp $
+$NetBSD: distinfo,v 1.5 2023/06/15 12:53:56 mef Exp $
 
-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
+BLAKE2s (R/insight_0.19.2.tar.gz) = 27546bc02180e245ac4839c3c831f807e1efe13e610bb99f4c6447b3489b6e8c
+SHA512 (R/insight_0.19.2.tar.gz) = 05ca3c0552b6d33fb654c29c77379f546fd56836f853c919903298f840b07a2a02ab60c6f37d2a93a4e91fabe95b3c013b90e33910d3295069abf66857595839
+Size (R/insight_0.19.2.tar.gz) = 930723 bytes