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Subject: CVS commit: pkgsrc/math/R-insight
From: Makoto Fujiwara
Date: 2023-06-15 14:53:56
Message id: 20230615125356.ED9F5FA89@cvs.NetBSD.org
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).
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