Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.28.1

Changes

• Methods for glmmTMB objects (ci(), model_parameters(), standard_error()) now support the vcov argument to compute robust standard errors.

• model_parameters() for marginaleffects objects is now more robust in detecting Bayesian models.

• Modified code base to address changes in the marginaleffects package from version 0.29.0 onwards.

Bug fixes

• Fixed issue with equivalence_test() for models of class glmmTMB with beta_family().

• exponentiate = TRUE in model_parameters() did not exponentiate location and scale parameters for models from package ordinal.

Scientific Software - Peer-reviewed - R
Published by strengejacke 4 months ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.28.0

Breaking Changes

• The experimental print_table() function was removed. The aim of this function was to test the implementation of the tinytable backend for printing. Now, tinytable is fully supported by insight::export_table() and thereby also by the various print() resp. display() methods for model parameters.

Changes

• All print_html() methods get an engine argument, to either use the gt package or the tinytable package for printing HTML tables. Since tinytable not only produces HTML tables, but rather different formats depending on the environment, print_html() may also generate a markdown table. Thus, the generic display() method can be used, too, which has a format argument that also supports "tt" for tinytable.

• Improved support for coxme models in model_parameters(). Random effects and group level estimates are now returned as well.

Bug fixes

• Fixed issue with models of class selection with multiple outcomes.

Scientific Software - Peer-reviewed - R
Published by strengejacke 5 months ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.27.0

Breaking Changes

• The standardize argument in factor_analysis() now defaults to FALSE.

• The rotation argument in factor_analysis() now defaults to "oblimin", because the former default of "none" rarely makes sense in the context of factor analysis. If you want to use no rotation, please set rotation = "none".

• The cor argument in n_factors() was renamed into correlation_matrix. In factor_analysis(), the cor argument was completely removed to avoid naming collision with the cor argument of psych::fa(), which now users can pass the cor argument to psych::fa() when using factor_analysis().

Changes

• factor_analysis() gets a .matrix method, including arguments n_obs and n_matrix, to compute factor analysis for a correlation matrix or covariance matrix.

• New function factor_scores() to extract factor scores from EFA (psych::fa() or factor_analysis()).

• Added and/or improved print-methods for all functions around PCA, FA and Omega.

• Improved efficiency in model_parameters() for models from packages brms and rstanarm.

• p_adjust for model_parameters() gets a new options, "sup-t", to calculate simultaneous confidence intervals.

Bug fixes

• bootstrap_model() did not work for intercept-only models. This has been fixed.

• Fixed issue with printing labels as pretty names for models from package pscl, i.e. print(model_parameters(model), pretty_names = "labels") now works as expected.

Scientific Software - Peer-reviewed - R
Published by strengejacke 6 months ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.26.0

Changes

• The effects argument in model_parameters() for classes merMod, glmmTMB, brmsfit and stanreg gets an additional "grouplevel" option, to return the group-level estimates for random effects.

• model_parameters() for Anova-objects gains a p_adjust argument, to apply p-adjustment where possible. Furthermore, for models from package afex, where p-adjustment was applied during model-fitting, the correct p-values are now returned (before, unadjusted p-values were returned in some cases).

• Revised code-base to address changes in latest insight update. Dealing with larger models (many parameters, many posterior samples) from packages brms and rstanarm is more efficient now. Furthermore, the options for the effects argument have a new behaviour. "all" only returns fixed effects and random effects variance components, but no longer the group level estimates. Use effects = "full" to return all parameters. This change is mainly to be more flexible and gain more efficiency for models with many parameters and / or many posterior draws.

• model_parameters() for Anova objects gains an include_intercept argument, to include intercepts in the Anova table, where possible.

Scientific Software - Peer-reviewed - R
Published by strengejacke 8 months ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.25.0

Changes

• model_parameters() for objects from the marginaleffects packages now calls bayestestR::describe_posterior() to process Bayesian models. This offers more flexibility in summarizing the posterior draws from marginaleffects.

• model_parameters() now shows a more informative coefficient name for binomial models with probit-link.

• Argument wb_component now defaults to FALSE.

• Improved support and printing for tests from package WRS2.

Bug fixes

• Fixed printing issue with model_parameters() for htest objects when printing into markdown or HTML format.

• Fixed printing issue with model_parameters() for mixed models when include_reference = TRUE.

Scientific Software - Peer-reviewed - R
Published by strengejacke 8 months ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.24.2

Changes

• The effects argument in model_parameters() for classes merMod, glmmTMB, brmsfit and stanreg gets an additional "random_total" option, to return the overall coefficient for random effects (sum of fixed and random effects).

Bug fixes

• Fixed issue in model_parameters() for objects from package marginaleffects where columns were renamed when their names equaled to certain reserved words.

Scientific Software - Peer-reviewed - R
Published by strengejacke 10 months ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.24.1

Changes

• model_parameters() now supports objects of class survfit.

• model_parameters() now gives informative error messages for more model classes than before when the function fails to extract model parameters.

• Improved information for credible intervals and sampling method from output of model_parameters() for Bayesian models.

Bug fixes

• Fixed issue when printing model_parameters() with models from mgcv::gam().

• Fixed issues due to breaking changes in the latest release of the datawizard package.

• Fixed issue with wrong column-header in printed output of model_parameters() for MASS::polr() models with probit-link.

Scientific Software - Peer-reviewed - R
Published by strengejacke 12 months ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.24.0

Breaking Changes

• The robust argument, which was deprecated for a long time, is now no longer supported. Please use vcov and vcov_args instead.

Changes

• Added support for coxph.panel models.

• Added support for anova() from models of the survey package.

• Documentation was re-organized and clarified, and the index reduced by removing redundant class-documentation.

Bug fixes

• Fixed bug in p_value() for objects of class averaging.

• Fixed bug when extracting 'pretty labels' for model parameters, which could fail when predictors were character vectors.

• Fixed bug with inaccurate standard errors for models from package fixest that used the sunab() function in the formula.

Scientific Software - Peer-reviewed - R
Published by strengejacke about 1 year ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.23.0

Breaking Changes

• Argument summary in model_parameters() is now deprecated. Please use include_info instead.

• Changed output style for the included additional information on model formula, sigma and R2 when printing model parameters. This information now also includes the RMSE.

Changes

• Used more accurate analytic approach to calculate normal distributions for the SGPV in equivalence_test() and used in p_significance().

• Added p_direction() methods for frequentist models. This is a convenient way to test the direction of the effect, which formerly was already (and still is) possible with pd = TRUE in model_parameters().

• p_function(), p_significance() and equivalence_test() get a vcov and vcov_args argument, so that results can be based on robust standard errors and confidence intervals.

• equivalence_test() and p_significance() work with objects returned by model_parameters().

• pool_parameters() now better deals with models with multiple components (e.g. zero-inflation or dispersion).

• Revision / enhancement of some documentation.

• Updated glmmTMB methods to work with the latest version of the package.

• Improved printing for simulate_parameters() for models from packages mclogit.

• print() for compare_parameters() now also puts factor levels into square brackets, like the print() method for model_parameters().

• include_reference now only adds the reference category of factors to the parameters table when those factors have appropriate contrasts (treatment or SAS contrasts).

Bug fixes

• Arguments like digits etc. were ignored in `model_parameters() for objects from the marginaleffects package.

Scientific Software - Peer-reviewed - R
Published by strengejacke about 1 year ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameter 0.22.2

New supported models

• Support for models glm_weightit, multinom_weightit and ordinal_weightit from package WeightIt.

Changes

• Added p_significance() methods for frequentist models.

• Methods for degrees_of_freedom() have been removed. degrees_of_freedom() now calls insight::get_df().

• model_parameters() for data frames and draws objects from package posterior also gets an exponentiate argument.

Bug fixes

• Fixed issue with warning for spuriously high coefficients for Stan-models (non-Gaussian).

Scientific Software - Peer-reviewed - R
Published by strengejacke over 1 year ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.22.1

Breaking changes

• Revised calculation of the second generation p-value (SGPV) in equivalence_test(), which should now be more accurate related to the proportion of the interval that falls inside the ROPE. Formerly, the confidence interval was simply treated as uniformly distributed when calculating the SGPV, now the interval is assumed to be normally distributed.

New supported models

• Support for svy2lme models from package svylme.

Changes

• standardize_parameters() now also prettifies labels of factors.

Bug fixes

• Fixed issue with equivalence_test() when ROPE range was not symmetrically centered around zero (e.g., range = c(-99, 0.1)).

• model_parameters() for anova() from mixed models now also includes the denominator degrees of freedom in the output (df_error).

• print(..., pretty_names = "labels") for tobit-models from package AER now include value labels, if available.

• Patch release, to ensure that performance runs with older version of datawizard on Mac OS X with R (old-release).

Scientific Software - Peer-reviewed - R
Published by strengejacke over 1 year ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.22.0

Breaking changes

• Deprecated arguments in model_parameters() for htest, aov and BFBayesFactor objects were removed.

• Argument effectsize_type is deprecated. Please use es_type now. This change was necessary to avoid conflicts with partial matching of argument names (here: effects).

New supported models

• Support for objects from stats::Box.test().

• Support for glmgee models from package glmtoolbox.

Bug fix

• Fixed edge case in predict() for factor_analysis().

• Fixed wrong ORCID in DESCRIPTION.

Scientific Software - Peer-reviewed - R
Published by strengejacke over 1 year ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.21.7

Changes

• Fixed issues related to latest release from marginaleffects.

Bug fixes

• Fixes issue in compare_parameters() for models from package blme.

• Fixed conflict in model_parameters() when both include_reference = TRUE and pretty_names = "labels" were used. Now, pretty labels are correctly updated and preserved.

Scientific Software - Peer-reviewed - R
Published by strengejacke over 1 year ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.21.6

New supported models

• Support for models of class serp (serp).

Changes

• include_reference can now directly be set to TRUE in model_parameters() and doesn't require a call to print() anymore.

• compare_parameters() gains a include_reference argument, to add the reference category of categorical predictors to the parameters table.

• print_md() for compare_parameters() now by default uses the tinytable package to create markdown tables. This allows better control for column heading spanning over multiple columns.

Bug fixes

• Fixed issue with parameter names for model_parameters() and objects from package epiR.

• Fixed issue with exponentiate = TRUE for model_parameters() with models of class clmm (package ordinal), when model had no component column (e.g., no scale or location parameters were returned).

• include_reference now also works when factor were created "on-the-fly" inside the model formula (i.e. y ~ as.factor(x)).

Scientific Software - Peer-reviewed - R
Published by strengejacke almost 2 years ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.21.5

Bug fixes

• Fixes CRAN check errors related to the changes in the latest update of marginaleffects.

Scientific Software - Peer-reviewed - R
Published by strengejacke almost 2 years ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.21.4

Breaking changes

• The exponentiate argument of model_parameters() for marginaleffects::predictions() now defaults to FALSE, in line with all the other model_parameters() methods.

Changes

• model_parameters() for models of package survey now gives informative messages when bootstrap = TRUE (which is currently not supported).

• n_factors() now also returns the explained variance for the number of factors as attributes.

• model_parameters() for objects of package metafor now warns when unsupported arguments (like vcov) are used.

• Improved documentation for pool_parameters().

Bug fixes

• print(include_reference = TRUE) for model_parameters() did not work when run inside a pipe-chain.

• Fixed issues with format() for objects returned by compare_parameters() that included mixed models.

Scientific Software - Peer-reviewed - R
Published by strengejacke almost 2 years ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.21.3

Changes

• principal_components() and factor_analysis() now also work when argument n = 1.

• print_md() for compare_parameters() now gains more arguments, similar to the print() method.

• bootstrap_parameters() and model_parameters() now accept bootstrapped samples returned by bootstrap_model().

• The print() method for model_parameters() now also yields a warning for models with logit-links when possible issues with (quasi) complete separation occur.

Bug fixes

• Fixed issue in print_html() for objects from package ggeffects.

• Fixed issues for nnet::multinom() with wide-format response variables (using cbind()).

• Minor fixes for print_html() method for model_parameters().

• Robust standard errors (argument vcov) now works for plm models.

Scientific Software - Peer-reviewed - R
Published by strengejacke about 2 years ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.21.2

Changes

• Minor improvements to factor analysis functions.

• The ci_digits argument of the print() method for model_parameters() now defaults to the same value of digits.

• model_parameters() for objects from package marginaleffects now also accepts the exponentiate argument.

• The print(), print_html(), print_md() and format() methods for model_parameters() get an include_reference argument, to add the reference category of categorical predictors to the parameters table.

Bug fixes

• Fixed issue with wrong calculation of test-statistic and p-values in model_parameters() for fixest models.

• Fixed issue with wrong column header for glm models with family = binomial("identiy").

• Minor fixes for dominance_analysis().

Scientific Software - Peer-reviewed - R
Published by strengejacke over 2 years ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.21.1

General

• Added support for models of class nestedLogit (nestedLogit).

Changes to functions

• model_parameters() now also prints correct "pretty names" when predictors where converted to ordered factors inside formulas, e.g. y ~ as.ordered(x).

• model_parameters() now prints a message when the vcov argument is provided and ci_method is explicitly set to "profile". Else, when vcov is not NULL and ci_method is NULL, it defaults to "wald", to return confidence intervals based on robust standard errors.

Scientific Software - Peer-reviewed - R
Published by strengejacke over 2 years ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.21.0

Breaking Changes

• It is no longer possible to calculate Satterthwaite-approximated degrees of freedom for mixed models from package nlme. This was based on the lavaSearch2 package, which no longer seems to support models of class lme.

Changes to functions

• Improved support for objects of class mipo for models with ordinal or categorical outcome.

Scientific Software - Peer-reviewed - R
Published by strengejacke over 2 years ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.20.3

General

• Added support for models of class hglm (hglm), mblogit (mclogit), fixest_multi (fixest), and phylolm / phyloglm (phylolm).

• as.data.frame methods for extracting posterior draws via bootstrap_model() have been retired. Instead, directly using bootstrap_model() is recommended.

Changes to functions

• equivalence_test() gets a method for ggeffects objects from package ggeffects.

• equivalence_test() now prints the SGPV column instead of % in ROPE. This is because the former % in ROPE actually was equivalent to the second generation p-value (SGPV) and refers to the proportion of the range of the confidence interval that is covered by the ROPE. However, % in ROPE did not refer to the probability mass of the underlying distribution of a confidence interval that was covered by the ROPE, hence the old column name was a bit misleading.

• Fixed issue in model_parameters.ggeffects() to address forthcoming changes in the ggeffects package.

Bug fixes

• When an invalid or not supported value for the p_adjust argument in model_parameters() is provided, the valid options were not shown in correct capital letters, where appropriate.

• Fixed bug in cluster_analysis() for include_factors = TRUE.

• Fixed warning in model_parameters() and ci() for models from package glmmTMB when ci_method was either "profile" or "uniroot".

Scientific Software - Peer-reviewed - R
Published by strengejacke almost 3 years ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.20.2

General

• Reduce unnecessary warnings.

• The deprecated argument df_method in model_parameters()was removed.

• Output from model_parameters() for objects returned by manova() and car::Manova() is now more consistent.

Bug fix

• Fixed issues in tests for mmrm models.

• Fixed issue in bootstrap_model() for models of class glmmTMB with dispersion parameters.

• Fixed failing examples.

Scientific Software - Peer-reviewed - R
Published by strengejacke almost 3 years ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.20.1

General

• Added support for models of class flic and flac (logistf), mmrm (mmrm).

Changes

• model_parameters() now includes a Group column for stanreg or brmsfit models with random effects.

• The print() method for model_parameters() now uses the same pattern to print random effect variances for Bayesian models as for frequentist models.

Bug fix

• Fixed issue with the print() method for compare_parameters(), which duplicated random effects parameters rows in some edge cases.

• Fixed issue with the print() method for compare_parameters(), which didn't work properly when ci=NULL.

Scientific Software - Peer-reviewed - R
Published by strengejacke almost 3 years ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.20.0

Breaking

• The deprecated argument df_method in model_parameters() is now defunct and throws an error when used.

• The deprecated functions ci_robust(), p_robust() and standard_error_robust have been removed. These were superseded by the vcov argument in ci(), p_value(), and standard_error(), respectively.

• The style argument in compare_parameters() was renamed into select.

New functions

• p_function(), to print and plot p-values and compatibility (confidence) intervals for statistical models, at different levels. This allows to see which estimates are most compatible with the model at various compatibility levels.

• p_calibrate(), to compute calibrated p-values.

Changes

• model_parameters() and compare_parameters() now use the unicode character for the multiplication-sign as interaction mark (i.e. \u00d7). Use options(parameters_interaction = <value>) or the argument interaction_mark to use a different character as interaction mark.

• The select argument in compare_parameters(), which is used to control the table column elements, now supports an experimental glue-like syntax. See this vignette Printing Model Parameters. Furthermore, the select argument can also be used in the print() method for model_parameters().

• print_html() gets a font_size and line_padding argument to tweak the appearance of HTML tables. Furthermore, arguments select and column_labels are new, to customize the column layout of tables. See examples in ?display.

• Consolidation of vignettes on standardization of model parameters.

• Minor speed improvements.

Bug fix

• model_parameters().BFBayesFactor no longer drops the BF column if the Bayes factor is NA.

• The print() and display() methods for model_parameters() from Bayesian models now pass the ... to insight::format_table(), allowing extra arguments to be recognized.

• Fixed footer message regarding the approximation method for CU and p-values for mixed models.

• Fixed issues in the print() method for compare_parameters() with mixed models, when some models contained within-between components (see wb_component) and others did not.

Scientific Software - Peer-reviewed - R
Published by strengejacke about 3 years ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.19.0

Breaking

• Arguments that calculate effectsize in model_parameters() for htest, Anova objects and objects of class BFBayesFactor were revised. Instead of single arguments for the different effectsizes, there is now one argument, effectsize_type. The reason behind this change is that meanwhile many new type of effectsizes have been added to the effectsize package, and the generic argument allows to make use of those effect sizes.

• The attribute name in PCA / EFA has been changed from data_set to dataset.

• The minimum needed R version has been bumped to 3.6.

• Removed deprecated argument parameters from model_parameters().

• standard_error_robust(), ci_robust() and p_value_robust() are now deprecated and superseded by the vcov and vcov_args arguments in the related methods standard_error(), ci() and p_value(), respectively.

• Following functions were moved from package parameters to performance: check_sphericity_bartlett(), check_kmo(), check_factorstructure() and check_clusterstructure().

Changes to functions

• Added sparse option to principal_components() for sparse PCA.

• The pretty_names argument from the print() method can now also be "labels", which will then use variable and value labels (if data is labelled) as pretty names. If no labels were found, default pretty names are used.

• bootstrap_model() for models of class glmmTMB and merMod gains a cluster argument to specify optional clusters when the parallel option is set to "snow".

• P-value adjustment (argument p_adjust in model_parameters()) is now performed after potential parameters were removed (using keep or drop), so adjusted p-values is only applied to the parameters of interest.

• Robust standard errors are now supported for fixest models with the vcov argument.

• print() for model_parameters() gains a footer argument, which can be used to suppress the footer in the output. Further more, if footer = "" or footer = FALSE in print_md(), no footer is printed.

• simulate_model() and simulate_parameters() now pass ... to insight::get_varcov(), to allow simulated draws to be based on heteroscedasticity consistent variance covariance matrices.

• The print() method for compare_parameters() was improved for models with multiple components (e.g., mixed models with fixed and random effects, or models with count- and zero-inflation parts). For these models, compare_parameters(effects = "all", component = "all") prints more nicely.

Bug fixes

• Fix erroneous warning for p-value adjustments when the differences between original and adjusted p-values were very small.

Scientific Software - Peer-reviewed - R
Published by strengejacke over 3 years ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.18.2

New functions

• New function dominance_analysis(), to compute dominance analysis statistics and designations.

Changes to functions

• Argument ci_random in model_parameters() defaults to NULL. It uses a heuristic to determine if random effects confidence intervals are likely to take a long time to compute, and automatically includes or excludes those confidence intervals. Set ci_random to TRUE or FALSE to explicitly calculate or omit confidence intervals for random effects.

Bug fixes

• Fix issues in pool_parameters() for certain models with special components (like MASS::polr()), that failed when argument component was set to "conditional" (the default).

• Fix issues in model_parameters() for multiple imputation models from package Hmisc.

Scientific Software - Peer-reviewed - R
Published by strengejacke over 3 years ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.8.3

Release for JOSS

Scientific Software - Peer-reviewed - R
Published by strengejacke over 5 years ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.8.2

Scientific Software - Peer-reviewed - R
Published by strengejacke over 5 years ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - parameters 0.8.1

Scientific Software - Peer-reviewed - R
Published by strengejacke over 5 years ago

Extracting, Computing and Exploring the Parameters of Statistical Models using R - 0.2.0

• CRAN Release (0.2.0)

Scientific Software - Peer-reviewed - R
Published by DominiqueMakowski over 6 years ago