Changelog • performance

performance 0.10.4

Changes to functions

icc() and r2_nakagawa() gain a ci_method argument, to either calculate confidence intervals using boot::boot() (instead of lmer::bootMer()) when ci_method = "boot" or analytical confidence intervals (ci_method = "analytical"). Use ci_method = "boot" when the default method fails to compute confidence intervals and use ci_method = "analytical" if bootstrapped intervals cannot be calculated at all. Note that the default computation method is preferred.
check_predictions() accepts a bandwidth argument (smoothing bandwidth), which is passed down to the plot() methods density-estimation.
check_predictions() gains a type argument, which is passed down to the plot() method to change plot-type (density or discrete dots/intervals). By default, type is set to "default" for models without discrete outcomes, and else type = "discrete_interval".
performance_accuracy() now includes confidence intervals, and reports those by default (the standard error is no longer reported, but still included).

Bug fixes

Fixed issue in check_collinearity() for fixest models that used i() to create interactions in formulas.

performance 0.10.3

CRAN release: 2023-04-07

New functions

item_discrimination(), to calculate the discrimination of a scale’s items.

Support for new models

model_performance(), check_overdispersion(), check_outliers() and r2() now work with objects of class fixest_multi (@etiennebacher, #554).
model_performance() can now return the “Weak instruments” statistic and p-value for models of class ivreg with metrics = "weak_instruments" (@etiennebacher, #560).
Support for mclogit models.

Changes to functions

test_*() functions now automatically fit a null-model when only one model objects was provided for testing multiple models.
Warnings in model_performance() for unsupported objects of class BFBayesFactor can now be suppressed with verbose = FALSE.
check_predictions() no longer fails with issues when re_formula = NULL for mixed models, but instead gives a warning and tries to compute posterior predictive checks with re_formuka = NA.
check_outliers() now also works for meta-analysis models from packages metafor and meta.
plot() for performance::check_model() no longer produces a normal QQ plot for GLMs. Instead, it now shows a half-normal QQ plot of the absolute value of the standardized deviance residuals.

Bug fixes

Fixed issue in print() method for check_collinearity(), which could mix up the correct order of parameters.

performance 0.10.2

CRAN release: 2023-01-12

General

Revised usage of insight::get_data() to meet forthcoming changes in the insight package.

Changes to functions

check_collinearity() now accepts NULL for the ci argument.

Bug fixes

Fixed issue in item_difficulty() with detecting the maximum values of an item set. Furthermore, item_difficulty() gets a maximum_value argument in case no item contains the maximum value due to missings.

performance 0.10.1

CRAN release: 2022-11-25

General

Minor improvements to the documentation.

Changes to functions

icc() and r2_nakagawa() get ci and iterations arguments, to compute confidence intervals for the ICC resp. R2, based on bootstrapped sampling.
r2() gets ci, to compute (analytical) confidence intervals for the R2.
The model underlying check_distribution() was now also trained to detect cauchy, half-cauchy and inverse-gamma distributions.
model_performance() now allows to include the ICC for Bayesian models.

Bug fixes

verbose didn’t work for r2_bayes() with BFBayesFactor objects.
Fixed issues in check_model() for models with convergence issues that lead to NA values in residuals.
Fixed bug in check_outliers whereby passing multiple elements to the threshold list generated an error (#496).
test_wald() now warns the user about inappropriate F test and calls test_likelihoodratio() for binomial models.
Fixed edge case for usage of parellel::detectCores() in check_outliers().

performance 0.10.0

CRAN release: 2022-10-03

Breaking Change

The minimum needed R version has been bumped to 3.6.
The alias performance_lrt() was removed. Use test_lrt() resp. test_likelihoodratio().

New functions

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

Changes to functions

check_normality(), check_homogeneity() and check_symmetry() now works for htest objects.
Print method for check_outliers() changed significantly: now states the methods, thresholds, and variables used, reports outliers per variable (for univariate methods) as well as any observation flagged for several variables/methods. Includes a new optional ID argument to add along the row number in the output (@rempsyc #443).
check_outliers() now uses more conventional outlier thresholds. The IQR and confidence interval methods now gain improved distance scores that are continuous instead of discrete.

Bug Fixes

Fixed wrong z-score values when using a vector instead of a data frame in check_outliers() (#476).
Fixed cronbachs_alpha() for objects from parameters::principal_component().

performance 0.9.2

CRAN release: 2022-08-10

General

print() methods for model_performance() and compare_performance() get a layout argument, which can be "horizontal" (default) or "vertical", to switch the layout of the printed table.
Improved speed performance for check_model() and some other performance_*() functions.
Improved support for models of class geeglm.

Changes to functions

check_model() gains a show_dots argument, to show or hide data points. This is particular useful for models with many observations, where generating the plot would be very slow.

Bug Fixes

Fixes wrong column names in model_performance() output for kmeans objects (#453)

performance 0.9.1

CRAN release: 2022-06-20

Breaking

The formerly “conditional” ICC in icc() is now named “unadjusted” ICC.

New functions

performance_cv() for cross-validated model performance.

Support for new models

Added support for models from package estimator.

Changes to functions

check_overdispersion() gets a plot() method.
check_outliers() now also works for models of classes gls and lme. As a consequence, check_model() will no longer fail for these models.
check_collinearity() now includes the confidence intervals for the VIFs and tolerance values.
model_performance() now also includes within-subject R2 measures, where applicable.
Improved handling of random effects in check_normality() (i.e. when argument effects = "random").

Bug fixes

check_predictions() did not work for GLMs with matrix-response.
check_predictions() did not work for logistic regression models (i.e. models with binary response) from package glmmTMB
item_split_half() did not work when the input data frame or matrix only contained two columns.
Fixed wrong computation of BIC in model_performance() when models had transformed response values.
Fixed issues in check_model() for GLMs with matrix-response.

performance 0.9.0

CRAN release: 2022-03-30

New functions

check_concurvity(), which returns GAM concurvity measures (comparable to collinearity checks).

Changes to functions

Check functions

check_predictions(), check_collinearity() and check_outliers() now support (mixed) regression models from BayesFactor.
check_zeroinflation() now also works for lme4::glmer.nb() models.
check_collinearity() better supports GAM models.

Test functions

test_performance() now calls test_lrt() or test_wald() instead of test_vuong() when package CompQuadForm is missing.
test_performance() and test_lrt() now compute the corrected log-likelihood when models with transformed response variables (such as log- or sqrt-transformations) are passed to the functions.

Model performance functions

performance_aic() now corrects the AIC value for models with transformed response variables. This also means that comparing models using compare_performance() allows comparisons of AIC values for models with and without transformed response variables.
Also, model_performance() now corrects both AIC and BIC values for models with transformed response variables.

Plotting and printing

The print() method for binned_residuals() now prints a short summary of the results (and no longer generates a plot). A plot() method was added to generate plots.
The plot() output for check_model() was revised:
- For binomial models, the constant variance plot was omitted, and a binned residuals plot included.
- The density-plot that showed normality of residuals was replaced by the posterior predictive check plot.

Bug fixes

model_performance() for models from lme4 did not report AICc when requested.
r2_nakagawa() messed up order of group levels when by_group was TRUE.

performance 0.8.0

CRAN release: 2021-10-01

Breaking Changes

The ci-level in r2() for Bayesian models now defaults to 0.95, to be in line with the latest changes in the bayestestR package.
S3-method dispatch for pp_check() was revised, to avoid problems with the bayesplot package, where the generic is located.

General

Minor revisions to wording for messages from some of the check-functions.
posterior_predictive_check() and check_predictions() were added as aliases for pp_check().

New functions

check_multimodal() and check_heterogeneity_bias(). These functions will be removed from the parameters packages in the future.

Changes to functions

r2() for linear models can now compute confidence intervals, via the ci argument.

Bug fixes

Fixed issues in check_model() for Bayesian models.
Fixed issue in pp_check() for models with transformed response variables, so now predictions and observed response values are on the same (transformed) scale.

performance 0.7.3

CRAN release: 2021-07-21

Changes to functions

check_outliers() has new ci (or hdi, eti) method to filter based on Confidence/Credible intervals.
compare_performance() now also accepts a list of model objects.
performance_roc() now also works for binomial models from other classes than glm.
Several functions, like icc() or r2_nakagawa(), now have an as.data.frame() method.
check_collinearity() now correctly handles objects from forthcoming afex update.

performance 0.7.2

CRAN release: 2021-05-17

New functions

performance_mae() to calculate the mean absolute error.

Bug fixes

Fixed issue with "data length differs from size of matrix" warnings in examples in forthcoming R 4.2.
Fixed issue in check_normality() for models with sample size larger than

5.000 observations.

Fixed issue in check_model() for glmmTMB models.
Fixed issue in check_collinearity() for glmmTMB models with zero-inflation, where the zero-inflated model was an intercept-only model.

performance 0.7.1

CRAN release: 2021-04-09

New supported models

Add support for model_fit (tidymodels).
model_performance supports kmeans models.

General

Give more informative warning when r2_bayes() for BFBayesFactor objects can’t be calculated.
Several check_*() functions now return informative messages for invalid model types as input.
r2() supports mhurdle (mhurdle) models.
Added print() methods for more classes of r2().
The performance_roc() and performance_accuracy() functions unfortunately had spelling mistakes in the output columns: Sensitivity was called Sensivity and Specificity was called Specifity. We think these are understandable mistakes :-)

Changes to functions

`check_model()`

check_model() gains more arguments, to customize plot appearance.
Added option to detrend QQ/PP plots in check_model().

`model_performance()`

The metrics argument from model_performance() and compare_performance() gains a "AICc" option, to also compute the 2nd order AIC.
"R2_adj" is now an explicit option in the metrics argument from model_performance() and compare_performance().

Other functions

The default-method for r2() now tries to compute an r-squared for all models that have no specific r2()-method yet, by using following formula: 1-sum((y-y_hat)^2)/sum((y-y_bar)^2))
The column name Parameter in check_collinearity() is now more appropriately named Term.

Bug fixes

test_likelihoodratio() now correctly sorts models with identical fixed effects part, but different other model parts (like zero-inflation).
Fixed incorrect computation of models from inverse-Gaussian families, or Gaussian families fitted with glm().
Fixed issue in performance_roc() for models where outcome was not 0/1 coded.
Fixed issue in performance_accuracy() for logistic regression models when method = "boot".
cronbachs_alpha() did not work for matrix-objects, as stated in the docs. It now does.

performance 0.7.0

CRAN release: 2021-02-03

General

Roll-back R dependency to R >= 3.4.

Breaking Changes

compare_performance() doesn’t return the models’ Bayes Factors, now returned by test_performance() and test_bf().

New functions to test or compare models

test_vuong(), to compare models using Vuong’s (1989) Test.
test_bf(), to compare models using Bayes factors.
test_likelihoodratio() as an alias for performance_lrt().
test_wald(), as a rough approximation for the LRT.
test_performance(), to run the most relevant and appropriate tests based on the input.

Changes to functions

`performance_lrt()`

performance_lrt() get an alias test_likelihoodratio().
Does not return AIC/BIC now (as they are not related to LRT per se and can be easily obtained with other functions).
Now contains a column with the difference in degrees of freedom between models.
Fixed column names for consistency.

`model_performance()`

Added more diagnostics to models of class ivreg.

Other functions

Revised computation of performance_mse(), to ensure that it’s always based on response residuals.
performance_aic() is now more robust.

Bug fixes

Fixed issue in icc() and variance_decomposition() for multivariate response models, where not all model parts contained random effects.
Fixed issue in compare_performance() with duplicated rows.
check_collinearity() no longer breaks for models with rank deficient model matrix, but gives a warning instead.
Fixed issue in check_homogeneity() for method = "auto", which wrongly tested the response variable, not the residuals.
Fixed issue in check_homogeneity() for edge cases where predictor had non-syntactic names.

performance 0.6.1

CRAN release: 2020-12-09

General

check_collinearity() gains a verbose argument, to toggle warnings and messages.

Bug fixes

Fixed examples, now using suggested packages only conditionally.

performance 0.6.0

CRAN release: 2020-12-01

General

model_performance() now supports margins, gamlss, stanmvreg and semLme.

New functions

r2_somers(), to compute Somers’ Dxy rank-correlation as R2-measure for logistic regression models.
display(), to print output from package-functions into different formats. print_md() is an alias for display(format = "markdown").

Changes to functions

`model_performance()`

model_performance() is now more robust and doesn’t fail if an index could not be computed. Instead, it returns all indices that were possible to calculate.
model_performance() gains a default-method that catches all model objects not previously supported. If model object is also not supported by the default-method, a warning is given.
model_performance() for metafor-models now includes the degrees of freedom for Cochran’s Q.

Other functions

performance_mse() and performance_rmse() now always try to return the (R)MSE on the response scale.
performance_accuracy() now accepts all types of linear or logistic regression models, even if these are not of class lm or glm.
performance_roc() now accepts all types of logistic regression models, even if these are not of class glm.
r2() for mixed models and r2_nakagawa() gain a tolerance-argument, to set the tolerance level for singularity checks when computing random effect variances for the conditional r-squared.

Bug fixes

Fixed issue in icc() introduced in the last update that make lme-models fail.
Fixed issue in performance_roc() for models with factors as response.

performance 0.5.1

CRAN release: 2020-10-29

Breaking changes

Column names for model_performance() and compare_performance() were changed to be in line with the easystats naming convention: LOGLOSS is now Log_loss, SCORE_LOG is Score_log and SCORE_SPHERICAL is now Score_spherical.

New functions

r2_posterior() for Bayesian models to obtain posterior distributions of R-squared.

Changes to functions

r2_bayes() works with Bayesian models from BayesFactor ( #143 ).
model_performance() works with Bayesian models from BayesFactor ( #150 ).
model_performance() now also includes the residual standard deviation.
Improved formatting for Bayes factors in compare_performance().
compare_performance() with rank = TRUE doesn’t use the BF values when BIC are present, to prevent “double-dipping” of the BIC values (#144).
The method argument in check_homogeneity() gains a "levene" option, to use Levene’s Test for homogeneity.

Bug fixes

Fix bug in compare_performance() when ... arguments were function calls to regression objects, instead of direct function calls.

performance 0.5.0

CRAN release: 2020-09-12

General

r2() and icc() support semLME models (package smicd).
check_heteroscedasticity() should now also work with zero-inflated mixed models from glmmTMB and GLMMadpative.
check_outliers() now returns a logical vector. Original numerical vector is still accessible via as.numeric().

New functions

pp_check() to compute posterior predictive checks for frequentist models.

Bug fixes

Fixed issue with incorrect labeling of groups from icc() when by_group = TRUE.
Fixed issue in check_heteroscedasticity() for mixed models where sigma could not be calculated in a straightforward way.
Fixed issues in check_zeroinflation() for MASS::glm.nb().
Fixed CRAN check issues.

performance 0.4.8

CRAN release: 2020-07-27

General

Removed suggested packages that have been removed from CRAN.

Changes to functions

icc() now also computes a “classical” ICC for brmsfit models. The former way of calculating an “ICC” for brmsfit models is now available as new function called variance_decomposition().

Bug fixes

Fix issue with new version of bigutilsr for check_outliers().
Fix issue with model order in performance_lrt().

performance 0.4.7

CRAN release: 2020-06-14

General

Support for models from package mfx.

Changes to functions

model_performance.rma() now includes results from heterogeneity test for meta-analysis objects.
check_normality() now also works for mixed models (with the limitation that studentized residuals are used).
check_normality() gets an effects-argument for mixed models, to check random effects for normality.

Bug fixes

Fixed issue in performance_accuracy() for binomial models when response variable had non-numeric factor levels.
Fixed issues in performance_roc(), which printed 1 - AUC instead of AUC.

performance 0.4.6

CRAN release: 2020-05-03

General

Minor revisions to model_performance() to meet changes in mlogit package.
Support for bayesx models.

Changes to functions

icc() gains a by_group argument, to compute ICCs per different group factors in mixed models with multiple levels or cross-classified design.
r2_nakagawa() gains a by_group argument, to compute explained variance at different levels (following the variance-reduction approach by Hox 2010).
performance_lrt() now works on lavaan objects.

Bug fixes

Fix issues in some functions for models with logical dependent variable.
Fix bug in check_itemscale(), which caused multiple computations of skewness statistics.
Fix issues in r2() for gam models.

performance 0.4.5

CRAN release: 2020-03-28

General

model_performance() and r2() now support rma-objects from package metafor, mlm and bife models.

Changes to functions

compare_performance() gets a bayesfactor argument, to include or exclude the Bayes factor for model comparisons in the output.
Added r2.aov().

Bug fixes

Fixed issue in performance_aic() for models from package survey, which returned three different AIC values. Now only the AIC value is returned.
Fixed issue in check_collinearity() for glmmTMB models when zero-inflated formula only had one predictor.
Fixed issue in check_model() for lme models.
Fixed issue in check_distribution() for brmsfit models.
Fixed issue in check_heteroscedasticity() for aov objects.
Fixed issues for lmrob and glmrob objects.