NEWS.md

parameters 0.12.1

New supported model classes

• blrm (rmsb), AKP, med1way, robtab (WRS2), epi.2by2 (epiR), mjoint (joineRML), mhurdle (mhurdle), sarlm (spatialreg), model_fit (tidymodels), BGGM (BGGM), mvord (mvord)

Changes to functions

model_parameters()

• model_parameters() for blavaan models is now fully treated as Bayesian model and thus relies on the functions from bayestestR (i.e. ROPE, Rhat or ESS are reported) .

• The effects-argument from model_parameters() for mixed models was revised and now shows the random effects variances by default (same functionality as random_parameters(), but mimicking the behaviour from broom.mixed::tidy()). When the group_level argument is set to TRUE, the conditional modes (BLUPs) of the random effects are shown.

• model_parameters() for mixed models now returns an Effects column even when there is just one type of "effects", to mimic the behaviour from broom.mixed::tidy(). In conjunction with standardize_names() users can get the same column names as in tidy() for model_parameters() objects.

• model_parameters() for t-tests now uses the group values as column names.

• print() for model_parameters() gains a zap_small argument, to avoid scientific notation for very small numbers. Instead, zap_small forces to round to the specified number of digits.

• To be internally consistent, the degrees of freedom column for lqm(m) and cgam(m) objects (with t-statistic) is called df_error.

• Minor improvements for models from quantreg.

• model_parameters supports rank-biserial, rank epsilon-squared, and Kendall's W as effect size measures for wilcox.test(), kruskal.test, and friedman.test, respectively.

Other functions

• describe_distribution() gets a quartiles argument to include 25th and 75th quartiles of a variable.

Bug fixes

• Fixed issue with non-initialized argument style in display() for compare_parameters().

• Make print() for compare_parameters() work with objects that have "simple" column names for confidence intervals with missing CI-level (i.e. when column is named "CI" instead of, say, "95% CI").

• Fixed issue with p_adjust in model_parameters(), which did not work for adjustment-methods "BY" and "BH".

• Fixed issue with show_sigma in print() for model_parameters().

• Fixed issue in model_parameters() with incorrect order of degrees of freedom.

parameters 0.12.0

General

• Roll-back R dependency to R >= 3.4.

• Bootstrapped estimates (from bootstrap_model() or bootstrap_parameters()) can be passed to emmeans to obtain bootstrapped estimates, contrasts, simple slopes (etc) and their CIs.

  • These can then be passed to model_parameters() and related functions to obtain standard errors, p-values, etc.

Breaking changes

• model_parameters() now always returns the confidence level for as additional CI column.

• The rule argument in equivalenct_test() defaults to "classic".

New supported model classes

• crr (cmprsk), leveneTest() (car), varest (vars), ergm (ergm), btergm (btergm), Rchoice (Rchoice), garch (tseries)

New functions

• compare_parameters() (and its alias compare_models()) to show / print parameters of multiple models in one table.

Changes to functions

• Estimation of bootstrapped p-values has been re-written to be more accurate.

• model_parameters() for mixed models gains an effects-argument, to return fixed, random or both fixed and random effects parameters.

• Revised printing for model_parameters() for metafor models.

• model_parameters() for metafor models now recognized confidence levels specified in the function call (via argument level).

• Improved support for effect sizes in model_parameters() from anova objects.

Bug fixes

• Fixed edge case when formatting parameters from polynomial terms with many degrees.

• Fixed issue with random sampling and dropped factor levels in bootstrap_model().

parameters 0.11.0

New supported model classes

• coxr (coxrobust), coeftest (lmtest), ivfixed (ivfixed), ivprobit (ivprobit), riskRegression (riskRegression), fitdistr (MASS), yuen, t1way, onesampb, mcp1 and mcp2 (WRS2), Anova.mlm (car), rqs (quantreg), lmodel2 (lmodel2), summary.lm, PMCMR, osrt and trendPMCMR (PMCMRplus), bamlss (bamlss).

New functions

Printing and table Formatting

• print_html() as an alias for display(format = "html"). This allows to print tabular outputs from data frames (as returned by most functions in parameters) into nicely rendered HTML markdown tables.

Changes to functions

• Added more effect size measures to model_parameters() for htest objects.

• model_parameters() for anova objects gains a power argument, to calculate the power for each parameter.

• ci() for models from lme4 and glmmTMB can now computed profiled confidence intervals, using method = "profile". Consequently, model_parameters() with df_method = "profile" also computes profiled confidence intervals. For models of class glmmTMB, option "uniroot" is also available.

Bug fixes

• model_parameters() for t-tests when standardize_d = TRUE, did not return columns for the group-specific means.

• Fixed issue in p_value() for fixest::feols().

• Fixed issue in model_parameters() for glmer() models with p-values that were calculated with df_method = "ml1" or df_method = "betwithin".

• Fixed issue in model_parameters() for multinomial models when response was a character vector (and no factor).

• Fixed issue in print_md() for model-parameters objects from Bayesian models.

• Fixed issues with printing of model parameters for multivariate response models from brms.

• Fixed issue with paired t-tests and model_parameters().

parameters 0.10.1

New functions

• format_p_adjust(), to create pretty names for p-adjustment methods.

Bug fixes

• Fixed breaking code / failing tests due to latest effectsize update.

• Fixed issue with model_parameters() for models of class mlm.

• Undocumented arguments digits, ci_digits and p_digits worked for print(), but not when directly called inside model_parameters(). Now, model_parameters(model, digits = 5, ci_digits = 8) works again.

• Fixed some minor printing-issues.

parameters 0.10.0

Breaking changes

• The default-method for effect sizes in model_parameters() for Anova-models (i.e. when arguments omega_squared, eta_squared or epsilon_squared are set to TRUE) is now "partial", as initially intended.

• Column names for degrees of freedom were revised. "df_residual" was replaced by the more generic "df_error". Moreover, models of class htest now also have the column name "df_error" and no longer "df" (where applicable).

• Some re-exports for functions that were moved to insight longer ago, were now removed.

New supported model classes

• Glm (rms), mediate (mediation).

• model_parameters() supports Gam models (gam), ridgelm (MASS), htest objects from oneway.test(), chisq.test(), prop.test(), mcnemar.test() and pairwise.htest objects, mcmc.list (e.g. from bayesGARCH).

New functions

Printing and table Formatting

• display(), to format output from package-functions into different formats.

• print_md() as an alias for display(format = "markdown"). This allows to print tabular outputs from data frames (as returned by most functions in parameters) into nicely rendered markdown tables.

• format(), to create a "pretty data frame" with nicer column names and formatted values. This is one of the worker-functions behind print() or print_md().

Changes to functions

model_parameters()

• model_parameters() for Anova-models (of class aov, anova etc.) gains a ci-argument, to add confidence intervals to effect size parameters.

• model_parameters() for htest objects gains a cramers_v and phi argument, to compute effect size parameters for objects from chisq.test(), and a standardized_D argument, to compute effect size parameters for objects from t.test().

• model_parameters() for metafor-models is more stable when called from inside functions.

• model_parameters() for metaBMA-models now includes prior information for the meta-parameters.

• model_parameters() for meta-analysis-models gains a include_studies-argument, to include or remove studies from the output.

• model_parameters() for gam-models now includes the residual df for smooth terms, and no longer the reference df.

• Slightly revised and improved the print() method for model_parameters().

Other functions

• describe_distribution() now includes the name of the centrality index in the CI-column, when centrality = "all".

• pool_parameters() gains a details-argument. For mixed models, and if details = TRUE, random effect variances will also be pooled.

Bug fixes

• Fixed issue in ci() for lme models with non-positive definite variance-covariance.

• Fixed issue in model_parameters() for nnet::multinom(), lqmm::lqm(), mgcv::gam(), and margins::margins() models, and models from package blme.

parameters 0.9.0

New supported model classes

• Support for maov (stats), HLfit (spaMM), scam (scam), preliminary support for emm_list (emmeans), merModList (merTools), meta_random, meta_bma and meta_fixed (metaBMA).

New functions

• pool_parameters(), to pool parameters estimates from multiple models.

• degroup(), as a more generic case for demean().

• center(), to center variables.

General

• Better support for (weighted) multivariate response models of class mlm for functions like model_parameters() or simulate_parameters().

• standardize_names() is now re-exported from the insight package.

Changes to functions

Printing model parameters

• print() for model_parameters() now names the coefficients column depending on the model type (i.e. "Odds Ratios" for logistic regression when exponentiate = TRUE etc.)

• print() for model_parameters() gains a show_sigma argument, to show or hide information on the residual standard deviation.

• print() for model_parameters() displays a message for Bayesian models, indicating which method to compute credible intervals was used.

Other changes

• data_partition() gets a seed argument, to explicitly set the seed before random sampling of test and training data.

• Revised parameters_table(), to improve readability of printed output.

Bug fixes

• Fixed issues in model_parameters() for vgam and mira objects.

• Fixed issue where model_parameters() for emmGrid objects falsely removed the Coefficient column.

• Fixed issue in parameters_type() for factors with different effects-coding than treatment contrasts.

• Fixed issues due to latest effectsize update.

parameters 0.8.6

Bug fixes

• Fixed issues with glmmTMB models with dispersion-parameter.

• Fixed issue where model_parameters() for glmmTMB models falsely removed the Component column.

• Fixed issue with missing CI columns in model_parameters() when standardize was one of the options except "refit".

• parameters_type() did not correctly detect interaction terms for specific patterns like scale() included in the interaction.

parameters 0.8.5

General

• Added vignette on model parameters and missing data.

• Update citation.

New supported model classes

• Support for mipo (mice), lqm and lqmm (lqmm). Preliminary support for semLME (smicd), mle2 (bbmle), mle (stats4)

• model_parameters() for objects of class mira (mice).

Changes to functions

• model_parameters() gets a specific behaviour for brms-meta-analysis models.

• model_parameters() for lavaan and blavaan now also prints self-defined parameters.

• model_parameters() for lavaan and blavaan gains more option for standardized parameters.

Bug fixes

• Fix issue in model_parameters() for coxph.penal models.

• Fix issue in model_parameters.metaplus() with random effects.

• Fix issue in check_heterogeneity() when x was a mixed model.

• Fix issue in check_heterogeneity() for data with missing values.

• Fix issue in dof_ml1() when random-effect terms where character vectors.

• Fix issue in print() method for model_parameters() that printed empty lines for rows with complete missing values. Empty lines are now removed.

• Fix issue in parameters_type() when exp() was used in a model formula.

parameters 0.8.2

New supported models

• metaplus (metaplus), glht (multcomp), glmm (glmm), manova (stats), crq and crqs (quantreg)

• Improved support for models from the rms package.

Changes to functions

• Improved parameters formatting for ordered factors in model_parameters() (and format_parameters()).

• Argument df_method can now also be applied to GLMs, to allow calculation of confidence intervals based on Wald-approximation, not profiled confidence intervals. This speeds up computation of CIs for models fit to large data sets.

• Improved select_parameters() for mixed models, and revised docs and associated vignette.

Bug fixes

• Allow threshold to be passed to efa_to_cfa() when the model is from factor_analysis().

• Allow correlation matrix to be passed to factor_analysis().

• Fix CRAN check issues.

• Fix issue in model_parameters() for models with non-estimable parameters or statistics.

• Fix issue in model_parameters() for plm models with only one parameter.

• Fix issue in check_heterogeneity() in case no predictor would cause heterogeneity bias.

• Make sure clubSandwich is used conditionally in all places, to properly pass CRAN checks.

parameters 0.8.0

New supported models

• robmixglm (robmixglm), betaor, betamfx, logitor, poissonirr, negbinirr, logitmfx, probitmfx, poissonmfx, negbinmfx (mfx), partial support emmGrid (emmeans)

Changes to functions

simulate_parameters() and simulate_model()

• has a nicer print() method.

• now also simulate parameters from the dispersion model for glmmTMB objects.

• gets a verbose argument, to show or hide warnings and messages.

Bug fixes

• fix issue with rank deficient models.

parameters 0.7.0

General

• We changed the computation of confidence intervals or standard errors, so these are now based on a t-distribution with degrees of freedom and not normal distribution assuming infinite degrees of freedom. This was implemented for most functions before and only affects few functions (like equivalence_test() or CIs for standardized parameters from model_parameters() when standardization method was "posthoc").

New supported models

• averaging (MuMIn), bayesx (R2BayesX), afex_aov (afex)

New functions

• check_heterogeneity() as a small helper to find variables that have a within- and between-effect related to a grouping variable (and thus, may result in heterogeneity bias, see this vignette).

Changes to functions

equivalence_test()

• gains a rule argument, so equivalence testing can be based on different approaches.

• for mixed models gains an effect argument, to perform equivalence testing on random effects.

• gains a p_values argument, to calculate p-values for the equivalence test.

• now supports more frequentist model objects.

describe_distribution()

• now works on grouped data frames.

• gains ci and iterations arguments, to compute confidence intervals based on bootstrapping.

• gains a iqr argument, to compute the interquartile range.

• SE column was removed.

model_parameters()

• model_parameters() for Stan-models (brms, rstanarm) gains a group_level argument to show or hide parameters for group levels of random effects.

• Improved accuracy of confidence intervals in model_parameters() with standardize = "basic" or standardize = "posthoc".

• model_parameters.merMod() no longer passes ... down to bootstrap-functions (i.e. when bootstrap = TRUE), as this might conflict with lme4::bootMer().

• For ordinal models (like MASS::polr() or ordinal::clm()), a Component column is added, indicating intercept categories ("alpha") and estimates ("beta").

• The select-argument from print.parameters_model() now gets a "minimal"-option as shortcut to print coefficients, confidence intervals and p-values only.

Other changes

• parameters_table() and print.parameters_model() now explicitly get arguments to define the digits for decimal places used in output.

• ci(), standard_error(), p_value() and model_parameters() for glmmTMB models now also works for dispersion models.

Bug fixes

• Fixed issue in equivalence_test() for mixed models.

• Fixed bug for model_parameters.anova(..., eta_squared = "partial") when called with non-mixed models.

• Fixed issue with wrong degrees of freedom in model_parameters() for gam models.

• Fixed issue with unused arguments in model_parameters().

parameters 0.6.1

General

• Remove 'Zelig' from suggested packages, as it was removed from CRAN.

Changes to functions

model_parameters()

• model_parameters() now also transforms standard errors when exponentiate = TRUE.

• model_parameters() for anova() from mixed models can now also compute effect sizes like eta squared.

• model_parameters() for aov() gains a type-argument to compute type-1, type-2 or type-3 sums of squares.

• model_parameters() for Bayesian models gains a standardize argument, to return standardized parameters from the posterior distribution.

• Improved print() method for model_parameters() for nested aov() (repeated measurements).

• You can now control whether demean() should add attributes to indicate within- and between-effects. This is only relevant for the print()-method of model_parameters().

Bug fixes

• Fixed model_parameters() for anova() from lmerTest models.

parameters 0.6.0

Breaking changes

• Alias model_bootstrap() was removed, please use bootstrap_model().

• Alias parameters_bootstrap() was removed, please use bootstrap_parameters().

• Alias model_simulate() was removed, please use simulate_model().

• Alias parameters_simulate() was removed, please use simulate_parameters().

• Alias parameters_selection() was removed, please use select_parameters().

• Alias parameters_reduction() was removed, please use reduce_parameters().

• Functions DDR(), ICA() and cmds() are no longer exported, as these were intended to be used internally by reduce_parameters() only.

• skewness() and kurtosis() always return a data frame.

New supported models

• Added support for arima (stats), bife (bife), bcplm and zcpglm (cplm)

Changes to functions

model_parameters()

• Improved print-method for model_parameters.brmsfit().

• Improved print-method for model_parameters.merMod() when fitting REWB-Models (see demean()).

• Improved efficiency for model_parameters() (for linear mixed models) when df_method = "kenward".

• model_parameters() gets a p_adjust-argument, to adjust p-values for multiple comparisons.

• Minor improvements for cluster_analysis() when method = "kmeans" and force = TRUE (factors now also work for kmeans-clustering).

p_value(), ci() and standard_error()

• p_value_kenward(), se_kenward() etc. now give a warning when model was not fitted by REML.

• Added ci(), standard_error() and p_value() for lavaan and blavaan objects.

• Added standard_error() for brmsfit and stanreg objects.

Other changes

• Run certain tests only locally, to reduce duration of CRAN checks.

• skewness(), kurtosis() and smoothness() get an iteration argument, to set the numbers of bootstrap replicates for computing standard errors.

• Improved print-method for factor_analysis().

• demean() now additionally converts factors with more than 2 levels to dummy-variables (binary), to mimic panelr-behaviour.

Bug fixes

• Fixed minor issue with the print()-method for model_parameters.befa().

• Fixed issues in model_parameters() (for linear mixed models) with wrong order of degrees of freedom when df_method was different from default.

• Fixed issues in model_parameters() (for linear mixed models) with accuracy of p-values when df_method = "kenward.

• Fixed issues in model_parameters() with wrong test statistic for lmerModLmerTest models.

• Fixed issue in format_parameters() (which is used to format output of model_parameters()) for factors, when variable name was also part of factor levels.

• Fixed issue in degrees_of_freedem() for logistf-models, which unintentionally printed the complete model summary.

• Fixed issue in model_parameters() for mlm models.

• Fixed issue in random_parameters() for uncorrelated random effects.