Deprecated functions and changes in selectors functions
all_categorical() are now compatible
with gtsummary version ≥ 2.0.0 (#270)scope_tidy() to scope a tidy tibble
allowing to tidy select (#270).select_to_varnames(),
.formula_list_to_named_list(),
.generic_selector() and .is_selector_scoped()
are now deprecated and will be removed in a future release: you may
consider cards::process_selectors() and
cards::process_formula_selectors() as alternatives
(#270)Fixes
model_get_model_frame.coxph() has been fixed to return
a correct model frame a subject identifier is passed to
survival::coxph() (#268)Documentation
New features
model_matrix_attr in
tidy_and_attach() and tidy_plus_plus() to
attach model frame and model matrix to the model as attributes for
saving some execution time (#254)tidy_add_n() now returns n_ind the number
of individuals, in addition to the number of observations (#251)tidy_parameters() calls now
parameters::model_parameters() with
pretty_names = FALSE for saving execution time (#259)|>),
requiring therefore R >= 4.2 (#262)Deprecated support
biglmm::bigglm() not supported anymore as
biglmm has been removed from CRANDeprecated functions
tidy_marginal_means() is now deprecated, following
deprecation of marginaleffects::marginal_means(). Use
instead tidy_marginal_predictions() with the option
newdata = "marginalmeans".tidy_margins() is now indicated as superseded and may
be deprecated if margins is removed from CRAN.
tidy_avg_slopes() could be used as an alternative.
(#252)Fixes
tidy_multgee() has been fixed to properly identify the
different y.levels (#260 @jackmwolf)tidy_marginal_predictions() has been updated to avoid
the use of the deprecated function
marginaleffects::datagridcf() (#256)New supported models
mmrm::mmrm() models (#228)survival::cch() models (#242)New features
tidy_post_fun argument in
tidy_plus_plus() (#235)Fix
tidy_marginal_predictions() (#245)supported_modelstidy_parameters() for mixed models
(#238)survey::svyglm() models with replicate
weights (#240)New features
MASS::contr.sdif() contrasts (#230)pscl::zeroinfl() and
pscl::hurdle() models (#232)betareg::betareg() models (#234)Fix
packageVersion() should be a character string
(#225)New features
tidy_add_estimate_to_reference_rows() now also populate
p-values and confidence intervals for sum contrasts (#220)nnet::multinom(), MASS::polr(),
ordinal::clm() and ordinal::clmm() models, as
long as the type of models is supported by the corresponding package,
for example, margins does not currently support
nnet::multinom() models (#215)Improvements
marginaleffects version 0.10.0 (#216)New features
broom.helpers functions.tidy_marginal_predictions(),
plot_marginal_predictions(),
tidy_all_effects(), and tidy_ggpredict()tidy_marginal_means()tidy_avg_comparisons() and
tidy_marginal_contrasts()tidy_avg_slopes()
and tidy_margins()model_list_higher_order_variables() to list
the highest order combinations of variables (#202)model_get_response_variable() to get the
name of the response variable (#202)seq_range() to generate a sequence
of values between the minimum and the maximum of a vector (#202)contrasts_adjust in
tidy_plus_plus(),
tidy_add_pairwise_contrasts() and
model_get_pairwise_contrasts() allowing to change the
adjustment method used to compute pairwise contrasts (#204)New features
tidy_add_pairwise_contrasts() and
model_get_pairwise_contrasts() to compute pairwise
contrasts of categorical variables with emmeans, and
corresponding new arguments in tidy_plus_plus() (#192)tidy_margins() to display Average Marginal
Effects (#195)tidy_all_effects() to display Marginal
Predictions (#195)tidy_ggpredict() to display Conditional
Predictions (#195)Bug fixes and improvements
exponentiate argument is not
appropriate (#197)New features
tidy_select_variables() now sorts the variables
according to include (#183)New supported models
logitr::logitr() models (#179)multgee::nomLORgee() and
multgee::ordLORgee() models (#185)Bug fixes and improvements
.get_package_dependencies() to be more
efficient. It now looks only at a single package description file
(#178).get_all_packages_dependencies() to list
all dependencies of all packages (#178).get_min_version_required() (#181)New features
.get_package_dependencies() listing all
dependencies, including minimum version required, of a package.
(#171).assert_package() now taking into
account the comparison operator (> or >=) when a minimum version
is required (#171)Bug fixes and improvements
tidyselect v1.2.0
(#173)mgcv::gam() models
(#175)New supported models
parsnip::model_fit objects (#161)biglm::bigglm() and
biglmm::bigglm() models (#155)fixest::feglm(),
fixest::femlm(), fixest::feols() and
fixest::feNmlm() (requires R>=4.1) (#167)New features
dplyr::vars() (also exported by
{gtsummary}) as a selector has now been deprecated. Users will be warned
that support for vars() will eventually be removed from the
package (#154).is_selector_scoped(), an internal function used in
generating custom selector functions, is now exported (#163)New features
.assert_package() now uses
rlang::check_installed() and
rlang::is_installed() to check whether needed packages are
installed. The rlang::check_installed() prompts user to
install needed package when run interactively. (#147)tidy_add_n() and model_get_n() support for
tidycmprsk::crr() models (#143)supported_models tibble (#145)Bug fixes
tidy_add_n() to
a mgcv::gam() model with smooth terms (#150)New supported models
plm::plm() models (#140)New features
.formula_list_to_named_list() now respects the
select_single= argument for all inputs types. Previously,
named lists were ignored..formula_list_to_named_list(null_allowed=) argument that
works in conjunction with type_check= asserting the
class/type of the RHS of the formula (or the value of the named list)
(#137).formula_list_to_named_list()
(#136)all_ran_pars() and
all_ran_vals()Bug fixes
.formula_list_to_named_list(type_check=) checks
RHS of a formula and the value of named list. (#138)New features
model_get_coefficients_type.tidycrr()
(#128)broom.helpers::tidy_parameters() to include the package
prefix. This message sometimes appears while running
gtsummary::tbl_regression() where some users may not be
aware where the tidy_paramters() function lives.
(#129).formula_list_to_named_list() improvement: it is now
possible to add a type check (#132).assert_package() and
.get_min_version_required() to check for a package’s
installation status and whether the installed version meets the minimum
required version from the DESCRIPTION file (#134)Bug fixes
nnet::multinom() models with a binary
outcome (#130)New supported models
glmmTMB::glmmTMB() models (#119)New features
list(trt ~ 1, all_continuous() ~ 2).~ <value> may be now used to
indicate everything() ~ <value>Bug fixes
lme4::glmer() (#116)New supported models
rstanarm::stan_glm() modelsVGAM::vglm() models (#105)New features
tidy_parameters() based on
parameters::model_parameters() (#104)tidy_with_broom_or_parameters()
(#104)tidy_plus_plus() now uses
tidy_with_broom_or_parameters()model_get_coefficients_type() now returns “prop_hazard”
for cloglog-binomial models (#106)Bug fixes
tidy_add_n() works with multinomial models when
y is not coded as a factor (#109)glue added to SuggestsNew features
model_get_coefficients_type() now returns
“relative_risk” for log-binomial models (#101)tidy_disambiguate_terms() for
disambiguating random-effect terms in mixed models and new options for
tidy_plus_plus(): disambiguate_terms
(TRUE by default) and disambiguate_sep
(#98)var_type column is now equal to
"ran_pars" or "ran_vals" for random-effect
parameters and values, based of the effect column returned
by broom.mixed::tidy() (#90)model_list_contrasts()tidy_add_n() to add the number of
observations (and for relevant models the number of events and exposure
time) (#64)add_n in tidy_plus_plus()
(#64)model_get_n(),
model_get_weights(), model_get_offset(),
model_get_response() and
model_compute_terms_contributions() (#64)New supported models
lfe::felm() models (#79)brms::brm() models (#89)cmprsk::crr() models (#91)stats::nls() models (#97)mgcv::gam() models. (#82)Bug fixes and other changes
strict argument removed
from tidy_identify_variables() (#99)usethis::ui_*() messaging with
cli::cli_*() (#94)tidy_add_term_labels() for variables with
non standard names (#77)rmarkdown
(#95)var_type
returned by tidy_identify_variables() is now equal to
"dichotomous" for categorical variables with only 2
levelstidy_identify_variables() now populates
variable column by term content, instead of
NA (#66)tidy_identify_variables(), the
variable column is now populated with the content of the
term column (#63).generic_selector(): makes it easy to create selecting
functions like all_continuous()..select_to_varnames(): converts selecting syntax into
character varnames.formula_list_to_named_list(): takes the formula
selecting syntax and converts it to a named list.all_continuous(),
all_categorical(), all_dichotomous(),
all_contrasts(), all_intercepts() and
all_interaction() for selecting variables from models
(#54)tidy_fun= (#49 @ddsjoberg)tidy_select_variables() to keep/drop
selected variables in the output (#45)tidy_add_coefficients_type() and
model_get_coefficients_type to get the type of coefficients
(generic, logistic, Poisson or proportional hazard) used by a model
(#46)tidy_add_contrasts() and
model_list_contrasts() now return an additional column
contrasts_typeno_reference_row argument for
tidy_add_reference_rows() (#47)model_get_nlevels to get the number of
levels of categorical variablesvar_nlevels returned by
tidy_identify_variables(),
model_identify_variables() and
tidy_plus_plus()model_list_terms_levels() and
categorical_terms_pattern in tidy_plus_plus()
and tidy_add_term_labels (#61)model_list_terms_levels() now returns additional
columns (level, reference_level,
contrasts_type, var_label,
var_levels and dichotomous)model_list_variables() now returns an additional
var_label columnexponentiate argument is now passed to the
tidy_*() functions, as an attribute attached to the tibble,
as well as custom labels (variable_labels and
term_labels)show_single_row argument now accepts tidyselect
notation (#51 @ddsjoberg)tidy_add_estimate_to_reference_rows() now relies on
emmeans for sum contrasts, allowing to cover a wider range
of modelstidy_* functions also inherits of
"broom.helpers" class (#56)interaction_sep argument has been added to
tidy_plus_plus().clean_backticks() and .escape_regex() are
now exportedtidy_add_header_rows() for
nnet::multinom models: label for header rows was missing
(#50)tidy_identify_variables() correctly
identify class “integer” for this type of variables (#57)tidy_add_header_rows() for continuous
variables with a non standard name (#70)