ggcoef_model | R Documentation |
ggcoef_model()
, ggcoef_table()
, ggcoef_dodged()
,
ggcoef_faceted()
and ggcoef_compare()
use broom.helpers::tidy_plus_plus()
to obtain a tibble
of the model coefficients,
apply additional data transformation and then pass the
produced tibble
to ggcoef_plot()
to generate the plot.
ggcoef_model(
model,
tidy_fun = broom.helpers::tidy_with_broom_or_parameters,
tidy_args = NULL,
conf.int = TRUE,
conf.level = 0.95,
exponentiate = FALSE,
variable_labels = NULL,
term_labels = NULL,
interaction_sep = " * ",
categorical_terms_pattern = "{level}",
add_reference_rows = TRUE,
no_reference_row = NULL,
intercept = FALSE,
include = dplyr::everything(),
group_by = broom.helpers::auto_group_by(),
group_labels = NULL,
add_pairwise_contrasts = FALSE,
pairwise_variables = broom.helpers::all_categorical(),
keep_model_terms = FALSE,
pairwise_reverse = TRUE,
emmeans_args = list(),
significance = 1 - conf.level,
significance_labels = NULL,
show_p_values = TRUE,
signif_stars = TRUE,
return_data = FALSE,
...
)
ggcoef_table(
model,
tidy_fun = broom.helpers::tidy_with_broom_or_parameters,
tidy_args = NULL,
conf.int = TRUE,
conf.level = 0.95,
exponentiate = FALSE,
variable_labels = NULL,
term_labels = NULL,
interaction_sep = " * ",
categorical_terms_pattern = "{level}",
add_reference_rows = TRUE,
no_reference_row = NULL,
intercept = FALSE,
include = dplyr::everything(),
group_by = broom.helpers::auto_group_by(),
group_labels = NULL,
add_pairwise_contrasts = FALSE,
pairwise_variables = broom.helpers::all_categorical(),
keep_model_terms = FALSE,
pairwise_reverse = TRUE,
emmeans_args = list(),
significance = 1 - conf.level,
significance_labels = NULL,
show_p_values = FALSE,
signif_stars = FALSE,
table_stat = c("estimate", "ci", "p.value"),
table_header = NULL,
table_text_size = 3,
table_stat_label = NULL,
ci_pattern = "{conf.low}, {conf.high}",
table_witdhs = c(3, 2),
...
)
ggcoef_dodged(
model,
tidy_fun = broom.helpers::tidy_with_broom_or_parameters,
tidy_args = NULL,
conf.int = TRUE,
conf.level = 0.95,
exponentiate = FALSE,
variable_labels = NULL,
term_labels = NULL,
interaction_sep = " * ",
categorical_terms_pattern = "{level}",
add_reference_rows = TRUE,
no_reference_row = NULL,
intercept = FALSE,
include = dplyr::everything(),
group_by = broom.helpers::auto_group_by(),
group_labels = NULL,
significance = 1 - conf.level,
significance_labels = NULL,
return_data = FALSE,
...
)
ggcoef_faceted(
model,
tidy_fun = broom.helpers::tidy_with_broom_or_parameters,
tidy_args = NULL,
conf.int = TRUE,
conf.level = 0.95,
exponentiate = FALSE,
variable_labels = NULL,
term_labels = NULL,
interaction_sep = " * ",
categorical_terms_pattern = "{level}",
add_reference_rows = TRUE,
no_reference_row = NULL,
intercept = FALSE,
include = dplyr::everything(),
group_by = broom.helpers::auto_group_by(),
group_labels = NULL,
significance = 1 - conf.level,
significance_labels = NULL,
return_data = FALSE,
...
)
ggcoef_compare(
models,
type = c("dodged", "faceted"),
tidy_fun = broom.helpers::tidy_with_broom_or_parameters,
tidy_args = NULL,
conf.int = TRUE,
conf.level = 0.95,
exponentiate = FALSE,
variable_labels = NULL,
term_labels = NULL,
interaction_sep = " * ",
categorical_terms_pattern = "{level}",
add_reference_rows = TRUE,
no_reference_row = NULL,
intercept = FALSE,
include = dplyr::everything(),
add_pairwise_contrasts = FALSE,
pairwise_variables = broom.helpers::all_categorical(),
keep_model_terms = FALSE,
pairwise_reverse = TRUE,
emmeans_args = list(),
significance = 1 - conf.level,
significance_labels = NULL,
return_data = FALSE,
...
)
ggcoef_plot(
data,
x = "estimate",
y = "label",
exponentiate = FALSE,
y_labeller = NULL,
point_size = 2,
point_stroke = 2,
point_fill = "white",
colour = NULL,
colour_guide = TRUE,
colour_lab = "",
colour_labels = ggplot2::waiver(),
shape = "significance",
shape_values = c(16, 21),
shape_guide = TRUE,
shape_lab = "",
errorbar = TRUE,
errorbar_height = 0.1,
errorbar_coloured = FALSE,
stripped_rows = TRUE,
strips_odd = "#11111111",
strips_even = "#00000000",
vline = TRUE,
vline_colour = "grey50",
dodged = FALSE,
dodged_width = 0.8,
facet_row = "var_label",
facet_col = NULL,
facet_labeller = "label_value",
plot_title = NULL
)
model |
a regression model object |
tidy_fun |
( |
tidy_args |
Additional arguments passed to
|
conf.int |
( |
conf.level |
the confidence level to use for the confidence
interval if |
exponentiate |
if |
variable_labels |
( |
term_labels |
( |
interaction_sep |
( |
categorical_terms_pattern |
( |
add_reference_rows |
( |
no_reference_row |
( |
intercept |
( |
include |
( |
group_by |
( |
group_labels |
( |
add_pairwise_contrasts |
( |
pairwise_variables |
( |
keep_model_terms |
( |
pairwise_reverse |
( |
emmeans_args |
( |
significance |
level (between 0 and 1) below which a
coefficient is consider to be significantly different from 0
(or 1 if |
significance_labels |
optional vector with custom labels for significance variable |
show_p_values |
if |
signif_stars |
if |
return_data |
if |
... |
parameters passed to |
table_stat |
statistics to display in the table, use any column name
returned by the tidier or |
table_header |
optional custom headers for the table |
table_text_size |
text size for the table |
table_stat_label |
optional named list of labeller functions for the displayed statistic (see examples) |
ci_pattern |
glue pattern for confidence intervals in the table |
table_witdhs |
relative widths of the forest plot and the coefficients table |
models |
named list of models |
type |
a dodged plot, a faceted plot or multiple table plots? |
data |
a data frame containing data to be plotted,
typically the output of |
x , y |
variables mapped to x and y axis |
y_labeller |
optional function to be applied on y labels (see examples) |
point_size |
size of the points |
point_stroke |
thickness of the points |
point_fill |
fill colour for the points |
colour |
optional variable name to be mapped to colour aesthetic |
colour_guide |
should colour guide be displayed in the legend? |
colour_lab |
label of the colour aesthetic in the legend |
colour_labels |
labels argument passed to
|
shape |
optional variable name to be mapped to the shape aesthetic |
shape_values |
values of the different shapes to use in
|
shape_guide |
should shape guide be displayed in the legend? |
shape_lab |
label of the shape aesthetic in the legend |
errorbar |
should error bars be plotted? |
errorbar_height |
height of error bars |
errorbar_coloured |
should error bars be colored as the points? |
stripped_rows |
should stripped rows be displayed in the background? |
strips_odd |
color of the odd rows |
strips_even |
color of the even rows |
vline |
should a vertical line be drawn at 0 (or 1 if
|
vline_colour |
colour of vertical line |
dodged |
should points be dodged (according to the colour aesthetic)? |
dodged_width |
width value for |
facet_row |
variable name to be used for row facets |
facet_col |
optional variable name to be used for column facets |
facet_labeller |
labeller function to be used for labeling facets;
if labels are too long, you can use |
plot_title |
an optional plot title |
For more control, you can use the argument return_data = TRUE
to
get the produced tibble
, apply any transformation of your own and
then pass your customized tibble
to ggcoef_plot()
.
A ggplot2
plot or a tibble
if return_data = TRUE
.
ggcoef_table()
: a variation of ggcoef_model()
adding a table
with estimates, confidence intervals and p-values
ggcoef_dodged()
: a dodged variation of ggcoef_model()
for
multi groups models
ggcoef_faceted()
: a faceted variation of ggcoef_model()
for
multi groups models
ggcoef_compare()
: designed for displaying several models on the same
plot.
ggcoef_plot()
: plot a tidy tibble
of coefficients
vignette("ggcoef_model")
mod <- lm(Sepal.Length ~ Sepal.Width + Species, data = iris)
ggcoef_model(mod)
ggcoef_table(mod)
ggcoef_table(mod, table_stat = c("estimate", "ci"))
ggcoef_table(
mod,
table_stat_label = list(
estimate = scales::label_number(.001)
)
)
ggcoef_table(mod, table_text_size = 5, table_witdhs = c(1, 1))
# a logistic regression example
d_titanic <- as.data.frame(Titanic)
d_titanic$Survived <- factor(d_titanic$Survived, c("No", "Yes"))
mod_titanic <- glm(
Survived ~ Sex * Age + Class,
weights = Freq,
data = d_titanic,
family = binomial
)
# use 'exponentiate = TRUE' to get the Odds Ratio
ggcoef_model(mod_titanic, exponentiate = TRUE)
ggcoef_table(mod_titanic, exponentiate = TRUE)
# display intercepts
ggcoef_model(mod_titanic, exponentiate = TRUE, intercept = TRUE)
# customize terms labels
ggcoef_model(
mod_titanic,
exponentiate = TRUE,
show_p_values = FALSE,
signif_stars = FALSE,
add_reference_rows = FALSE,
categorical_terms_pattern = "{level} (ref: {reference_level})",
interaction_sep = " x ",
y_labeller = scales::label_wrap(15)
)
# display only a subset of terms
ggcoef_model(mod_titanic, exponentiate = TRUE, include = c("Age", "Class"))
# do not change points' shape based on significance
ggcoef_model(mod_titanic, exponentiate = TRUE, significance = NULL)
# a black and white version
ggcoef_model(
mod_titanic,
exponentiate = TRUE,
colour = NULL, stripped_rows = FALSE
)
# show dichotomous terms on one row
ggcoef_model(
mod_titanic,
exponentiate = TRUE,
no_reference_row = broom.helpers::all_dichotomous(),
categorical_terms_pattern =
"{ifelse(dichotomous, paste0(level, ' / ', reference_level), level)}",
show_p_values = FALSE
)
data(tips, package = "reshape")
mod_simple <- lm(tip ~ day + time + total_bill, data = tips)
ggcoef_model(mod_simple)
# custom variable labels
# you can use the labelled package to define variable labels
# before computing model
if (requireNamespace("labelled")) {
tips_labelled <- tips |>
labelled::set_variable_labels(
day = "Day of the week",
time = "Lunch or Dinner",
total_bill = "Bill's total"
)
mod_labelled <- lm(tip ~ day + time + total_bill, data = tips_labelled)
ggcoef_model(mod_labelled)
}
# you can provide custom variable labels with 'variable_labels'
ggcoef_model(
mod_simple,
variable_labels = c(
day = "Week day",
time = "Time (lunch or dinner ?)",
total_bill = "Total of the bill"
)
)
# if labels are too long, you can use 'facet_labeller' to wrap them
ggcoef_model(
mod_simple,
variable_labels = c(
day = "Week day",
time = "Time (lunch or dinner ?)",
total_bill = "Total of the bill"
),
facet_labeller = ggplot2::label_wrap_gen(10)
)
# do not display variable facets but add colour guide
ggcoef_model(mod_simple, facet_row = NULL, colour_guide = TRUE)
# works also with with polynomial terms
mod_poly <- lm(
tip ~ poly(total_bill, 3) + day,
data = tips,
)
ggcoef_model(mod_poly)
# or with different type of contrasts
# for sum contrasts, the value of the reference term is computed
if (requireNamespace("emmeans")) {
mod2 <- lm(
tip ~ day + time + sex,
data = tips,
contrasts = list(time = contr.sum, day = contr.treatment(4, base = 3))
)
ggcoef_model(mod2)
}
# multinomial model
mod <- nnet::multinom(grade ~ stage + trt + age, data = gtsummary::trial)
ggcoef_model(mod, exponentiate = TRUE)
ggcoef_table(mod, group_labels = c(II = "Stage 2 vs. 1"))
ggcoef_dodged(mod, exponentiate = TRUE)
ggcoef_faceted(mod, exponentiate = TRUE)
library(pscl)
data("bioChemists", package = "pscl")
mod <- zeroinfl(art ~ fem * mar | fem + mar, data = bioChemists)
ggcoef_model(mod)
ggcoef_table(mod)
ggcoef_dodged(mod)
ggcoef_faceted(
mod,
group_labels = c(conditional = "Count", zero_inflated = "Zero-inflated")
)
mod2 <- zeroinfl(art ~ fem + mar | 1, data = bioChemists)
ggcoef_table(mod2)
ggcoef_table(mod2, intercept = TRUE)
# Use ggcoef_compare() for comparing several models on the same plot
mod1 <- lm(Fertility ~ ., data = swiss)
mod2 <- step(mod1, trace = 0)
mod3 <- lm(Fertility ~ Agriculture + Education * Catholic, data = swiss)
models <- list(
"Full model" = mod1,
"Simplified model" = mod2,
"With interaction" = mod3
)
ggcoef_compare(models)
ggcoef_compare(models, type = "faceted")
# you can reverse the vertical position of the point by using a negative
# value for dodged_width (but it will produce some warnings)
ggcoef_compare(models, dodged_width = -.9)
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