data-raw/old/e_plot_model_contrasts_20230304.R
In erikerhardt/erikmisc: Erik Erhardt's miscellaneous functions for solving complex data analysis workflows
#' Compute and plot all contrasts and test results from a linear model by automating the use of emmeans tables and plots.
#'
#' Variable labels can be provided by labelling your data with the labelled::var_label() command.
#'
#' Plot interpretation:
#' This EMM plot (Estimated Marginal Means, aka Least-Squares Means) is only
#' available when conditioning on one variable. The blue bars are confidence
#' intervals for the EMMs; don't ever use confidence intervals for EMMs to perform
#' comparisons --- they can be very misleading. The red arrows are for the
#' comparisons between means; the degree to which the "comparison arrows" overlap
#' reflects as much as possible the significance of the comparison of the two
#' estimates. If an arrow from one mean overlaps an arrow from another group, the
#' difference is not significant, based on the adjust setting (which defaults to
#' "tukey").
#'
#' @param fit (required) model object: lm, glm, lmerModLmerTest (from \code{lme4::lmer}, or lmerMod (from \code{lmerTest::as_lmerModLmerTest})
#' @param dat_cont (required) data used for the lm object (only used for variable labels using labelled::var_label()
#' @param choose_contrasts is a list of effects to plot, such as c("hp", "vs:wt"); NULL does all in model.
#' @param sw_table_in_plot T/F put table of results in caption of plot
#' @param adjust_method see `?emmeans::summary.emmGrid`
#' @param CI_level level from `?emmeans::emmeans`
#' @param sw_glm_scale for glm fit, choose results on the "link" (default) or "response" scale
#' @param sw_print T/F whether to print results as this function runs
#' @param sw_marginal_even_if_interaction T/F whether to also calculate marginal results when involved in interaction(s)
#' @param sw_TWI_plots_keep two-way interaction plots are plotted for each variable conditional on the other. Plots are created separately ("singles") or together in a grid ("both"), and "all" keeps the singles and the grid version.
#' @param sw_TWI_both_orientation "tall" or "wide" orientation for when both two-way interaction plots are combined in a grid
#' @param sw_plot_quantiles_values "quantiles" or "values" to specify whether to plot quantiles of the numeric variable or specified values
#' @param plot_quantiles quantiles plotted for numeric:numeric interaction plots, if \code{sw_plot_quantiles_values} is "quantiles"
#' @param sw_quantile_type quantile type as specified in \code{?stats::quantile}.
#' @param plot_values a named list for values plotted for a single specified numeric:numeric interaction plot, if \code{sw_plot_quantiles_values} is "values". Specify a specific contrast, for example: \code{choose_contrasts = "disp:hp"}. Then specify the values for each variable, for example: \code{plot_values = list(hp = c(75, 100, 150, 200, 250), disp = c(80, 120, 200, 350, 450))}
#' @param emmip_rg.limit from emmeans package, increase from 10000 if "Error: The rows of your requested reference grid would be 10000, which exceeds the limit of XXXXX (not including any multivariate responses)."
#'
#' @return out a list of three lists: "plots", "tables" , and "text", each have results for each contrast that was computed. "plots" is a list of ggplot objects to plot separately or arrange in a grid. "tables" is a list of emmeans tables to print. "text" is the caption text for the plots.
#' @import dplyr
#' @import ggplot2
#' @import emmeans
#' @importFrom labelled var_label
#' @importFrom stringr fixed
#' @importFrom stringr str_detect
#' @importFrom stringr str_split
#' @importFrom stringr str_split_fixed
#' @importFrom gridExtra arrangeGrob
#' @importFrom ggpubr as_ggplot
#' @importFrom purrr pluck
#' @importFrom stats as.formula
#' @importFrom stats quantile
#' @importFrom stats anova
#' @importFrom stats terms.formula
#' @importFrom cowplot plot_grid
#' @export
#'
#' @examples
#' # Data for testing
#' dat_cont <-
#' dat_mtcars_e
#'
#' # Set specific model with some interactions
#' form_model <-
#' mpg ~ cyl + disp + hp + wt + vs + am + cyl:vs + disp:hp + hp:vs
#'
#' fit <-
#' lm(
#' formula = form_model
#' , data = dat_cont
#' )
#'
#' car::Anova(fit) #, type = 3)
#' summary(fit)
#'
#' # all contrasts from model
#' fit_contrasts <-
#' e_plot_model_contrasts(
#' fit = fit
#' , dat_cont = dat_cont
#' , sw_print = FALSE
#' , sw_table_in_plot = FALSE
#' , sw_TWI_plots_keep = "singles"
#' , sw_quantile_type = 1
#' )
#' fit_contrasts$tables # to print tables
#' fit_contrasts$plots # to print plots
#' fit_contrasts$text # to print caption text
#'
#'
#' ## To plot all contrasts in a plot grid:
#' # Since plot interactions have sublists of plots, we want to pull those out
#' # into a one-level plot list.
#' # The code here works for sw_TWI_plots_keep = "singles"
#' # which will make each plot the same size in the plot_grid() below.
#' # For a publications, you'll want to manually choose which plots to show.
#'
#' # index for plot list,
#' # needed since interactions add 2 plots to the list, so the number of terms
#' # is not necessarily the same as the number of plots.
#' i_list <- 0
#' # initialize a list of plots
#' p_list <- list()
#'
#' for (i_term in 1:length(fit_contrasts$plots)) {
#' ## i_term = 1
#'
#' # extract the name of the plot
#' n_list <- names(fit_contrasts$plots)[i_term]
#'
#' # test whether the name has a colon ":"; if so, it's an interaction
#' if (stringr::str_detect(string = n_list, pattern = stringr::fixed(":"))) {
#' # an two-way interaction has two plots
#'
#' # first plot
#' i_list <- i_list + 1
#' p_list[[ i_list ]] <- fit_contrasts$plots[[ i_term ]][[ 1 ]]
#'
#' # second plot
#' i_list <- i_list + 1
#' p_list[[ i_list ]] <- fit_contrasts$plots[[ i_term ]][[ 2 ]]
#'
#' } else {
#' # not an interaction, only one plot
#'
#' i_list <- i_list + 1
#' p_list[[ i_list ]] <- fit_contrasts$plots[[ i_term ]]
#'
#' } # if
#' } # for
#'
#' p_arranged <-
#' cowplot::plot_grid(
#' plotlist = p_list
#' , nrow = NULL
#' , ncol = 3
#' , labels = "AUTO"
#' )
#'
#' p_arranged |> print()
#'
#'
#'
#'
#'
#' # one specific numeric:numeric contrast with specified values
#' fit_contrasts <-
#' e_plot_model_contrasts(
#' fit = fit
#' , dat_cont = dat_cont
#' , choose_contrasts = "disp:hp"
#' , sw_table_in_plot = TRUE
#' , adjust_method = c("none", "tukey", "scheffe", "sidak", "bonferroni"
#' , "dunnettx", "mvt")[4] # see ?emmeans::summary.emmGrid
#' , CI_level = 0.95
#' , sw_glm_scale = c("link", "response")[1]
#' , sw_print = FALSE
#' , sw_marginal_even_if_interaction = TRUE
#' , sw_TWI_plots_keep = c("singles", "both", "all")[3]
#' , sw_TWI_both_orientation = c("tall", "wide")[1]
#' , sw_plot_quantiles_values = c("quantiles", "values")[2] # for numeric:numeric plots
#' , plot_quantiles = c(0.05, 0.25, 0.50, 0.75, 0.95) # for numeric:numeric plots
#' , sw_quantile_type = 1
#' , plot_values = list(hp = c(75, 100, 150, 200, 250)
#' , disp = c(80, 120, 200, 350, 450)) # for numeric:numeric plots
#' )
#' fit_contrasts$plots$`disp:hp`$both
#'
#'
#' \dontrun{
#' ## GLM on logit and probability scales
#'
#' dat_cont <-
#' dat_cont |>
#' dplyr::mutate(
#' am_01 =
#' dplyr::case_when(
#' am == "manual" ~ 0
#' , am == "automatic" ~ 1
#' )
#' )
#' labelled::var_label(dat_cont[["am_01"]]) <- labelled::var_label(dat_cont[["am"]])
#'
#' # numeric:factor interaction
#' fit_glm <-
#' glm(
#' cbind(am_01, 1 - am_01) ~
#' vs + hp + vs:hp
#' , family = binomial
#' , data = dat_cont
#' )
#'
#' car::Anova(fit_glm, type = 3)
#' summary(fit_glm)
#'
#' # all contrasts from model, logit scale
#' fit_contrasts <-
#' e_plot_model_contrasts(
#' fit = fit_glm
#' , dat_cont = dat_cont
#' , sw_glm_scale = c("link", "response")[1]
#' , sw_print = FALSE
#' , sw_marginal_even_if_interaction = TRUE
#' , sw_TWI_plots_keep = "both"
#' )
#' fit_contrasts
#'
#' # all contrasts from model, probability scale
#' fit_contrasts <-
#' e_plot_model_contrasts(
#' fit = fit_glm
#' , dat_cont = dat_cont
#' , sw_glm_scale = c("link", "response")[2]
#' , sw_print = FALSE
#' , sw_marginal_even_if_interaction = TRUE
#' , sw_TWI_plots_keep = "both"
#' )
#' fit_contrasts
#'
#'
#' # numeric:numeric interaction
#' fit_glm <-
#' glm(
#' cbind(am_01, 1 - am_01) ~
#' disp + hp + disp:hp
#' , family = binomial
#' , data = dat_cont
#' )
#'
#' car::Anova(fit_glm, type = 3)
#' summary(fit_glm)
#'
#' fit_contrasts <-
#' e_plot_model_contrasts(
#' fit = fit_glm
#' , dat_cont = dat_cont
#' , sw_glm_scale = c("link", "response")[2]
#' , sw_print = FALSE
#' , sw_TWI_plots_keep = "both"
#' )
#' fit_contrasts
#'
#'
#' # factor:factor interaction
#' fit_glm <-
#' glm(
#' cbind(am_01, 1 - am_01) ~
#' vs + cyl + vs:cyl
#' , family = binomial
#' , data = dat_cont
#' )
#'
#' car::Anova(fit_glm) #, type = 3)
#' summary(fit_glm)
#'
#' fit_contrasts <-
#' e_plot_model_contrasts(
#' fit = fit_glm
#' , dat_cont = dat_cont
#' , sw_glm_scale = c("link", "response")[2]
#' , sw_print = FALSE
#' , sw_TWI_plots_keep = "both"
#' )
#' fit_contrasts
#'
#'
#' ## lme4::lmer mixed-effects model
#' fit_lmer <-
#' lme4::lmer(
#' formula = Reaction ~ Days + (Days | Subject)
#' , data = lme4::sleepstudy
#' )
#'
#' fit_lmer_contrasts <-
#' e_plot_model_contrasts(
#' fit = fit_lmer
#' , dat_cont = lme4::sleepstudy
#' , sw_print = FALSE
#' , sw_table_in_plot = FALSE
#' )
#' fit_lmer_contrasts
#'
#'
#' ## lmerTest::as_lmerModLmerTest mixed-effects model
#'
#' fit_lmer <-
#' lmerTest::as_lmerModLmerTest(fit_lmer)
#'
#' fit_lmer_contrasts <-
#' e_plot_model_contrasts(
#' fit = fit_lmer
#' , dat_cont = lme4::sleepstudy
#' , sw_print = FALSE
#' , sw_table_in_plot = FALSE
#' )
#' fit_lmer_contrasts
#' }
#'
e_plot_model_contrasts <-
function(
fit = NULL
, dat_cont = NULL
, choose_contrasts = NULL
, sw_table_in_plot = TRUE
, adjust_method = c("none", "tukey", "scheffe", "sidak", "bonferroni", "dunnettx", "mvt")[4] # see ?emmeans::summary.emmGrid
, CI_level = 0.95
, sw_glm_scale = c("link", "response")[1]
, sw_print = TRUE
, sw_marginal_even_if_interaction = FALSE
, sw_TWI_plots_keep = c("singles", "both", "all")[3]
, sw_TWI_both_orientation = c("wide", "tall")[1]
, sw_plot_quantiles_values = c("quantiles", "values")[1] # for numeric:numeric plots
, plot_quantiles = c(0.05, 0.25, 0.50, 0.75, 0.95) # for numeric:numeric plots
, sw_quantile_type = 7
, plot_values = NULL # for numeric:numeric plots
, emmip_rg.limit = 10000
) {
###### START Example dataset for testing
##
## library(tidyverse)
##
## choose_contrasts = NULL
## sw_table_in_plot = TRUE
## adjust_method = c("none", "tukey", "scheffe", "sidak", "bonferroni", "dunnettx", "mvt")[4] # see ?emmeans::summary.emmGrid
## CI_level = 0.95
## sw_print = TRUE
## sw_marginal_even_if_interaction = TRUE
## sw_TWI_plots_keep = c("singles", "both", "all")[3]
## sw_TWI_both_orientation = c("tall", "wide")[1]
## sw_plot_quantiles_values = c("quantiles", "values")[1] # for numeric:numeric plots
## plot_quantiles = c(0.05, 0.25, 0.50, 0.75, 0.95) # for numeric:numeric plots
## plot_values = c(-1, 0, 1) # for numeric:numeric plots
##
## # Data for testing
## dat_cont <-
## dat_mtcars_e |>
## as_tibble(
## rownames = "model"
## ) |>
## mutate(
## cyl = cyl |> factor(levels = c(4, 6, 8), labels = c("four", "six", "eight"))
## , vs = vs |> factor(levels = c(0, 1), labels = c("V-shaped", "straight"))
## , am = am |> factor(levels = c(0, 1), labels = c("automatic", "manual"))
## )
##
## # Label columns
## dat_labels <-
## tribble(
## ~var, ~label
## , "model" , "Model"
## , "mpg" , "Miles/(US) gallon"
## , "cyl" , "Number of cylinders"
## , "disp" , "Displacement (cu.in.)"
## , "hp" , "Gross horsepower"
## , "drat" , "Rear axle ratio"
## , "wt" , "Weight (1000 lbs)"
## , "qsec" , "1/4 mile time"
## , "vs" , "Engine" # (0 = V-shaped, 1 = straight)"
## , "am" , "Transmission" # (0 = automatic, 1 = manual)"
## , "gear" , "Number of forward gears"
## , "carb" , "Number of carburetors"
## )
##
## for (i_row in 1:nrow(dat_labels)) {
## labelled::var_label(dat_cont[[dat_labels[["var"]][i_row] ]]) <- dat_labels[["label"]][i_row]
## }
##
## ## form_model <-
## ## stats::as.formula(
## ## paste0(
## ## "mpg"
## ## , " ~ "
## ## , "("
## ## , " cyl"
## ## , " + disp"
## ## , " + hp"
## ## #, " + drat"
## ## , " + wt"
## ## #, " + qsec"
## ## , " + vs"
## ## , " + am"
## ## , " + gear"
## ## , " + carb"
## ## , ")^2" # all two-way interaction pairs
## ## )
## ## )
## ##
## ## fit <-
## ## lm(
## ## formula = form_model
## ## , data = dat_cont
## ## )
## ##
## ## ## AIC
## ## # option: test="F" includes additional information
## ## # for parameter estimate tests that we're familiar with
## ## # option: for BIC, include k=log(nrow( [data.frame name] ))
## ## fit <-
## ## step(
## ## fit
## ## , direction = "both"
## ## , test = "F"
## ## , k = log(nrow( dat_cont ))
## ## , trace = 0
## ## )
##
## # Set specific model with some interactions
## form_model <-
## mpg ~ cyl + disp + hp + wt + vs + am + cyl:vs + disp:hp + hp:vs
##
##
## fit <-
## lm(
## formula = form_model
## , data = dat_cont
## )
## stats::anova(fit)
## summary(fit)
##
##
## e_plot_model_contrasts(
## fit = fit
## , dat_cont = dat_cont
## , choose_contrasts = NULL
## , sw_table_in_plot = TRUE
## , adjust_method = c("none", "tukey", "scheffe", "sidak", "bonferroni", "dunnettx", "mvt")[4] # see ?emmeans::summary.emmGrid
## , CI_level = 0.95
## , sw_print = TRUE
## , sw_marginal_even_if_interaction = TRUE
## , sw_TWI_plots_keep = c("singles", "both", "all")[3]
## , sw_TWI_both_orientation = c("tall", "wide")[1]
## , plot_quantiles = c(0.05, 0.25, 0.50, 0.75, 0.95) # for numeric:numeric plots
## )
##
##
## e_plot_model_contrasts(
## fit = fit
## , dat_cont = dat_cont
## , choose_contrasts = "disp:hp"
## , sw_table_in_plot = TRUE
## , adjust_method = c("none", "tukey", "scheffe", "sidak", "bonferroni", "dunnettx", "mvt")[4] # see ?emmeans::summary.emmGrid
## , CI_level = 0.95
## , sw_print = TRUE
## , sw_marginal_even_if_interaction = TRUE
## , sw_TWI_plots_keep = c("singles", "both", "all")[1]
## , sw_TWI_both_orientation = c("tall", "wide")[1]
## , sw_plot_quantiles_values = c("quantiles", "values")[2] # for numeric:numeric plots
## , plot_quantiles = c(0.05, 0.25, 0.50, 0.75, 0.95) # for numeric:numeric plots
## , plot_values = list(hp = c(75, 100, 150, 200, 250), disp = c(80, 120, 200, 350, 450)) # for numeric:numeric plots
## )
##
##
###### END Example dataset for testing
# give error if two main inputs aren't specified
if (is.null(fit) | is.null(dat_cont)) {
stop("erikmisc::e_plot_model_contrasts() \"fit\" and \"dat_cont\" arguments are required.")
return(NULL)
}
# indicates, "lm", "glm", or "lmerMod" (future, another method based on the call)
fit_model_type <-
#as.character(fit$call)[1]
class(fit)[1]
if (fit_model_type %notin% c("lm", "glm", "lmerModLmerTest", "lmerMod")) {
message(paste0("e_plot_model_contrasts: fit class\"", fit_model_type, "\" not tested."))
}
# BEGIN Capture warnings to take actions
message_involve_interaction <-
"NOTE: Results may be misleading due to involvement in interactions\n"
# END Capture warnings to take actions
# confidence limits (CL) column names differ depending on method and rank deficiency
# provide a list of possibilities to look for from the summary tables
col_names_LCL <- c("lower.CL", "asymp.LCL")
col_names_UCL <- c("upper.CL", "asymp.UCL")
# subset to include only complete observations for variables used
if (fit_model_type %in% c("lm")) {
temp_var_list <- names(attr(fit$terms, "dataClasses"))
dat_cont <- na.omit(dat_cont[, temp_var_list])
rm(temp_var_list)
}
if (fit_model_type %in% c("glm")) {
temp_var_list <- names(attr(fit$terms, "dataClasses"))
# strip variable name out of cbind() statement
if(any(stringr::str_detect(temp_var_list, stringr::fixed("cbind(")))) {
temp_ind <- which(stringr::str_detect(temp_var_list, stringr::fixed("cbind(")))
temp_var_list[temp_ind] <-
stringr::str_split(
stringr::str_split(
string = temp_var_list[temp_ind]
, pattern = stringr::fixed("cbind(")
, simplify = TRUE
)[2]
, pattern = stringr::fixed(",")
, simplify = TRUE
)[1]
}
dat_cont <- na.omit(dat_cont[, temp_var_list])
rm(temp_var_list, temp_ind)
}
if (fit_model_type %in% c("lmerModLmerTest", "lmerMod")) {
temp_var_list <- names(fit@frame)
dat_cont <- na.omit(dat_cont[, temp_var_list])
rm(temp_var_list)
}
# check for label, create label if unlabelled
for (n_col in names(dat_cont)) {
## n_col = names(dat_cont)[1]
if (is.null(labelled::var_label(dat_cont[[n_col]]))) {
labelled::var_label(dat_cont[[n_col]]) <- n_col
}
}
# labelled::var_label(fit$model[[1]])
# extract variables
var_name_y <-
as.character(formula(fit))[2]
var_name_x <-
stringr::str_split(
string = attr(terms.formula(formula(fit)), "term.labels") #as.character(formula(fit))[3]
, pattern = stringr::fixed(" + ")
) |>
unlist()
if (fit_model_type == "glm" & stringr::str_detect(var_name_y, pattern = stringr::fixed("cbind("))) {
# the y-variable usually looks like "cbind(y, 1-y)", so strip out the variable name
var_name_y <-
var_name_y |>
stringr::str_split_fixed(
pattern = stringr::fixed(",")
, n = 2
) |>
as.character() |>
purrr::pluck(1) |>
stringr::str_split_fixed(
pattern = stringr::fixed("cbind(")
, n = 2
) |>
as.character() |>
purrr::pluck(2)
}
# restrict to chosen contrasts
if (!is.null(choose_contrasts)) {
# for chosen contrasts, copy and reverse order of two-way interactions
# to make sure there's a match
## https://stackoverflow.com/questions/49141253/how-to-reverse-the-delimited-parts-of-a-string
choose_contrasts_rev <-
sapply(
stringr::str_split(
string = choose_contrasts
, pattern = stringr::fixed(":")
)
, function(x) {
paste0(rev(x), collapse = ":")
}
)
# restrict to chosen
var_name_x <-
var_name_x[which(var_name_x %in% c(choose_contrasts, choose_contrasts_rev))]
}
# output list of tables and plots
out <- list()
out[["tables"]] <- list()
out[["plots" ]] <- list()
out[["text" ]] <- list()
## For each covariate, compute contrasts
for (i_var_x in seq_along(var_name_x)) {
#### "cyl" "disp" "hp" "wt" "vs" "am" "cyl:vs" "disp:hp" "hp:vs"
## i_var_x = 1 # factor , has interaction
## i_var_x = 2 # numeric, has interaction
## i_var_x = 3 # numeric, has interaction
## i_var_x = 4 # numeric
## i_var_x = 5 # factor , has interaction
## i_var_x = 6 # factor
## i_var_x = 7 # factor:factor one pair NA, cyleight:vsstraight
## i_var_x = 8 # numeric:numeric
## i_var_x = 9 # numeric:factor
## i_var_x = length(var_name_x)
# get x variable(s)
var_xs <-
stringr::str_split(
string = var_name_x[i_var_x]
, pattern = stringr::fixed(":")
) |>
unlist()
# Main effect
if (length(var_xs) == 1) {
text_marginal_even_if_interaction <- NULL
# First check if effect is involved in interactions
check_message <-
e_message_capture(
emmeans::emmeans(
object = fit
, specs = var_xs
)
)(1)
if (check_message$logs[[1]]$message == message_involve_interaction) {
if(sw_marginal_even_if_interaction) {
text_marginal_even_if_interaction <- paste0(check_message$logs[[1]]$message, "\n")
message(paste0("e_plot_model_contrasts: Continuing with \"", var_xs, "\" even though involved in interactions."))
} else {
message(paste0("e_plot_model_contrasts: Skipping \"", var_xs, "\" since involved in interactions."))
next
}
}
### if numeric
if ( inherits(dat_cont[[var_xs]], c("numeric", "integer")) ) {
## Table
if (fit_model_type == "glm" & sw_glm_scale == "response") {
# response scale
cont_fit <-
emmeans::emtrends(
object = fit
, specs = var_xs
, var = var_xs
#, transform = "response" # updated in emmeans 1.7.3
, regrid = "response"
)
} else {
# default scale
cont_fit <-
emmeans::emtrends(
object = fit
, specs = var_xs
, var = var_xs
##, transform = "response" # updated in emmeans 1.7.3
#, regrid = "response"
)
}
# confidence limit (CL) column names
col_name_LCL <- names(summary(cont_fit))[which(names(summary(cont_fit)) %in% col_names_LCL)]
col_name_UCL <- names(summary(cont_fit))[which(names(summary(cont_fit)) %in% col_names_UCL)]
out[["tables"]][[ var_name_x[i_var_x] ]][["est" ]] <- cont_fit
out[["tables"]][[ var_name_x[i_var_x] ]][["cont" ]] <- NULL
## Plot
# CI text
# is.null is for when no values could be estimated
#CLs#if(!is.null(summary(cont_fit)[["lower.CL"]])) {
if(!is.null(summary(cont_fit)[[col_name_LCL]])) {
text_cont <- summary(cont_fit)[[ var_xs[1] ]]
ind_trend <- which(stringr::str_detect(names(summary(cont_fit)), stringr::fixed(".trend")))
text_est <- summary(cont_fit)[[ind_trend]] # 2
text_LCL <- summary(cont_fit)[[col_name_LCL]]
text_UCL <- summary(cont_fit)[[col_name_UCL]]
text_CI <-
paste0(
"Estimate", " (n = ", nrow(dat_cont), ")", ": "
, "(at mean = ", signif(text_cont, 3), ")"
, ": "
, signif(text_est, 3)
, ", "
, round(CI_level * 100, 1), "% CI: "
, "("
, signif(text_LCL, 3)
, ", "
, signif(text_UCL, 3)
, ")"
, collapse = "\n"
)
} else {
text_CI <- NULL
}
text_averaged <-
paste0("Tables: ", attributes(summary(cont_fit))$mesg)
form_var <- stats::as.formula(paste0("~", var_xs))
if (fit_model_type == "glm" & sw_glm_scale == "response") {
## ?emmeans::ref_grid for cov.reduce option
# response scale
at_list <- list()
at_list[[var_xs]] <- unique(quantile(dat_cont[[var_xs]], probs = seq(0, 1, by = 0.01)))
p <-
emmeans::emmip(
object = fit
, formula = form_var
#, cov.reduce = range
, at = at_list
, rg.limit = emmip_rg.limit
#, transform = "response" # updated in emmeans 1.7.3
, regrid = "response"
)
} else {
# default scale
p <-
emmeans::emmip(
object = fit
, formula = form_var
, cov.reduce = range
, rg.limit = emmip_rg.limit
)
}
text_averaged_plot <-
paste0("Plot: ", attributes(p$data)$mesg)
text_long <-
paste0(
text_marginal_even_if_interaction
, text_CI
, "\n"
#, text_diff
#, "\n"
, text_averaged
, "\n"
, text_averaged_plot
)
text_short <-
paste0(
text_marginal_even_if_interaction
# text_CI
#, "\n"
#, text_diff
#, "\n"
#, text_averaged
#, "\n"
, text_averaged_plot
)
if (sw_table_in_plot) {
text_caption <- text_long
} else {
text_caption <- text_short
}
if (!(fit_model_type == "glm")) {
y_label <- paste0("Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character() )
} else {
if (sw_glm_scale == "response") {
# response scale
y_label <- paste0("(Response-scale) Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
} else {
# default scale
y_label <- paste0("(Link-scale) Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
}
}
p <- p + labs(
title = paste0("Main effect of ", labelled::var_label(dat_cont[[var_xs]]) |> as.character())
, subtitle = var_name_x[i_var_x]
, x = labelled::var_label(dat_cont[[var_xs]]) |> as.character()
, y = y_label
, caption = text_caption
)
p <- p + theme_bw()
p <- p + theme(plot.caption = element_text(hjust = 0)) # Default is hjust=1
#p <- p + theme(axis.text.x = element_text(angle = 15, vjust = 1, hjust = 1))
if(sw_print) {
print(p)
}
out[["plots" ]][[ var_name_x[i_var_x] ]] <- p
out[["text" ]][[ var_name_x[i_var_x] ]] <- text_long |> stringr::str_split(pattern = "\n")
} # numeric
### if factor
if ( inherits(dat_cont[[var_xs]], "factor") ) {
## Table
# if a factor, then compute the contrast and statistics and create plot
if (fit_model_type == "glm" & sw_glm_scale == "response") {
# response scale
cont_fit <-
emmeans::emmeans(
object = fit
, specs = var_xs
#, by =
#, simple = "each", combine = FALSE
, adjust = adjust_method
, level = CI_level
, type = "response"
)
} else {
# default scale
cont_fit <-
emmeans::emmeans(
object = fit
, specs = var_xs
#, by =
#, simple = "each", combine = FALSE
, adjust = adjust_method
, level = CI_level
#, type = "response"
)
}
cont_pairs <- cont_fit |> pairs(adjust = adjust_method)
# confidence limit (CL) column names
col_name_LCL <- names(summary(cont_fit))[which(names(summary(cont_fit)) %in% col_names_LCL)]
col_name_UCL <- names(summary(cont_fit))[which(names(summary(cont_fit)) %in% col_names_UCL)]
if(sw_print) {
cont_fit |> print()
cont_pairs |> print()
}
out[["tables"]][[ var_name_x[i_var_x] ]][["est" ]] <- cont_fit
out[["tables"]][[ var_name_x[i_var_x] ]][["cont" ]] <- cont_pairs
#CLs#col_name_LCL <- "lower.CL"
#CLs#col_name_UCL <- "upper.CL"
#CLs#
#CLs## ## lmer fit issue can cause a cont_fit to not provide an estimate
#CLs## # fit warnings:
#CLs## # fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
#CLs## # if the estimate is NA, then the column headers differ, too.
#CLs#if (!(col_name_LCL %in% names(summary(cont_fit)))) {
#CLs# col_name_LCL <- "asymp.LCL"
#CLs# col_name_UCL <- "asymp.UCL"
#CLs#}
## Plot
# CI text
text_cont <- summary(cont_fit)[[var_xs]]
if (fit_model_type == "glm" & sw_glm_scale == "response") {
# response scale
text_est <- summary(cont_fit)[["prob"]]
} else {
# default scale
text_est <- summary(cont_fit)[["emmean"]]
}
text_LCL <- summary(cont_fit)[[col_name_LCL]]
text_UCL <- summary(cont_fit)[[col_name_UCL]]
# sample size
n_this <- dat_cont[[var_xs]] |> table()
text_CI <-
paste0(
"Estimate", " (n = ", n_this, ")", ": "
, text_cont
, " = "
, signif(text_est, 3)
, ", "
, round(CI_level * 100, 1), "% CI: "
, "("
, signif(text_LCL, 3)
, ", "
, signif(text_UCL, 3)
, ")"
, collapse = "\n"
)
# Contrast text
text_cont <- summary(cont_pairs)[["contrast"]]
if (fit_model_type == "glm" & sw_glm_scale == "response") {
# response scale
text_est <- summary(cont_pairs)[["odds.ratio"]]
} else {
# default scale
text_est <- summary(cont_pairs)[["estimate"]]
}
text_pval <- summary(cont_pairs)[["p.value"]]
text_diff <-
paste0(
"Contrast: "
, text_cont
, " = "
, signif(text_est, 3)
, ", p-value = "
, round(text_pval, 4)
, collapse = "\n"
)
text_averaged <-
paste0(attributes(summary(cont_pairs))$mesg, collapse = "\n")
text_long <-
paste0(
text_marginal_even_if_interaction
, text_CI
, "\n"
, text_diff
, "\n"
, text_averaged
)
text_short <-
paste0(
text_marginal_even_if_interaction
# text_CI
#, "\n"
#, text_diff
#, "\n"
, text_averaged
)
if (sw_table_in_plot) {
text_caption <- text_long
} else {
text_caption <- text_short
}
p <-
plot(
cont_fit
, comparisons = TRUE
, adjust = adjust_method
, horizontal = TRUE #FALSE
#, by = "surv_prog.factor"
#, type = "scale" #"response"
)
if (!(fit_model_type == "glm")) {
x_label <- paste0("Estimate of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
} else {
if (sw_glm_scale == "response") {
# response scale
x_label <- paste0("(Response-scale) Estimate of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
} else {
# default scale
x_label <- paste0("(Link-scale) Estimate of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
}
}
p <- p + labs(
title = paste0("Main effect of ", labelled::var_label(dat_cont[[var_xs]]) |> as.character())
, subtitle = var_name_x[i_var_x]
, x = x_label
, y = labelled::var_label(dat_cont[[var_xs]]) |> as.character()
, caption = text_caption
)
p <- p + theme_bw()
p <- p + theme(plot.caption = element_text(hjust = 0)) # Default is hjust=1
#p <- p + theme(axis.text.x = element_text(angle = 15, vjust = 1, hjust = 1))
if(sw_print) {
print(p)
}
out[["plots" ]][[ var_name_x[i_var_x] ]] <- p
out[["text" ]][[ var_name_x[i_var_x] ]] <- text_long |> stringr::str_split(pattern = "\n")
} # factor
} # 1 Main effect
# Two-way interaction
if (length(var_xs) == 2) {
### if factor:factor
if (all(inherits(dat_cont[[ var_xs[1] ]], "factor"), inherits(dat_cont[[ var_xs[2] ]], "factor"))) {
# do this twice, reversing the order of the factors
for (i_repeat in 1:2) {
## i_repeat = 1
## Repeat, but reverse factors
if (i_repeat == 2) {
var_xs <- rev(var_xs)
}
## Table
# if a factor, then compute the contrast and statistics and create plot
if (fit_model_type == "glm" & sw_glm_scale == "response") {
# response scale
cont_fit <-
emmeans::emmeans(
object = fit
, specs = var_xs[1]
, by = var_xs[2]
#, simple = "each", combine = FALSE
, adjust = adjust_method
, level = CI_level
, type = "response"
)
} else {
# default scale
cont_fit <-
emmeans::emmeans(
object = fit
, specs = var_xs[1]
, by = var_xs[2]
#, simple = "each", combine = FALSE
, adjust = adjust_method
, level = CI_level
)
}
cont_pairs <- cont_fit |> pairs(adjust = adjust_method)
# confidence limit (CL) column names
col_name_LCL <- names(summary(cont_fit))[which(names(summary(cont_fit)) %in% col_names_LCL)]
col_name_UCL <- names(summary(cont_fit))[which(names(summary(cont_fit)) %in% col_names_UCL)]
if(sw_print) {
cont_fit |> print()
cont_pairs |> print()
}
out[["tables"]][[ var_name_x[i_var_x] ]][["est" ]] <- cont_fit
out[["tables"]][[ var_name_x[i_var_x] ]][["cont" ]] <- cont_pairs
# levels of variables
levels_specs <- levels(cont_fit)[[ var_xs[1] ]]
levels_by <- levels(cont_fit)[[ var_xs[2] ]]
## Plot
# CI and Contrast text
text_CI <- NULL
text_diff <- NULL
i_row_cont_fit = 0
for (i_by in seq_along(levels_by)) {
## i_by = 1
text_CI <-
paste0(
text_CI
, paste0(var_xs[2], " = ", levels_by[i_by], ":\n")
)
text_diff <-
paste0(
text_diff
, paste0(var_xs[2], " = ", levels_by[i_by], ":\n")
)
## Estimates
# CI text
summary_cont_fit <-
cont_fit |>
summary() |>
as.data.frame()
# only rows of this "by" variable
summary_cont_fit_by <-
summary_cont_fit[summary_cont_fit[[ var_xs[2] ]] == levels_by[i_by], ]
for (i_row in seq_len(nrow(summary_cont_fit_by))) {
# i_row = 1
text_cont <- summary_cont_fit_by[[ var_xs[1] ]] [i_row]
if (fit_model_type == "glm" & sw_glm_scale == "response") {
# response scale
text_est <- summary_cont_fit_by[["prob"]] [i_row]
} else {
# default scale
text_est <- summary_cont_fit_by[["emmean"]] [i_row]
}
text_LCL <- summary_cont_fit_by[[col_name_LCL]][i_row]
text_UCL <- summary_cont_fit_by[[col_name_UCL]][i_row]
# sample size
n_this <-
dat_cont[
(dat_cont[[ var_xs[1] ]] == levels_specs[i_row]) &
(dat_cont[[ var_xs[2] ]] == levels_by[i_by])
, ] |> nrow()
text_CI <-
paste0(
text_CI
#, "Estimate: "
, "Estimate", " (n = ", n_this, ")", ": "
, text_cont
, " = "
, signif(text_est, 3)
, ", "
, round(CI_level * 100, 1), "% CI: "
, "("
, signif(text_LCL, 3)
, ", "
, signif(text_UCL, 3)
, ")"
, "\n"
#, collapse = "\n"
)
} # i_row
## Contrasts
# CI text
summary_cont_pairs <-
cont_pairs |>
summary() |>
as.data.frame()
# only rows of this "by" variable
summary_cont_pairs_by <-
summary_cont_pairs[summary_cont_pairs[[ var_xs[2] ]] == levels_by[i_by], ]
for (i_row in seq_len(nrow(summary_cont_pairs_by))) {
# i_row = 1
# Contrast text
text_cont <- summary_cont_pairs_by[["contrast"]][i_row]
if (fit_model_type == "glm" & sw_glm_scale == "response") {
# response scale
text_est <- summary_cont_pairs_by[["odds.ratio"]][i_row]
} else {
# default scale
text_est <- summary_cont_pairs_by[["estimate"]][i_row]
}
text_pval <- summary_cont_pairs_by[["p.value"]] [i_row]
text_diff <-
paste0(
text_diff
, "Contrast: "
, text_cont
, " = "
, signif(text_est, 3)
, ", p-value = "
, round(text_pval, 4)
, "\n"
#, collapse = "\n"
)
} # i_row
} # i_by
text_averaged <-
paste0(attributes(summary(cont_pairs))$mesg, collapse = "\n")
text_long <-
paste0(
text_CI
, "\n"
, text_diff
, "\n"
, text_averaged
)
text_short <-
paste0(
# text_CI
#, "\n"
#, text_diff
#, "\n"
text_averaged
)
if (sw_table_in_plot) {
text_caption <- text_long
} else {
text_caption <- text_short
}
# if error: "Error: Aborted -- Some comparison arrows have negative length!"
# then remove comprisons
sw_try_ok <-
!e_is_error(
try(
plot(
cont_fit
, comparisons = TRUE
)
)
)
if(sw_try_ok) {
p <-
plot(
cont_fit
, comparisons = TRUE
, adjust = adjust_method
, horizontal = TRUE #FALSE
#, by = "surv_prog.factor"
)
} else {
message(paste0(" e_plot_model_contrasts: Due to error, no comparison arrows for: ", var_xs))
text_caption <-
paste0(
text_caption
, "\n"
, "Due to error, no comparison arrows are plotted"
)
p <-
plot(
cont_fit
#, comparisons = TRUE
, adjust = adjust_method
, horizontal = TRUE #FALSE
#, by = "surv_prog.factor"
)
} # if sw_try_ok
if (!(fit_model_type == "glm")) {
x_label <- paste0("Estimate of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
} else {
if (sw_glm_scale == "response") {
# response scale
x_label <- paste0("(Response-scale) Estimate of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
} else {
# default scale
x_label <- paste0("(Link-scale) Estimate of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
}
}
p <- p + labs(
title = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
, subtitle = var_name_x[i_var_x]
, x = x_label
, y = labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character()
, caption = text_caption
)
p <- p + theme_bw()
p <- p + theme(plot.caption = element_text(hjust = 0)) # Default is hjust=1
#p <- p + theme(axis.text.x = element_text(angle = 15, vjust = 1, hjust = 1))
if(sw_print) {
print(p)
}
if (i_repeat == 1) {
p1 <- p
}
if (i_repeat == 2) {
p2 <- p
}
if(sw_TWI_plots_keep %in% c("singles", "both", "all")[c(1, 3)]) {
out[["plots" ]][[ var_name_x[i_var_x] ]][[i_repeat]] <- p
}
out[["text" ]][[ var_name_x[i_var_x] ]][[i_repeat]] <- text_long |> stringr::str_split(pattern = "\n")
} # i_repeat
if(sw_TWI_plots_keep %in% c("singles", "both", "all")[c(2, 3)]) {
# prepare for group plot
p1 <- p1 +
labs(title = NULL, tag = "A")
p2 <- p2 +
labs(title = NULL, tag = "B")
## Arrange in a grid
#library(gridExtra)
#library(grid)
if (sw_TWI_both_orientation == c("tall", "wide")[1]) {
lay_grid <-
rbind(
c(1)
, c(2)
)
#p2 <- p2 + labs(title = NULL)
# p_arranged <-
# #gridExtra::grid.arrange(
# gridExtra::arrangeGrob(
# grobs = list(p1, p2)
# , layout_matrix = lay_grid
# #, top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
# #, bottom = "bottom\ntitle"
# #, left = "left label"
# #, right = "right label"
# ) |>
# ggpubr::as_ggplot()
}
if (sw_TWI_both_orientation == c("tall", "wide")[2]) {
lay_grid <-
rbind(
c(1, 2)
#, c(2)
)
#p1 <- p1 + labs(title = NULL)
#p2 <- p2 + labs(title = NULL)
# p_arranged <-
# #gridExtra::grid.arrange(
# gridExtra::arrangeGrob(
# grobs = list(p1, p2)
# , layout_matrix = lay_grid
# , top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
# #, bottom = "bottom\ntitle"
# #, left = "left label"
# #, right = "right label"
# ) |>
# ggpubr::as_ggplot()
}
p_arranged <-
#gridExtra::grid.arrange(
gridExtra::arrangeGrob(
grobs = list(p1, p2)
, layout_matrix = lay_grid
, top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
#, bottom = "bottom\ntitle"
#, left = "left label"
#, right = "right label"
) |>
ggpubr::as_ggplot()
if(sw_print) {
print(p_arranged)
}
out[["plots" ]][[ var_name_x[i_var_x] ]][["both"]] <- p_arranged
} # sw_TWI_plots_keep
} # factor:factor
### if factor:numeric
if (any(inherits(dat_cont[[ var_xs[1] ]], "factor"), inherits(dat_cont[[ var_xs[2] ]], "factor") ) &
any(inherits(dat_cont[[ var_xs[1] ]], c("numeric", "integer")), inherits(dat_cont[[ var_xs[2] ]], c("numeric", "integer")) )
) {
# make first variable the factor and second numeric
if(inherits(dat_cont[[ var_xs[2] ]], "factor")) {
var_xs <- rev(var_xs)
}
## Table
form_var_fac <- stats::as.formula(paste0("pairwise", " ~ ", var_xs[1]))
if (fit_model_type == "glm" & sw_glm_scale == "response") {
# response scale
cont_fit <-
emmeans::emtrends(
object = fit
, specs = form_var_fac
, var = var_xs[2]
, adjust = adjust_method
, level = CI_level
#, transform = "response" # updated in emmeans 1.7.3
, regrid = "response"
)
} else {
# default scale
cont_fit <-
emmeans::emtrends(
object = fit
, specs = form_var_fac
, var = var_xs[2] ## 8/18/2022 1:29PM XXX Should this be "3"
, adjust = adjust_method
, level = CI_level
##, transform = "response" # updated in emmeans 1.7.3
#, regrid = "response"
)
}
# confidence limit (CL) column names
col_name_LCL <- names(summary(cont_fit)$emtrends)[which(names(summary(cont_fit)$emtrends) %in% col_names_LCL)]
col_name_UCL <- names(summary(cont_fit)$emtrends)[which(names(summary(cont_fit)$emtrends) %in% col_names_UCL)]
out[["tables"]][[ var_name_x[i_var_x] ]][["est" ]] <- cont_fit$emtrends
out[["tables"]][[ var_name_x[i_var_x] ]][["cont" ]] <- cont_fit$contrasts
## Plot
# CI text
# is.null is for when no values could be estimated
#CLs#if(!is.null(summary(cont_fit$emtrends)[["lower.CL"]])) {
if(!is.null(summary(cont_fit$emtrends)[[col_name_LCL]])) {
text_cont <- summary(cont_fit$emtrends)[[ var_xs[1] ]]
ind_trend <- which(stringr::str_detect(names(summary(cont_fit$emtrends)), stringr::fixed(".trend")))
text_est <- summary(cont_fit$emtrends)[[ind_trend]] # 2
text_LCL <- summary(cont_fit$emtrends)[[col_name_LCL]]
text_UCL <- summary(cont_fit$emtrends)[[col_name_UCL]]
# sample size
n_this <- dat_cont[[ var_xs[1] ]] |> table()
text_CI <-
paste0(
"Estimate", " (n = ", n_this, ")", ": "
, text_cont
, " = "
, signif(text_est, 3)
, ", "
, round(CI_level * 100, 1), "% CI: "
, "("
, signif(text_LCL, 3)
, ", "
, signif(text_UCL, 3)
, ")"
, collapse = "\n"
)
# Contrast text
text_cont <- summary(cont_fit$contrasts)[["contrast"]]
text_est <- summary(cont_fit$contrasts)[["estimate"]]
text_pval <- summary(cont_fit$contrasts)[["p.value"]]
text_diff <-
paste0(
"Contrast: "
, text_cont
, " = "
, signif(text_est, 3)
, ", p-value = "
, round(text_pval, 4)
, collapse = "\n"
)
} else {
text_CI <- NULL
}
text_averaged <-
attributes(summary(cont_fit$contrasts))$mesg
text_long <-
paste0(
text_CI
, "\n"
, text_diff
, "\n"
, text_averaged
)
text_short <-
paste0(
# text_CI
#, "\n"
#, text_diff
#, "\n"
text_averaged
)
if (sw_table_in_plot) {
text_caption <- text_long
} else {
text_caption <- text_short
}
p1 <- plot(cont_fit)
p1 <- p1 + theme_bw()
p1 <- p1 + labs(
title = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
, subtitle = var_name_x[i_var_x]
, x = paste0("Estimated slope for:\n", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character() )
, y = labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character()
#, colour = labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character()
, caption = text_caption
#, tag = "A"
)
p1 <- p1 + theme(plot.caption = element_text(hjust = 0)) # Default is hjust=1
if(sw_TWI_plots_keep %in% c("singles", "both", "all")[c(1, 3)]) {
out[["plots" ]][[ var_name_x[i_var_x] ]][[1]] <- p1
}
out[["text" ]][[ var_name_x[i_var_x] ]][[1]] <- text_long |> stringr::str_split(pattern = "\n")
form_var_fac_num <- stats::as.formula(paste0(var_xs[1], " ~ ", var_xs[2]))
# 12/20/2021 removed because it was removing the table in plot
# text_long <-
# paste0(
# text_averaged
# )
# text_short <-
# paste0(
# text_averaged
# )
# if (sw_table_in_plot) {
# text_caption <- text_long
# } else {
# text_caption <- text_short
# }
if (fit_model_type == "glm" & sw_glm_scale == "response") {
## ?emmeans::ref_grid for cov.reduce option
# response scale
at_list <- list()
at_list[[var_xs[2]]] <- unique(quantile(dat_cont[[var_xs[2]]], probs = seq(0, 1, by = 0.01)))
p2 <- emmeans::emmip(
object = fit
, formula = form_var_fac_num
#, cov.reduce = range
, at = at_list
, rg.limit = emmip_rg.limit
#, transform = "response" # updated in emmeans 1.7.3
, regrid = "response"
)
} else {
# default scale
p2 <- emmeans::emmip(
object = fit
, formula = form_var_fac_num
, cov.reduce = range
, rg.limit = emmip_rg.limit
)
}
if (!(fit_model_type == "glm")) {
y_label <- paste0("Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character() )
} else {
if (sw_glm_scale == "response") {
# response scale
y_label <- paste0("(Response-scale) Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
} else {
# default scale
y_label <- paste0("(Link-scale) Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
}
}
p2 <- p2 + theme_bw()
p2 <- p2 + labs(
title = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
, subtitle = var_name_x[i_var_x]
, x = labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character()
, y = y_label
, colour = labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character()
, caption = text_caption
#, tag = "B"
)
p2 <- p2 + theme(plot.caption = element_text(hjust = 0)) # Default is hjust=1
if(sw_TWI_plots_keep %in% c("singles", "both", "all")[c(1, 3)]) {
out[["plots" ]][[ var_name_x[i_var_x] ]][[2]] <- p2
}
out[["text" ]][[ var_name_x[i_var_x] ]][[2]] <- text_long |> stringr::str_split(pattern = "\n")
if(sw_TWI_plots_keep %in% c("singles", "both", "all")[c(2, 3)]) {
# prepare for group plot
p1 <- p1 +
labs(title = NULL, tag = "A")
p2 <- p2 +
labs(title = NULL, tag = "B")
## Arrange in a grid
#library(gridExtra)
#library(grid)
if (sw_TWI_both_orientation == c("tall", "wide")[1]) {
lay_grid <-
rbind(
c(1)
, c(2)
)
#p2 <- p2 + labs(title = NULL)
# p_arranged <-
# #gridExtra::grid.arrange(
# gridExtra::arrangeGrob(
# grobs = list(p1, p2)
# , layout_matrix = lay_grid
# #, top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
# #, bottom = "bottom\ntitle"
# #, left = "left label"
# #, right = "right label"
# ) |>
# ggpubr::as_ggplot()
}
if (sw_TWI_both_orientation == c("tall", "wide")[2]) {
lay_grid <-
rbind(
c(1, 2)
#, c(2)
)
#p1 <- p1 + labs(title = NULL)
#p2 <- p2 + labs(title = NULL)
# p_arranged <-
# #gridExtra::grid.arrange(
# gridExtra::arrangeGrob(
# grobs = list(p1, p2)
# , layout_matrix = lay_grid
# , top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
# #, bottom = "bottom\ntitle"
# #, left = "left label"
# #, right = "right label"
# ) |>
# ggpubr::as_ggplot()
}
p_arranged <-
#gridExtra::grid.arrange(
gridExtra::arrangeGrob(
grobs = list(p1, p2)
, layout_matrix = lay_grid
, top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
#, bottom = "bottom\ntitle"
#, left = "left label"
#, right = "right label"
) |>
ggpubr::as_ggplot()
if(sw_print) {
print(p_arranged)
}
out[["plots" ]][[ var_name_x[i_var_x] ]][["both"]] <- p_arranged
} # sw_TWI_plots_keep
} # factor:numeric
### if numeric:numeric
if ( all(inherits(dat_cont[[ var_xs[1] ]], c("numeric", "integer")), inherits(dat_cont[[ var_xs[2] ]], c("numeric", "integer"))) ) {
# do this twice, reversing the order of the factors
for (i_repeat in 1:2) {
## i_repeat = 1
## Repeat, but reverse factors
if (i_repeat == 2) {
var_xs <- rev(var_xs)
}
form_var_num_num <- stats::as.formula(paste0(var_xs[1], " ~ ", var_xs[2]))
# this is the common every-variable situation
if (sw_plot_quantiles_values == "quantiles" | is.null(plot_values)) {
# values of numeric variables for plotting
at_list <- list()
at_list[[ var_xs[1] ]] <-
dat_cont[[ var_xs[1] ]] |> stats::quantile(probs = plot_quantiles, type = sw_quantile_type) |> unique()
at_list[[ var_xs[2] ]] <-
#dat_cont[[ var_xs[2] ]] |> stats::quantile(probs = plot_quantiles, type = sw_quantile_type) |> unique()
dat_cont[[ var_xs[2] ]] |> stats::quantile(probs = seq(0, 1, by = 0.01)) |> unique()
}
# this is for a specific numeric:numeric interaction
if (sw_plot_quantiles_values == "values") {
# values of numeric variables for plotting
at_list <- list()
at_list[[ var_xs[1] ]] <-
plot_values[[ var_xs[1] ]]
at_list[[ var_xs[2] ]] <-
plot_values[[ var_xs[2] ]]
}
if (fit_model_type == "glm" & sw_glm_scale == "response") {
## ?emmeans::ref_grid for cov.reduce option
# response scale
fit_emm_at <-
emmeans::ref_grid(
object = fit
, at = at_list
#, type = "response"
#, transform = "response" # updated in emmeans 1.7.3
, regrid = "response"
)
} else {
# default scale
fit_emm_at <-
emmeans::ref_grid(
object = fit
, at = at_list
)
}
## Table
#form_var_fac <- stats::as.formula(paste0("pairwise", " ~ ", var_xs[1]))
out[["tables"]][[ var_name_x[i_var_x] ]][["est" ]] <- NULL
out[["tables"]][[ var_name_x[i_var_x] ]][["cont" ]] <- NULL
## Plot
p <- emmeans::emmip(
object = fit_emm_at
, formula = form_var_num_num
#, cov.reduce = range #not originally here, but maybe belongs
, rg.limit = emmip_rg.limit
)
text_averaged_plot <-
attributes(p$data)$mesg
# this is the common every-variable situation
if (sw_plot_quantiles_values == "quantiles" | is.null(plot_values)) {
text_long <-
paste0(
paste0("Quantiles plotted: ", paste(plot_quantiles, collapse = ", "), ";\n may be fewer if quantiles are not unique values.")
, "\n"
, text_averaged_plot
)
text_short <-
paste0(
paste0("Quantiles plotted: ", paste(plot_quantiles, collapse = ", "), ";\n may be fewer if quantiles are not unique values.")
, "\n"
, text_averaged_plot
)
}
# this is for a specific numeric:numeric interaction
if (sw_plot_quantiles_values == "values") {
text_long <-
paste0(
paste0("Specified values plotted.")
, "\n"
, text_averaged_plot
)
text_short <-
paste0(
paste0("Specified values plotted.")
, "\n"
, text_averaged_plot
)
}
if (sw_table_in_plot) {
text_caption <- text_long
} else {
text_caption <- text_short
}
if (!(fit_model_type == "glm")) {
y_label <- paste0("Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character() )
} else {
if (sw_glm_scale == "response") {
# response scale
y_label <- paste0("(Response-scale) Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
} else {
# default scale
y_label <- paste0("(Link-scale) Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
}
}
p <- p + labs(
title = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
, subtitle = var_name_x[i_var_x]
, x = labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character()
, y = y_label
, colour = labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character()
, caption = text_caption
#, tag = "A"
)
p <- p + theme_bw()
p <- p + theme(plot.caption = element_text(hjust = 0)) # Default is hjust=1
#p <- p + theme(axis.text.x = element_text(angle = 15, vjust = 1, hjust = 1))
if(sw_print) {
print(p)
}
if (i_repeat == 1) {
p1 <- p
}
if (i_repeat == 2) {
p2 <- p
}
if(sw_TWI_plots_keep %in% c("singles", "both", "all")[c(1, 3)]) {
out[["plots" ]][[ var_name_x[i_var_x] ]][[i_repeat]] <- p
}
out[["text" ]][[ var_name_x[i_var_x] ]][[i_repeat]] <- text_long |> stringr::str_split(pattern = "\n")
} # i_repeat
if(sw_TWI_plots_keep %in% c("singles", "both", "all")[c(2, 3)]) {
# prepare for group plot
p1 <- p1 +
labs(title = NULL, tag = "A")
p2 <- p2 +
labs(title = NULL, tag = "B")
## Arrange in a grid
#library(gridExtra)
#library(grid)
if (sw_TWI_both_orientation == c("tall", "wide")[1]) {
lay_grid <-
rbind(
c(1)
, c(2)
)
#p2 <- p2 + labs(title = NULL)
# p_arranged <-
# #gridExtra::grid.arrange(
# gridExtra::arrangeGrob(
# grobs = list(p1, p2)
# , layout_matrix = lay_grid
# #, top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
# #, bottom = "bottom\ntitle"
# #, left = "left label"
# #, right = "right label"
# ) |>
# ggpubr::as_ggplot()
}
if (sw_TWI_both_orientation == c("tall", "wide")[2]) {
lay_grid <-
rbind(
c(1, 2)
#, c(2)
)
#p1 <- p1 + labs(title = NULL)
#p2 <- p2 + labs(title = NULL)
# p_arranged <-
# #gridExtra::grid.arrange(
# gridExtra::arrangeGrob(
# grobs = list(p1, p2)
# , layout_matrix = lay_grid
# , top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
# #, bottom = "bottom\ntitle"
# #, left = "left label"
# #, right = "right label"
# ) |>
# ggpubr::as_ggplot()
}
p_arranged <-
#gridExtra::grid.arrange(
gridExtra::arrangeGrob(
grobs = list(p1, p2)
, layout_matrix = lay_grid
, top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
#, bottom = "bottom\ntitle"
#, left = "left label"
#, right = "right label"
) |>
ggpubr::as_ggplot()
if(sw_print) {
print(p_arranged)
}
out[["plots" ]][[ var_name_x[i_var_x] ]][["both"]] <- p_arranged
} # sw_TWI_plots_keep
} # numeric:numeric
} # 2 Two-way interaction
} # i_var_x
invisible(out)
} # end of e_plot_model_contrasts()
erikerhardt/erikmisc documentation built on April 17, 2025, 10:48 a.m.
R Package Documentation
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#' Compute and plot all contrasts and test results from a linear model by automating the use of emmeans tables and plots.
#'
#' Variable labels can be provided by labelling your data with the labelled::var_label() command.
#'
#' Plot interpretation:
#' This EMM plot (Estimated Marginal Means, aka Least-Squares Means) is only
#' available when conditioning on one variable. The blue bars are confidence
#' intervals for the EMMs; don't ever use confidence intervals for EMMs to perform
#' comparisons --- they can be very misleading. The red arrows are for the
#' comparisons between means; the degree to which the "comparison arrows" overlap
#' reflects as much as possible the significance of the comparison of the two
#' estimates. If an arrow from one mean overlaps an arrow from another group, the
#' difference is not significant, based on the adjust setting (which defaults to
#' "tukey").
#'
#' @param fit (required) model object: lm, glm, lmerModLmerTest (from \code{lme4::lmer}, or lmerMod (from \code{lmerTest::as_lmerModLmerTest})
#' @param dat_cont (required) data used for the lm object (only used for variable labels using labelled::var_label()
#' @param choose_contrasts is a list of effects to plot, such as c("hp", "vs:wt"); NULL does all in model.
#' @param sw_table_in_plot T/F put table of results in caption of plot
#' @param adjust_method see `?emmeans::summary.emmGrid`
#' @param CI_level level from `?emmeans::emmeans`
#' @param sw_glm_scale for glm fit, choose results on the "link" (default) or "response" scale
#' @param sw_print T/F whether to print results as this function runs
#' @param sw_marginal_even_if_interaction T/F whether to also calculate marginal results when involved in interaction(s)
#' @param sw_TWI_plots_keep two-way interaction plots are plotted for each variable conditional on the other. Plots are created separately ("singles") or together in a grid ("both"), and "all" keeps the singles and the grid version.
#' @param sw_TWI_both_orientation "tall" or "wide" orientation for when both two-way interaction plots are combined in a grid
#' @param sw_plot_quantiles_values "quantiles" or "values" to specify whether to plot quantiles of the numeric variable or specified values
#' @param plot_quantiles quantiles plotted for numeric:numeric interaction plots, if \code{sw_plot_quantiles_values} is "quantiles"
#' @param sw_quantile_type quantile type as specified in \code{?stats::quantile}.
#' @param plot_values a named list for values plotted for a single specified numeric:numeric interaction plot, if \code{sw_plot_quantiles_values} is "values". Specify a specific contrast, for example: \code{choose_contrasts = "disp:hp"}. Then specify the values for each variable, for example: \code{plot_values = list(hp = c(75, 100, 150, 200, 250), disp = c(80, 120, 200, 350, 450))}
#' @param emmip_rg.limit from emmeans package, increase from 10000 if "Error: The rows of your requested reference grid would be 10000, which exceeds the limit of XXXXX (not including any multivariate responses)."
#'
#' @return out a list of three lists: "plots", "tables" , and "text", each have results for each contrast that was computed. "plots" is a list of ggplot objects to plot separately or arrange in a grid. "tables" is a list of emmeans tables to print. "text" is the caption text for the plots.
#' @import dplyr
#' @import ggplot2
#' @import emmeans
#' @importFrom labelled var_label
#' @importFrom stringr fixed
#' @importFrom stringr str_detect
#' @importFrom stringr str_split
#' @importFrom stringr str_split_fixed
#' @importFrom gridExtra arrangeGrob
#' @importFrom ggpubr as_ggplot
#' @importFrom purrr pluck
#' @importFrom stats as.formula
#' @importFrom stats quantile
#' @importFrom stats anova
#' @importFrom stats terms.formula
#' @importFrom cowplot plot_grid
#' @export
#'
#' @examples
#' # Data for testing
#' dat_cont <-
#' dat_mtcars_e
#'
#' # Set specific model with some interactions
#' form_model <-
#' mpg ~ cyl + disp + hp + wt + vs + am + cyl:vs + disp:hp + hp:vs
#'
#' fit <-
#' lm(
#' formula = form_model
#' , data = dat_cont
#' )
#'
#' car::Anova(fit) #, type = 3)
#' summary(fit)
#'
#' # all contrasts from model
#' fit_contrasts <-
#' e_plot_model_contrasts(
#' fit = fit
#' , dat_cont = dat_cont
#' , sw_print = FALSE
#' , sw_table_in_plot = FALSE
#' , sw_TWI_plots_keep = "singles"
#' , sw_quantile_type = 1
#' )
#' fit_contrasts$tables # to print tables
#' fit_contrasts$plots # to print plots
#' fit_contrasts$text # to print caption text
#'
#'
#' ## To plot all contrasts in a plot grid:
#' # Since plot interactions have sublists of plots, we want to pull those out
#' # into a one-level plot list.
#' # The code here works for sw_TWI_plots_keep = "singles"
#' # which will make each plot the same size in the plot_grid() below.
#' # For a publications, you'll want to manually choose which plots to show.
#'
#' # index for plot list,
#' # needed since interactions add 2 plots to the list, so the number of terms
#' # is not necessarily the same as the number of plots.
#' i_list <- 0
#' # initialize a list of plots
#' p_list <- list()
#'
#' for (i_term in 1:length(fit_contrasts$plots)) {
#' ## i_term = 1
#'
#' # extract the name of the plot
#' n_list <- names(fit_contrasts$plots)[i_term]
#'
#' # test whether the name has a colon ":"; if so, it's an interaction
#' if (stringr::str_detect(string = n_list, pattern = stringr::fixed(":"))) {
#' # an two-way interaction has two plots
#'
#' # first plot
#' i_list <- i_list + 1
#' p_list[[ i_list ]] <- fit_contrasts$plots[[ i_term ]][[ 1 ]]
#'
#' # second plot
#' i_list <- i_list + 1
#' p_list[[ i_list ]] <- fit_contrasts$plots[[ i_term ]][[ 2 ]]
#'
#' } else {
#' # not an interaction, only one plot
#'
#' i_list <- i_list + 1
#' p_list[[ i_list ]] <- fit_contrasts$plots[[ i_term ]]
#'
#' } # if
#' } # for
#'
#' p_arranged <-
#' cowplot::plot_grid(
#' plotlist = p_list
#' , nrow = NULL
#' , ncol = 3
#' , labels = "AUTO"
#' )
#'
#' p_arranged |> print()
#'
#'
#'
#'
#'
#' # one specific numeric:numeric contrast with specified values
#' fit_contrasts <-
#' e_plot_model_contrasts(
#' fit = fit
#' , dat_cont = dat_cont
#' , choose_contrasts = "disp:hp"
#' , sw_table_in_plot = TRUE
#' , adjust_method = c("none", "tukey", "scheffe", "sidak", "bonferroni"
#' , "dunnettx", "mvt")[4] # see ?emmeans::summary.emmGrid
#' , CI_level = 0.95
#' , sw_glm_scale = c("link", "response")[1]
#' , sw_print = FALSE
#' , sw_marginal_even_if_interaction = TRUE
#' , sw_TWI_plots_keep = c("singles", "both", "all")[3]
#' , sw_TWI_both_orientation = c("tall", "wide")[1]
#' , sw_plot_quantiles_values = c("quantiles", "values")[2] # for numeric:numeric plots
#' , plot_quantiles = c(0.05, 0.25, 0.50, 0.75, 0.95) # for numeric:numeric plots
#' , sw_quantile_type = 1
#' , plot_values = list(hp = c(75, 100, 150, 200, 250)
#' , disp = c(80, 120, 200, 350, 450)) # for numeric:numeric plots
#' )
#' fit_contrasts$plots$`disp:hp`$both
#'
#'
#' \dontrun{
#' ## GLM on logit and probability scales
#'
#' dat_cont <-
#' dat_cont |>
#' dplyr::mutate(
#' am_01 =
#' dplyr::case_when(
#' am == "manual" ~ 0
#' , am == "automatic" ~ 1
#' )
#' )
#' labelled::var_label(dat_cont[["am_01"]]) <- labelled::var_label(dat_cont[["am"]])
#'
#' # numeric:factor interaction
#' fit_glm <-
#' glm(
#' cbind(am_01, 1 - am_01) ~
#' vs + hp + vs:hp
#' , family = binomial
#' , data = dat_cont
#' )
#'
#' car::Anova(fit_glm, type = 3)
#' summary(fit_glm)
#'
#' # all contrasts from model, logit scale
#' fit_contrasts <-
#' e_plot_model_contrasts(
#' fit = fit_glm
#' , dat_cont = dat_cont
#' , sw_glm_scale = c("link", "response")[1]
#' , sw_print = FALSE
#' , sw_marginal_even_if_interaction = TRUE
#' , sw_TWI_plots_keep = "both"
#' )
#' fit_contrasts
#'
#' # all contrasts from model, probability scale
#' fit_contrasts <-
#' e_plot_model_contrasts(
#' fit = fit_glm
#' , dat_cont = dat_cont
#' , sw_glm_scale = c("link", "response")[2]
#' , sw_print = FALSE
#' , sw_marginal_even_if_interaction = TRUE
#' , sw_TWI_plots_keep = "both"
#' )
#' fit_contrasts
#'
#'
#' # numeric:numeric interaction
#' fit_glm <-
#' glm(
#' cbind(am_01, 1 - am_01) ~
#' disp + hp + disp:hp
#' , family = binomial
#' , data = dat_cont
#' )
#'
#' car::Anova(fit_glm, type = 3)
#' summary(fit_glm)
#'
#' fit_contrasts <-
#' e_plot_model_contrasts(
#' fit = fit_glm
#' , dat_cont = dat_cont
#' , sw_glm_scale = c("link", "response")[2]
#' , sw_print = FALSE
#' , sw_TWI_plots_keep = "both"
#' )
#' fit_contrasts
#'
#'
#' # factor:factor interaction
#' fit_glm <-
#' glm(
#' cbind(am_01, 1 - am_01) ~
#' vs + cyl + vs:cyl
#' , family = binomial
#' , data = dat_cont
#' )
#'
#' car::Anova(fit_glm) #, type = 3)
#' summary(fit_glm)
#'
#' fit_contrasts <-
#' e_plot_model_contrasts(
#' fit = fit_glm
#' , dat_cont = dat_cont
#' , sw_glm_scale = c("link", "response")[2]
#' , sw_print = FALSE
#' , sw_TWI_plots_keep = "both"
#' )
#' fit_contrasts
#'
#'
#' ## lme4::lmer mixed-effects model
#' fit_lmer <-
#' lme4::lmer(
#' formula = Reaction ~ Days + (Days | Subject)
#' , data = lme4::sleepstudy
#' )
#'
#' fit_lmer_contrasts <-
#' e_plot_model_contrasts(
#' fit = fit_lmer
#' , dat_cont = lme4::sleepstudy
#' , sw_print = FALSE
#' , sw_table_in_plot = FALSE
#' )
#' fit_lmer_contrasts
#'
#'
#' ## lmerTest::as_lmerModLmerTest mixed-effects model
#'
#' fit_lmer <-
#' lmerTest::as_lmerModLmerTest(fit_lmer)
#'
#' fit_lmer_contrasts <-
#' e_plot_model_contrasts(
#' fit = fit_lmer
#' , dat_cont = lme4::sleepstudy
#' , sw_print = FALSE
#' , sw_table_in_plot = FALSE
#' )
#' fit_lmer_contrasts
#' }
#'
e_plot_model_contrasts <-
function(
fit = NULL
, dat_cont = NULL
, choose_contrasts = NULL
, sw_table_in_plot = TRUE
, adjust_method = c("none", "tukey", "scheffe", "sidak", "bonferroni", "dunnettx", "mvt")[4] # see ?emmeans::summary.emmGrid
, CI_level = 0.95
, sw_glm_scale = c("link", "response")[1]
, sw_print = TRUE
, sw_marginal_even_if_interaction = FALSE
, sw_TWI_plots_keep = c("singles", "both", "all")[3]
, sw_TWI_both_orientation = c("wide", "tall")[1]
, sw_plot_quantiles_values = c("quantiles", "values")[1] # for numeric:numeric plots
, plot_quantiles = c(0.05, 0.25, 0.50, 0.75, 0.95) # for numeric:numeric plots
, sw_quantile_type = 7
, plot_values = NULL # for numeric:numeric plots
, emmip_rg.limit = 10000
) {
###### START Example dataset for testing
##
## library(tidyverse)
##
## choose_contrasts = NULL
## sw_table_in_plot = TRUE
## adjust_method = c("none", "tukey", "scheffe", "sidak", "bonferroni", "dunnettx", "mvt")[4] # see ?emmeans::summary.emmGrid
## CI_level = 0.95
## sw_print = TRUE
## sw_marginal_even_if_interaction = TRUE
## sw_TWI_plots_keep = c("singles", "both", "all")[3]
## sw_TWI_both_orientation = c("tall", "wide")[1]
## sw_plot_quantiles_values = c("quantiles", "values")[1] # for numeric:numeric plots
## plot_quantiles = c(0.05, 0.25, 0.50, 0.75, 0.95) # for numeric:numeric plots
## plot_values = c(-1, 0, 1) # for numeric:numeric plots
##
## # Data for testing
## dat_cont <-
## dat_mtcars_e |>
## as_tibble(
## rownames = "model"
## ) |>
## mutate(
## cyl = cyl |> factor(levels = c(4, 6, 8), labels = c("four", "six", "eight"))
## , vs = vs |> factor(levels = c(0, 1), labels = c("V-shaped", "straight"))
## , am = am |> factor(levels = c(0, 1), labels = c("automatic", "manual"))
## )
##
## # Label columns
## dat_labels <-
## tribble(
## ~var, ~label
## , "model" , "Model"
## , "mpg" , "Miles/(US) gallon"
## , "cyl" , "Number of cylinders"
## , "disp" , "Displacement (cu.in.)"
## , "hp" , "Gross horsepower"
## , "drat" , "Rear axle ratio"
## , "wt" , "Weight (1000 lbs)"
## , "qsec" , "1/4 mile time"
## , "vs" , "Engine" # (0 = V-shaped, 1 = straight)"
## , "am" , "Transmission" # (0 = automatic, 1 = manual)"
## , "gear" , "Number of forward gears"
## , "carb" , "Number of carburetors"
## )
##
## for (i_row in 1:nrow(dat_labels)) {
## labelled::var_label(dat_cont[[dat_labels[["var"]][i_row] ]]) <- dat_labels[["label"]][i_row]
## }
##
## ## form_model <-
## ## stats::as.formula(
## ## paste0(
## ## "mpg"
## ## , " ~ "
## ## , "("
## ## , " cyl"
## ## , " + disp"
## ## , " + hp"
## ## #, " + drat"
## ## , " + wt"
## ## #, " + qsec"
## ## , " + vs"
## ## , " + am"
## ## , " + gear"
## ## , " + carb"
## ## , ")^2" # all two-way interaction pairs
## ## )
## ## )
## ##
## ## fit <-
## ## lm(
## ## formula = form_model
## ## , data = dat_cont
## ## )
## ##
## ## ## AIC
## ## # option: test="F" includes additional information
## ## # for parameter estimate tests that we're familiar with
## ## # option: for BIC, include k=log(nrow( [data.frame name] ))
## ## fit <-
## ## step(
## ## fit
## ## , direction = "both"
## ## , test = "F"
## ## , k = log(nrow( dat_cont ))
## ## , trace = 0
## ## )
##
## # Set specific model with some interactions
## form_model <-
## mpg ~ cyl + disp + hp + wt + vs + am + cyl:vs + disp:hp + hp:vs
##
##
## fit <-
## lm(
## formula = form_model
## , data = dat_cont
## )
## stats::anova(fit)
## summary(fit)
##
##
## e_plot_model_contrasts(
## fit = fit
## , dat_cont = dat_cont
## , choose_contrasts = NULL
## , sw_table_in_plot = TRUE
## , adjust_method = c("none", "tukey", "scheffe", "sidak", "bonferroni", "dunnettx", "mvt")[4] # see ?emmeans::summary.emmGrid
## , CI_level = 0.95
## , sw_print = TRUE
## , sw_marginal_even_if_interaction = TRUE
## , sw_TWI_plots_keep = c("singles", "both", "all")[3]
## , sw_TWI_both_orientation = c("tall", "wide")[1]
## , plot_quantiles = c(0.05, 0.25, 0.50, 0.75, 0.95) # for numeric:numeric plots
## )
##
##
## e_plot_model_contrasts(
## fit = fit
## , dat_cont = dat_cont
## , choose_contrasts = "disp:hp"
## , sw_table_in_plot = TRUE
## , adjust_method = c("none", "tukey", "scheffe", "sidak", "bonferroni", "dunnettx", "mvt")[4] # see ?emmeans::summary.emmGrid
## , CI_level = 0.95
## , sw_print = TRUE
## , sw_marginal_even_if_interaction = TRUE
## , sw_TWI_plots_keep = c("singles", "both", "all")[1]
## , sw_TWI_both_orientation = c("tall", "wide")[1]
## , sw_plot_quantiles_values = c("quantiles", "values")[2] # for numeric:numeric plots
## , plot_quantiles = c(0.05, 0.25, 0.50, 0.75, 0.95) # for numeric:numeric plots
## , plot_values = list(hp = c(75, 100, 150, 200, 250), disp = c(80, 120, 200, 350, 450)) # for numeric:numeric plots
## )
##
##
###### END Example dataset for testing
# give error if two main inputs aren't specified
if (is.null(fit) | is.null(dat_cont)) {
stop("erikmisc::e_plot_model_contrasts() \"fit\" and \"dat_cont\" arguments are required.")
return(NULL)
}
# indicates, "lm", "glm", or "lmerMod" (future, another method based on the call)
fit_model_type <-
#as.character(fit$call)[1]
class(fit)[1]
if (fit_model_type %notin% c("lm", "glm", "lmerModLmerTest", "lmerMod")) {
message(paste0("e_plot_model_contrasts: fit class\"", fit_model_type, "\" not tested."))
}
# BEGIN Capture warnings to take actions
message_involve_interaction <-
"NOTE: Results may be misleading due to involvement in interactions\n"
# END Capture warnings to take actions
# confidence limits (CL) column names differ depending on method and rank deficiency
# provide a list of possibilities to look for from the summary tables
col_names_LCL <- c("lower.CL", "asymp.LCL")
col_names_UCL <- c("upper.CL", "asymp.UCL")
# subset to include only complete observations for variables used
if (fit_model_type %in% c("lm")) {
temp_var_list <- names(attr(fit$terms, "dataClasses"))
dat_cont <- na.omit(dat_cont[, temp_var_list])
rm(temp_var_list)
}
if (fit_model_type %in% c("glm")) {
temp_var_list <- names(attr(fit$terms, "dataClasses"))
# strip variable name out of cbind() statement
if(any(stringr::str_detect(temp_var_list, stringr::fixed("cbind(")))) {
temp_ind <- which(stringr::str_detect(temp_var_list, stringr::fixed("cbind(")))
temp_var_list[temp_ind] <-
stringr::str_split(
stringr::str_split(
string = temp_var_list[temp_ind]
, pattern = stringr::fixed("cbind(")
, simplify = TRUE
)[2]
, pattern = stringr::fixed(",")
, simplify = TRUE
)[1]
}
dat_cont <- na.omit(dat_cont[, temp_var_list])
rm(temp_var_list, temp_ind)
}
if (fit_model_type %in% c("lmerModLmerTest", "lmerMod")) {
temp_var_list <- names(fit@frame)
dat_cont <- na.omit(dat_cont[, temp_var_list])
rm(temp_var_list)
}
# check for label, create label if unlabelled
for (n_col in names(dat_cont)) {
## n_col = names(dat_cont)[1]
if (is.null(labelled::var_label(dat_cont[[n_col]]))) {
labelled::var_label(dat_cont[[n_col]]) <- n_col
}
}
# labelled::var_label(fit$model[[1]])
# extract variables
var_name_y <-
as.character(formula(fit))[2]
var_name_x <-
stringr::str_split(
string = attr(terms.formula(formula(fit)), "term.labels") #as.character(formula(fit))[3]
, pattern = stringr::fixed(" + ")
) |>
unlist()
if (fit_model_type == "glm" & stringr::str_detect(var_name_y, pattern = stringr::fixed("cbind("))) {
# the y-variable usually looks like "cbind(y, 1-y)", so strip out the variable name
var_name_y <-
var_name_y |>
stringr::str_split_fixed(
pattern = stringr::fixed(",")
, n = 2
) |>
as.character() |>
purrr::pluck(1) |>
stringr::str_split_fixed(
pattern = stringr::fixed("cbind(")
, n = 2
) |>
as.character() |>
purrr::pluck(2)
}
# restrict to chosen contrasts
if (!is.null(choose_contrasts)) {
# for chosen contrasts, copy and reverse order of two-way interactions
# to make sure there's a match
## https://stackoverflow.com/questions/49141253/how-to-reverse-the-delimited-parts-of-a-string
choose_contrasts_rev <-
sapply(
stringr::str_split(
string = choose_contrasts
, pattern = stringr::fixed(":")
)
, function(x) {
paste0(rev(x), collapse = ":")
}
)
# restrict to chosen
var_name_x <-
var_name_x[which(var_name_x %in% c(choose_contrasts, choose_contrasts_rev))]
}
# output list of tables and plots
out <- list()
out[["tables"]] <- list()
out[["plots" ]] <- list()
out[["text" ]] <- list()
## For each covariate, compute contrasts
for (i_var_x in seq_along(var_name_x)) {
#### "cyl" "disp" "hp" "wt" "vs" "am" "cyl:vs" "disp:hp" "hp:vs"
## i_var_x = 1 # factor , has interaction
## i_var_x = 2 # numeric, has interaction
## i_var_x = 3 # numeric, has interaction
## i_var_x = 4 # numeric
## i_var_x = 5 # factor , has interaction
## i_var_x = 6 # factor
## i_var_x = 7 # factor:factor one pair NA, cyleight:vsstraight
## i_var_x = 8 # numeric:numeric
## i_var_x = 9 # numeric:factor
## i_var_x = length(var_name_x)
# get x variable(s)
var_xs <-
stringr::str_split(
string = var_name_x[i_var_x]
, pattern = stringr::fixed(":")
) |>
unlist()
# Main effect
if (length(var_xs) == 1) {
text_marginal_even_if_interaction <- NULL
# First check if effect is involved in interactions
check_message <-
e_message_capture(
emmeans::emmeans(
object = fit
, specs = var_xs
)
)(1)
if (check_message$logs[[1]]$message == message_involve_interaction) {
if(sw_marginal_even_if_interaction) {
text_marginal_even_if_interaction <- paste0(check_message$logs[[1]]$message, "\n")
message(paste0("e_plot_model_contrasts: Continuing with \"", var_xs, "\" even though involved in interactions."))
} else {
message(paste0("e_plot_model_contrasts: Skipping \"", var_xs, "\" since involved in interactions."))
next
}
}
### if numeric
if ( inherits(dat_cont[[var_xs]], c("numeric", "integer")) ) {
## Table
if (fit_model_type == "glm" & sw_glm_scale == "response") {
# response scale
cont_fit <-
emmeans::emtrends(
object = fit
, specs = var_xs
, var = var_xs
#, transform = "response" # updated in emmeans 1.7.3
, regrid = "response"
)
} else {
# default scale
cont_fit <-
emmeans::emtrends(
object = fit
, specs = var_xs
, var = var_xs
##, transform = "response" # updated in emmeans 1.7.3
#, regrid = "response"
)
}
# confidence limit (CL) column names
col_name_LCL <- names(summary(cont_fit))[which(names(summary(cont_fit)) %in% col_names_LCL)]
col_name_UCL <- names(summary(cont_fit))[which(names(summary(cont_fit)) %in% col_names_UCL)]
out[["tables"]][[ var_name_x[i_var_x] ]][["est" ]] <- cont_fit
out[["tables"]][[ var_name_x[i_var_x] ]][["cont" ]] <- NULL
## Plot
# CI text
# is.null is for when no values could be estimated
#CLs#if(!is.null(summary(cont_fit)[["lower.CL"]])) {
if(!is.null(summary(cont_fit)[[col_name_LCL]])) {
text_cont <- summary(cont_fit)[[ var_xs[1] ]]
ind_trend <- which(stringr::str_detect(names(summary(cont_fit)), stringr::fixed(".trend")))
text_est <- summary(cont_fit)[[ind_trend]] # 2
text_LCL <- summary(cont_fit)[[col_name_LCL]]
text_UCL <- summary(cont_fit)[[col_name_UCL]]
text_CI <-
paste0(
"Estimate", " (n = ", nrow(dat_cont), ")", ": "
, "(at mean = ", signif(text_cont, 3), ")"
, ": "
, signif(text_est, 3)
, ", "
, round(CI_level * 100, 1), "% CI: "
, "("
, signif(text_LCL, 3)
, ", "
, signif(text_UCL, 3)
, ")"
, collapse = "\n"
)
} else {
text_CI <- NULL
}
text_averaged <-
paste0("Tables: ", attributes(summary(cont_fit))$mesg)
form_var <- stats::as.formula(paste0("~", var_xs))
if (fit_model_type == "glm" & sw_glm_scale == "response") {
## ?emmeans::ref_grid for cov.reduce option
# response scale
at_list <- list()
at_list[[var_xs]] <- unique(quantile(dat_cont[[var_xs]], probs = seq(0, 1, by = 0.01)))
p <-
emmeans::emmip(
object = fit
, formula = form_var
#, cov.reduce = range
, at = at_list
, rg.limit = emmip_rg.limit
#, transform = "response" # updated in emmeans 1.7.3
, regrid = "response"
)
} else {
# default scale
p <-
emmeans::emmip(
object = fit
, formula = form_var
, cov.reduce = range
, rg.limit = emmip_rg.limit
)
}
text_averaged_plot <-
paste0("Plot: ", attributes(p$data)$mesg)
text_long <-
paste0(
text_marginal_even_if_interaction
, text_CI
, "\n"
#, text_diff
#, "\n"
, text_averaged
, "\n"
, text_averaged_plot
)
text_short <-
paste0(
text_marginal_even_if_interaction
# text_CI
#, "\n"
#, text_diff
#, "\n"
#, text_averaged
#, "\n"
, text_averaged_plot
)
if (sw_table_in_plot) {
text_caption <- text_long
} else {
text_caption <- text_short
}
if (!(fit_model_type == "glm")) {
y_label <- paste0("Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character() )
} else {
if (sw_glm_scale == "response") {
# response scale
y_label <- paste0("(Response-scale) Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
} else {
# default scale
y_label <- paste0("(Link-scale) Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
}
}
p <- p + labs(
title = paste0("Main effect of ", labelled::var_label(dat_cont[[var_xs]]) |> as.character())
, subtitle = var_name_x[i_var_x]
, x = labelled::var_label(dat_cont[[var_xs]]) |> as.character()
, y = y_label
, caption = text_caption
)
p <- p + theme_bw()
p <- p + theme(plot.caption = element_text(hjust = 0)) # Default is hjust=1
#p <- p + theme(axis.text.x = element_text(angle = 15, vjust = 1, hjust = 1))
if(sw_print) {
print(p)
}
out[["plots" ]][[ var_name_x[i_var_x] ]] <- p
out[["text" ]][[ var_name_x[i_var_x] ]] <- text_long |> stringr::str_split(pattern = "\n")
} # numeric
### if factor
if ( inherits(dat_cont[[var_xs]], "factor") ) {
## Table
# if a factor, then compute the contrast and statistics and create plot
if (fit_model_type == "glm" & sw_glm_scale == "response") {
# response scale
cont_fit <-
emmeans::emmeans(
object = fit
, specs = var_xs
#, by =
#, simple = "each", combine = FALSE
, adjust = adjust_method
, level = CI_level
, type = "response"
)
} else {
# default scale
cont_fit <-
emmeans::emmeans(
object = fit
, specs = var_xs
#, by =
#, simple = "each", combine = FALSE
, adjust = adjust_method
, level = CI_level
#, type = "response"
)
}
cont_pairs <- cont_fit |> pairs(adjust = adjust_method)
# confidence limit (CL) column names
col_name_LCL <- names(summary(cont_fit))[which(names(summary(cont_fit)) %in% col_names_LCL)]
col_name_UCL <- names(summary(cont_fit))[which(names(summary(cont_fit)) %in% col_names_UCL)]
if(sw_print) {
cont_fit |> print()
cont_pairs |> print()
}
out[["tables"]][[ var_name_x[i_var_x] ]][["est" ]] <- cont_fit
out[["tables"]][[ var_name_x[i_var_x] ]][["cont" ]] <- cont_pairs
#CLs#col_name_LCL <- "lower.CL"
#CLs#col_name_UCL <- "upper.CL"
#CLs#
#CLs## ## lmer fit issue can cause a cont_fit to not provide an estimate
#CLs## # fit warnings:
#CLs## # fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
#CLs## # if the estimate is NA, then the column headers differ, too.
#CLs#if (!(col_name_LCL %in% names(summary(cont_fit)))) {
#CLs# col_name_LCL <- "asymp.LCL"
#CLs# col_name_UCL <- "asymp.UCL"
#CLs#}
## Plot
# CI text
text_cont <- summary(cont_fit)[[var_xs]]
if (fit_model_type == "glm" & sw_glm_scale == "response") {
# response scale
text_est <- summary(cont_fit)[["prob"]]
} else {
# default scale
text_est <- summary(cont_fit)[["emmean"]]
}
text_LCL <- summary(cont_fit)[[col_name_LCL]]
text_UCL <- summary(cont_fit)[[col_name_UCL]]
# sample size
n_this <- dat_cont[[var_xs]] |> table()
text_CI <-
paste0(
"Estimate", " (n = ", n_this, ")", ": "
, text_cont
, " = "
, signif(text_est, 3)
, ", "
, round(CI_level * 100, 1), "% CI: "
, "("
, signif(text_LCL, 3)
, ", "
, signif(text_UCL, 3)
, ")"
, collapse = "\n"
)
# Contrast text
text_cont <- summary(cont_pairs)[["contrast"]]
if (fit_model_type == "glm" & sw_glm_scale == "response") {
# response scale
text_est <- summary(cont_pairs)[["odds.ratio"]]
} else {
# default scale
text_est <- summary(cont_pairs)[["estimate"]]
}
text_pval <- summary(cont_pairs)[["p.value"]]
text_diff <-
paste0(
"Contrast: "
, text_cont
, " = "
, signif(text_est, 3)
, ", p-value = "
, round(text_pval, 4)
, collapse = "\n"
)
text_averaged <-
paste0(attributes(summary(cont_pairs))$mesg, collapse = "\n")
text_long <-
paste0(
text_marginal_even_if_interaction
, text_CI
, "\n"
, text_diff
, "\n"
, text_averaged
)
text_short <-
paste0(
text_marginal_even_if_interaction
# text_CI
#, "\n"
#, text_diff
#, "\n"
, text_averaged
)
if (sw_table_in_plot) {
text_caption <- text_long
} else {
text_caption <- text_short
}
p <-
plot(
cont_fit
, comparisons = TRUE
, adjust = adjust_method
, horizontal = TRUE #FALSE
#, by = "surv_prog.factor"
#, type = "scale" #"response"
)
if (!(fit_model_type == "glm")) {
x_label <- paste0("Estimate of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
} else {
if (sw_glm_scale == "response") {
# response scale
x_label <- paste0("(Response-scale) Estimate of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
} else {
# default scale
x_label <- paste0("(Link-scale) Estimate of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
}
}
p <- p + labs(
title = paste0("Main effect of ", labelled::var_label(dat_cont[[var_xs]]) |> as.character())
, subtitle = var_name_x[i_var_x]
, x = x_label
, y = labelled::var_label(dat_cont[[var_xs]]) |> as.character()
, caption = text_caption
)
p <- p + theme_bw()
p <- p + theme(plot.caption = element_text(hjust = 0)) # Default is hjust=1
#p <- p + theme(axis.text.x = element_text(angle = 15, vjust = 1, hjust = 1))
if(sw_print) {
print(p)
}
out[["plots" ]][[ var_name_x[i_var_x] ]] <- p
out[["text" ]][[ var_name_x[i_var_x] ]] <- text_long |> stringr::str_split(pattern = "\n")
} # factor
} # 1 Main effect
# Two-way interaction
if (length(var_xs) == 2) {
### if factor:factor
if (all(inherits(dat_cont[[ var_xs[1] ]], "factor"), inherits(dat_cont[[ var_xs[2] ]], "factor"))) {
# do this twice, reversing the order of the factors
for (i_repeat in 1:2) {
## i_repeat = 1
## Repeat, but reverse factors
if (i_repeat == 2) {
var_xs <- rev(var_xs)
}
## Table
# if a factor, then compute the contrast and statistics and create plot
if (fit_model_type == "glm" & sw_glm_scale == "response") {
# response scale
cont_fit <-
emmeans::emmeans(
object = fit
, specs = var_xs[1]
, by = var_xs[2]
#, simple = "each", combine = FALSE
, adjust = adjust_method
, level = CI_level
, type = "response"
)
} else {
# default scale
cont_fit <-
emmeans::emmeans(
object = fit
, specs = var_xs[1]
, by = var_xs[2]
#, simple = "each", combine = FALSE
, adjust = adjust_method
, level = CI_level
)
}
cont_pairs <- cont_fit |> pairs(adjust = adjust_method)
# confidence limit (CL) column names
col_name_LCL <- names(summary(cont_fit))[which(names(summary(cont_fit)) %in% col_names_LCL)]
col_name_UCL <- names(summary(cont_fit))[which(names(summary(cont_fit)) %in% col_names_UCL)]
if(sw_print) {
cont_fit |> print()
cont_pairs |> print()
}
out[["tables"]][[ var_name_x[i_var_x] ]][["est" ]] <- cont_fit
out[["tables"]][[ var_name_x[i_var_x] ]][["cont" ]] <- cont_pairs
# levels of variables
levels_specs <- levels(cont_fit)[[ var_xs[1] ]]
levels_by <- levels(cont_fit)[[ var_xs[2] ]]
## Plot
# CI and Contrast text
text_CI <- NULL
text_diff <- NULL
i_row_cont_fit = 0
for (i_by in seq_along(levels_by)) {
## i_by = 1
text_CI <-
paste0(
text_CI
, paste0(var_xs[2], " = ", levels_by[i_by], ":\n")
)
text_diff <-
paste0(
text_diff
, paste0(var_xs[2], " = ", levels_by[i_by], ":\n")
)
## Estimates
# CI text
summary_cont_fit <-
cont_fit |>
summary() |>
as.data.frame()
# only rows of this "by" variable
summary_cont_fit_by <-
summary_cont_fit[summary_cont_fit[[ var_xs[2] ]] == levels_by[i_by], ]
for (i_row in seq_len(nrow(summary_cont_fit_by))) {
# i_row = 1
text_cont <- summary_cont_fit_by[[ var_xs[1] ]] [i_row]
if (fit_model_type == "glm" & sw_glm_scale == "response") {
# response scale
text_est <- summary_cont_fit_by[["prob"]] [i_row]
} else {
# default scale
text_est <- summary_cont_fit_by[["emmean"]] [i_row]
}
text_LCL <- summary_cont_fit_by[[col_name_LCL]][i_row]
text_UCL <- summary_cont_fit_by[[col_name_UCL]][i_row]
# sample size
n_this <-
dat_cont[
(dat_cont[[ var_xs[1] ]] == levels_specs[i_row]) &
(dat_cont[[ var_xs[2] ]] == levels_by[i_by])
, ] |> nrow()
text_CI <-
paste0(
text_CI
#, "Estimate: "
, "Estimate", " (n = ", n_this, ")", ": "
, text_cont
, " = "
, signif(text_est, 3)
, ", "
, round(CI_level * 100, 1), "% CI: "
, "("
, signif(text_LCL, 3)
, ", "
, signif(text_UCL, 3)
, ")"
, "\n"
#, collapse = "\n"
)
} # i_row
## Contrasts
# CI text
summary_cont_pairs <-
cont_pairs |>
summary() |>
as.data.frame()
# only rows of this "by" variable
summary_cont_pairs_by <-
summary_cont_pairs[summary_cont_pairs[[ var_xs[2] ]] == levels_by[i_by], ]
for (i_row in seq_len(nrow(summary_cont_pairs_by))) {
# i_row = 1
# Contrast text
text_cont <- summary_cont_pairs_by[["contrast"]][i_row]
if (fit_model_type == "glm" & sw_glm_scale == "response") {
# response scale
text_est <- summary_cont_pairs_by[["odds.ratio"]][i_row]
} else {
# default scale
text_est <- summary_cont_pairs_by[["estimate"]][i_row]
}
text_pval <- summary_cont_pairs_by[["p.value"]] [i_row]
text_diff <-
paste0(
text_diff
, "Contrast: "
, text_cont
, " = "
, signif(text_est, 3)
, ", p-value = "
, round(text_pval, 4)
, "\n"
#, collapse = "\n"
)
} # i_row
} # i_by
text_averaged <-
paste0(attributes(summary(cont_pairs))$mesg, collapse = "\n")
text_long <-
paste0(
text_CI
, "\n"
, text_diff
, "\n"
, text_averaged
)
text_short <-
paste0(
# text_CI
#, "\n"
#, text_diff
#, "\n"
text_averaged
)
if (sw_table_in_plot) {
text_caption <- text_long
} else {
text_caption <- text_short
}
# if error: "Error: Aborted -- Some comparison arrows have negative length!"
# then remove comprisons
sw_try_ok <-
!e_is_error(
try(
plot(
cont_fit
, comparisons = TRUE
)
)
)
if(sw_try_ok) {
p <-
plot(
cont_fit
, comparisons = TRUE
, adjust = adjust_method
, horizontal = TRUE #FALSE
#, by = "surv_prog.factor"
)
} else {
message(paste0(" e_plot_model_contrasts: Due to error, no comparison arrows for: ", var_xs))
text_caption <-
paste0(
text_caption
, "\n"
, "Due to error, no comparison arrows are plotted"
)
p <-
plot(
cont_fit
#, comparisons = TRUE
, adjust = adjust_method
, horizontal = TRUE #FALSE
#, by = "surv_prog.factor"
)
} # if sw_try_ok
if (!(fit_model_type == "glm")) {
x_label <- paste0("Estimate of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
} else {
if (sw_glm_scale == "response") {
# response scale
x_label <- paste0("(Response-scale) Estimate of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
} else {
# default scale
x_label <- paste0("(Link-scale) Estimate of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
}
}
p <- p + labs(
title = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
, subtitle = var_name_x[i_var_x]
, x = x_label
, y = labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character()
, caption = text_caption
)
p <- p + theme_bw()
p <- p + theme(plot.caption = element_text(hjust = 0)) # Default is hjust=1
#p <- p + theme(axis.text.x = element_text(angle = 15, vjust = 1, hjust = 1))
if(sw_print) {
print(p)
}
if (i_repeat == 1) {
p1 <- p
}
if (i_repeat == 2) {
p2 <- p
}
if(sw_TWI_plots_keep %in% c("singles", "both", "all")[c(1, 3)]) {
out[["plots" ]][[ var_name_x[i_var_x] ]][[i_repeat]] <- p
}
out[["text" ]][[ var_name_x[i_var_x] ]][[i_repeat]] <- text_long |> stringr::str_split(pattern = "\n")
} # i_repeat
if(sw_TWI_plots_keep %in% c("singles", "both", "all")[c(2, 3)]) {
# prepare for group plot
p1 <- p1 +
labs(title = NULL, tag = "A")
p2 <- p2 +
labs(title = NULL, tag = "B")
## Arrange in a grid
#library(gridExtra)
#library(grid)
if (sw_TWI_both_orientation == c("tall", "wide")[1]) {
lay_grid <-
rbind(
c(1)
, c(2)
)
#p2 <- p2 + labs(title = NULL)
# p_arranged <-
# #gridExtra::grid.arrange(
# gridExtra::arrangeGrob(
# grobs = list(p1, p2)
# , layout_matrix = lay_grid
# #, top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
# #, bottom = "bottom\ntitle"
# #, left = "left label"
# #, right = "right label"
# ) |>
# ggpubr::as_ggplot()
}
if (sw_TWI_both_orientation == c("tall", "wide")[2]) {
lay_grid <-
rbind(
c(1, 2)
#, c(2)
)
#p1 <- p1 + labs(title = NULL)
#p2 <- p2 + labs(title = NULL)
# p_arranged <-
# #gridExtra::grid.arrange(
# gridExtra::arrangeGrob(
# grobs = list(p1, p2)
# , layout_matrix = lay_grid
# , top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
# #, bottom = "bottom\ntitle"
# #, left = "left label"
# #, right = "right label"
# ) |>
# ggpubr::as_ggplot()
}
p_arranged <-
#gridExtra::grid.arrange(
gridExtra::arrangeGrob(
grobs = list(p1, p2)
, layout_matrix = lay_grid
, top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
#, bottom = "bottom\ntitle"
#, left = "left label"
#, right = "right label"
) |>
ggpubr::as_ggplot()
if(sw_print) {
print(p_arranged)
}
out[["plots" ]][[ var_name_x[i_var_x] ]][["both"]] <- p_arranged
} # sw_TWI_plots_keep
} # factor:factor
### if factor:numeric
if (any(inherits(dat_cont[[ var_xs[1] ]], "factor"), inherits(dat_cont[[ var_xs[2] ]], "factor") ) &
any(inherits(dat_cont[[ var_xs[1] ]], c("numeric", "integer")), inherits(dat_cont[[ var_xs[2] ]], c("numeric", "integer")) )
) {
# make first variable the factor and second numeric
if(inherits(dat_cont[[ var_xs[2] ]], "factor")) {
var_xs <- rev(var_xs)
}
## Table
form_var_fac <- stats::as.formula(paste0("pairwise", " ~ ", var_xs[1]))
if (fit_model_type == "glm" & sw_glm_scale == "response") {
# response scale
cont_fit <-
emmeans::emtrends(
object = fit
, specs = form_var_fac
, var = var_xs[2]
, adjust = adjust_method
, level = CI_level
#, transform = "response" # updated in emmeans 1.7.3
, regrid = "response"
)
} else {
# default scale
cont_fit <-
emmeans::emtrends(
object = fit
, specs = form_var_fac
, var = var_xs[2] ## 8/18/2022 1:29PM XXX Should this be "3"
, adjust = adjust_method
, level = CI_level
##, transform = "response" # updated in emmeans 1.7.3
#, regrid = "response"
)
}
# confidence limit (CL) column names
col_name_LCL <- names(summary(cont_fit)$emtrends)[which(names(summary(cont_fit)$emtrends) %in% col_names_LCL)]
col_name_UCL <- names(summary(cont_fit)$emtrends)[which(names(summary(cont_fit)$emtrends) %in% col_names_UCL)]
out[["tables"]][[ var_name_x[i_var_x] ]][["est" ]] <- cont_fit$emtrends
out[["tables"]][[ var_name_x[i_var_x] ]][["cont" ]] <- cont_fit$contrasts
## Plot
# CI text
# is.null is for when no values could be estimated
#CLs#if(!is.null(summary(cont_fit$emtrends)[["lower.CL"]])) {
if(!is.null(summary(cont_fit$emtrends)[[col_name_LCL]])) {
text_cont <- summary(cont_fit$emtrends)[[ var_xs[1] ]]
ind_trend <- which(stringr::str_detect(names(summary(cont_fit$emtrends)), stringr::fixed(".trend")))
text_est <- summary(cont_fit$emtrends)[[ind_trend]] # 2
text_LCL <- summary(cont_fit$emtrends)[[col_name_LCL]]
text_UCL <- summary(cont_fit$emtrends)[[col_name_UCL]]
# sample size
n_this <- dat_cont[[ var_xs[1] ]] |> table()
text_CI <-
paste0(
"Estimate", " (n = ", n_this, ")", ": "
, text_cont
, " = "
, signif(text_est, 3)
, ", "
, round(CI_level * 100, 1), "% CI: "
, "("
, signif(text_LCL, 3)
, ", "
, signif(text_UCL, 3)
, ")"
, collapse = "\n"
)
# Contrast text
text_cont <- summary(cont_fit$contrasts)[["contrast"]]
text_est <- summary(cont_fit$contrasts)[["estimate"]]
text_pval <- summary(cont_fit$contrasts)[["p.value"]]
text_diff <-
paste0(
"Contrast: "
, text_cont
, " = "
, signif(text_est, 3)
, ", p-value = "
, round(text_pval, 4)
, collapse = "\n"
)
} else {
text_CI <- NULL
}
text_averaged <-
attributes(summary(cont_fit$contrasts))$mesg
text_long <-
paste0(
text_CI
, "\n"
, text_diff
, "\n"
, text_averaged
)
text_short <-
paste0(
# text_CI
#, "\n"
#, text_diff
#, "\n"
text_averaged
)
if (sw_table_in_plot) {
text_caption <- text_long
} else {
text_caption <- text_short
}
p1 <- plot(cont_fit)
p1 <- p1 + theme_bw()
p1 <- p1 + labs(
title = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
, subtitle = var_name_x[i_var_x]
, x = paste0("Estimated slope for:\n", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character() )
, y = labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character()
#, colour = labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character()
, caption = text_caption
#, tag = "A"
)
p1 <- p1 + theme(plot.caption = element_text(hjust = 0)) # Default is hjust=1
if(sw_TWI_plots_keep %in% c("singles", "both", "all")[c(1, 3)]) {
out[["plots" ]][[ var_name_x[i_var_x] ]][[1]] <- p1
}
out[["text" ]][[ var_name_x[i_var_x] ]][[1]] <- text_long |> stringr::str_split(pattern = "\n")
form_var_fac_num <- stats::as.formula(paste0(var_xs[1], " ~ ", var_xs[2]))
# 12/20/2021 removed because it was removing the table in plot
# text_long <-
# paste0(
# text_averaged
# )
# text_short <-
# paste0(
# text_averaged
# )
# if (sw_table_in_plot) {
# text_caption <- text_long
# } else {
# text_caption <- text_short
# }
if (fit_model_type == "glm" & sw_glm_scale == "response") {
## ?emmeans::ref_grid for cov.reduce option
# response scale
at_list <- list()
at_list[[var_xs[2]]] <- unique(quantile(dat_cont[[var_xs[2]]], probs = seq(0, 1, by = 0.01)))
p2 <- emmeans::emmip(
object = fit
, formula = form_var_fac_num
#, cov.reduce = range
, at = at_list
, rg.limit = emmip_rg.limit
#, transform = "response" # updated in emmeans 1.7.3
, regrid = "response"
)
} else {
# default scale
p2 <- emmeans::emmip(
object = fit
, formula = form_var_fac_num
, cov.reduce = range
, rg.limit = emmip_rg.limit
)
}
if (!(fit_model_type == "glm")) {
y_label <- paste0("Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character() )
} else {
if (sw_glm_scale == "response") {
# response scale
y_label <- paste0("(Response-scale) Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
} else {
# default scale
y_label <- paste0("(Link-scale) Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
}
}
p2 <- p2 + theme_bw()
p2 <- p2 + labs(
title = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
, subtitle = var_name_x[i_var_x]
, x = labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character()
, y = y_label
, colour = labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character()
, caption = text_caption
#, tag = "B"
)
p2 <- p2 + theme(plot.caption = element_text(hjust = 0)) # Default is hjust=1
if(sw_TWI_plots_keep %in% c("singles", "both", "all")[c(1, 3)]) {
out[["plots" ]][[ var_name_x[i_var_x] ]][[2]] <- p2
}
out[["text" ]][[ var_name_x[i_var_x] ]][[2]] <- text_long |> stringr::str_split(pattern = "\n")
if(sw_TWI_plots_keep %in% c("singles", "both", "all")[c(2, 3)]) {
# prepare for group plot
p1 <- p1 +
labs(title = NULL, tag = "A")
p2 <- p2 +
labs(title = NULL, tag = "B")
## Arrange in a grid
#library(gridExtra)
#library(grid)
if (sw_TWI_both_orientation == c("tall", "wide")[1]) {
lay_grid <-
rbind(
c(1)
, c(2)
)
#p2 <- p2 + labs(title = NULL)
# p_arranged <-
# #gridExtra::grid.arrange(
# gridExtra::arrangeGrob(
# grobs = list(p1, p2)
# , layout_matrix = lay_grid
# #, top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
# #, bottom = "bottom\ntitle"
# #, left = "left label"
# #, right = "right label"
# ) |>
# ggpubr::as_ggplot()
}
if (sw_TWI_both_orientation == c("tall", "wide")[2]) {
lay_grid <-
rbind(
c(1, 2)
#, c(2)
)
#p1 <- p1 + labs(title = NULL)
#p2 <- p2 + labs(title = NULL)
# p_arranged <-
# #gridExtra::grid.arrange(
# gridExtra::arrangeGrob(
# grobs = list(p1, p2)
# , layout_matrix = lay_grid
# , top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
# #, bottom = "bottom\ntitle"
# #, left = "left label"
# #, right = "right label"
# ) |>
# ggpubr::as_ggplot()
}
p_arranged <-
#gridExtra::grid.arrange(
gridExtra::arrangeGrob(
grobs = list(p1, p2)
, layout_matrix = lay_grid
, top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
#, bottom = "bottom\ntitle"
#, left = "left label"
#, right = "right label"
) |>
ggpubr::as_ggplot()
if(sw_print) {
print(p_arranged)
}
out[["plots" ]][[ var_name_x[i_var_x] ]][["both"]] <- p_arranged
} # sw_TWI_plots_keep
} # factor:numeric
### if numeric:numeric
if ( all(inherits(dat_cont[[ var_xs[1] ]], c("numeric", "integer")), inherits(dat_cont[[ var_xs[2] ]], c("numeric", "integer"))) ) {
# do this twice, reversing the order of the factors
for (i_repeat in 1:2) {
## i_repeat = 1
## Repeat, but reverse factors
if (i_repeat == 2) {
var_xs <- rev(var_xs)
}
form_var_num_num <- stats::as.formula(paste0(var_xs[1], " ~ ", var_xs[2]))
# this is the common every-variable situation
if (sw_plot_quantiles_values == "quantiles" | is.null(plot_values)) {
# values of numeric variables for plotting
at_list <- list()
at_list[[ var_xs[1] ]] <-
dat_cont[[ var_xs[1] ]] |> stats::quantile(probs = plot_quantiles, type = sw_quantile_type) |> unique()
at_list[[ var_xs[2] ]] <-
#dat_cont[[ var_xs[2] ]] |> stats::quantile(probs = plot_quantiles, type = sw_quantile_type) |> unique()
dat_cont[[ var_xs[2] ]] |> stats::quantile(probs = seq(0, 1, by = 0.01)) |> unique()
}
# this is for a specific numeric:numeric interaction
if (sw_plot_quantiles_values == "values") {
# values of numeric variables for plotting
at_list <- list()
at_list[[ var_xs[1] ]] <-
plot_values[[ var_xs[1] ]]
at_list[[ var_xs[2] ]] <-
plot_values[[ var_xs[2] ]]
}
if (fit_model_type == "glm" & sw_glm_scale == "response") {
## ?emmeans::ref_grid for cov.reduce option
# response scale
fit_emm_at <-
emmeans::ref_grid(
object = fit
, at = at_list
#, type = "response"
#, transform = "response" # updated in emmeans 1.7.3
, regrid = "response"
)
} else {
# default scale
fit_emm_at <-
emmeans::ref_grid(
object = fit
, at = at_list
)
}
## Table
#form_var_fac <- stats::as.formula(paste0("pairwise", " ~ ", var_xs[1]))
out[["tables"]][[ var_name_x[i_var_x] ]][["est" ]] <- NULL
out[["tables"]][[ var_name_x[i_var_x] ]][["cont" ]] <- NULL
## Plot
p <- emmeans::emmip(
object = fit_emm_at
, formula = form_var_num_num
#, cov.reduce = range #not originally here, but maybe belongs
, rg.limit = emmip_rg.limit
)
text_averaged_plot <-
attributes(p$data)$mesg
# this is the common every-variable situation
if (sw_plot_quantiles_values == "quantiles" | is.null(plot_values)) {
text_long <-
paste0(
paste0("Quantiles plotted: ", paste(plot_quantiles, collapse = ", "), ";\n may be fewer if quantiles are not unique values.")
, "\n"
, text_averaged_plot
)
text_short <-
paste0(
paste0("Quantiles plotted: ", paste(plot_quantiles, collapse = ", "), ";\n may be fewer if quantiles are not unique values.")
, "\n"
, text_averaged_plot
)
}
# this is for a specific numeric:numeric interaction
if (sw_plot_quantiles_values == "values") {
text_long <-
paste0(
paste0("Specified values plotted.")
, "\n"
, text_averaged_plot
)
text_short <-
paste0(
paste0("Specified values plotted.")
, "\n"
, text_averaged_plot
)
}
if (sw_table_in_plot) {
text_caption <- text_long
} else {
text_caption <- text_short
}
if (!(fit_model_type == "glm")) {
y_label <- paste0("Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character() )
} else {
if (sw_glm_scale == "response") {
# response scale
y_label <- paste0("(Response-scale) Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
} else {
# default scale
y_label <- paste0("(Link-scale) Linear prediction of:\n", labelled::var_label(dat_cont[[var_name_y]]) |> as.character())
}
}
p <- p + labs(
title = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
, subtitle = var_name_x[i_var_x]
, x = labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character()
, y = y_label
, colour = labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character()
, caption = text_caption
#, tag = "A"
)
p <- p + theme_bw()
p <- p + theme(plot.caption = element_text(hjust = 0)) # Default is hjust=1
#p <- p + theme(axis.text.x = element_text(angle = 15, vjust = 1, hjust = 1))
if(sw_print) {
print(p)
}
if (i_repeat == 1) {
p1 <- p
}
if (i_repeat == 2) {
p2 <- p
}
if(sw_TWI_plots_keep %in% c("singles", "both", "all")[c(1, 3)]) {
out[["plots" ]][[ var_name_x[i_var_x] ]][[i_repeat]] <- p
}
out[["text" ]][[ var_name_x[i_var_x] ]][[i_repeat]] <- text_long |> stringr::str_split(pattern = "\n")
} # i_repeat
if(sw_TWI_plots_keep %in% c("singles", "both", "all")[c(2, 3)]) {
# prepare for group plot
p1 <- p1 +
labs(title = NULL, tag = "A")
p2 <- p2 +
labs(title = NULL, tag = "B")
## Arrange in a grid
#library(gridExtra)
#library(grid)
if (sw_TWI_both_orientation == c("tall", "wide")[1]) {
lay_grid <-
rbind(
c(1)
, c(2)
)
#p2 <- p2 + labs(title = NULL)
# p_arranged <-
# #gridExtra::grid.arrange(
# gridExtra::arrangeGrob(
# grobs = list(p1, p2)
# , layout_matrix = lay_grid
# #, top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
# #, bottom = "bottom\ntitle"
# #, left = "left label"
# #, right = "right label"
# ) |>
# ggpubr::as_ggplot()
}
if (sw_TWI_both_orientation == c("tall", "wide")[2]) {
lay_grid <-
rbind(
c(1, 2)
#, c(2)
)
#p1 <- p1 + labs(title = NULL)
#p2 <- p2 + labs(title = NULL)
# p_arranged <-
# #gridExtra::grid.arrange(
# gridExtra::arrangeGrob(
# grobs = list(p1, p2)
# , layout_matrix = lay_grid
# , top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
# #, bottom = "bottom\ntitle"
# #, left = "left label"
# #, right = "right label"
# ) |>
# ggpubr::as_ggplot()
}
p_arranged <-
#gridExtra::grid.arrange(
gridExtra::arrangeGrob(
grobs = list(p1, p2)
, layout_matrix = lay_grid
, top = paste0("Interaction of ", labelled::var_label(dat_cont[[ var_xs[1] ]]) |> as.character(), " and ", labelled::var_label(dat_cont[[ var_xs[2] ]]) |> as.character())
#, bottom = "bottom\ntitle"
#, left = "left label"
#, right = "right label"
) |>
ggpubr::as_ggplot()
if(sw_print) {
print(p_arranged)
}
out[["plots" ]][[ var_name_x[i_var_x] ]][["both"]] <- p_arranged
} # sw_TWI_plots_keep
} # numeric:numeric
} # 2 Two-way interaction
} # i_var_x
invisible(out)
} # end of e_plot_model_contrasts()
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