Regression models forest plot

Data

We use the R dataset lung in the survival package.
We can select variables and change their names using the transmute() function, or add labels to our variables of interest using the apply_labels function:

# Libraries
library(survival)
library(dplyr)
library(expss) # for apply_labels function

# Data used
pretty_lung <- lung %>%
  transmute(time,
    status = status - 1,
    age,
    sex = factor(sex, labels = c("Male", "Female")),
    ph.ecog = factor(ph.ecog),
    meal.cal
  ) %>%
  apply_labels(
    age = "Age", 
    sex = "Sex", 
    ph.ecog = "ECOG", 
    meal.cal = "Meal Cal"
)


pretty_lung format :

A data frame with 228 observations on the following 6 variables :
time Survival time in days
status Censoring status 0=censored, 1=dead
age Age in years
sex Patient sex
ph.ecog ECOG performance score. 0=asymptomatic, 1= symptomatic but completely ambulatory, 2= in bed <50% of the day, 3= in bed > 50% of the day but not bedbound, 4 = bedbound
meal.cal Calories consumed at meals 




#Head of dataset
knitr::kable(head(pretty_lung,8), align = "l")
time status age sex ph.ecog meal.cal
306 1 74 Male 1 1175
455 1 68 Male 0 1225
1010 0 56 Male 0 NA
210 1 57 Male 1 1150
883 1 60 Male 0 NA
1022 0 74 Male 1 513
310 1 68 Female 2 384
361 1 71 Female 2 538



forestmodel package

The forest_model function produce a forest plot based on a regression model

forest_model(
model, regression model produced by lm, glm, coxph
panels = default_forest_panels(model, factor_separate_line = factor_separate_line), list with details of the panels
covariates = NULL, a character vector optionally listing the variables to include in the plot
exponentiate = NULL, whether the numbers on the x scale should be exponentiated for plotting
funcs = NULL, optional list of functions required for formatting panels$display
factor_separate_line = FALSE, whether to show the factor variable name on a separate line
format_options = forest_model_format_options(), formatting options as a list as generated by forest_model_format_options
theme = theme_forest(), theme to apply to the plot
limits = NULL, limits of the forest plot on the X-axis
breaks = NULL, breaks to appear on the X-axis
return_data = FALSE, return the data to produce the plot as well as the plot itself
recalculate_width = TRUE, TRUE to recalculate panel widths using the current device or the desired plot width in inches
recalculate_height = TRUE, TRUE to shrink text size using the current device or the desired plot height in inches
model_list = NULL, list of models to incorporate into a single forest plot
merge_models = FALSE, if TRUE, merge all models in one section
exclude_infinite_cis = TRUE, whether to exclude points and confidence intervals that go to positive or negative infinity from plotting
...
)

Multivariate - Forest plot based on a logistic model

We use the function forest_model to print the forest plot : 

library(forestmodel)

model <- glm(status ~ age + sex + ph.ecog + meal.cal, data=pretty_lung)
class(model) <- c("myglm",class(model)) # to use by default Wald CI
confint.myglm <- confint.default

print(forest_model(model))



Multivariate - Forest plot based on a cox model

We use the function forest_model to print the forest plot : 

library(forestmodel)

model <- coxph(Surv(time, status) ~ ., data=pretty_lung)
model$xlevels <- unname(model$xlevels) # to retrieve labels for categorical variables (only for cox models)

print(forest_model(model))



Univariate - Forest plot based on several logistic models

We use the function forest_model to print the forest plot : 

library(forestmodel)

covariates <- c('age','sex')
univ_formulas <- sapply(covariates, function(x) as.formula(paste('status~', x)))
univ_models <- lapply(univ_formulas, function(x){
  model <- glm(x, family='binomial', data=pretty_lung)
  class(model) <- c("myglm",class(model)) # to use by default Wald CI
  return(model)
})
confint.myglm <- confint.default

print(forest_model(model_list = univ_models, covariates = covariates, merge_models = T))

Univariate - Forest plot based on several Cox models

We use the function forest_model to print the forest plot : 

library(forestmodel)

covariates <- c('age','sex','ph.ecog','meal.cal')
univ_formulas <- sapply(covariates, function(x) as.formula(paste('Surv(time, status)~', x)))
univ_models <- lapply(univ_formulas, function(x){
  model <- coxph(x, data=pretty_lung)
  model$xlevels <- unname(model$xlevels) # to retrieve labels for categorical variables (only for cox models)
  return(model)
})

print(forest_model(model_list = univ_models, covariates = covariates, merge_models = T))




Contact

This document is a work of the statistics team in the Biostatistics and Medical Information Department at Saint-Louis Hospital in Paris (SBIM).
Based on The R Graph Gallery by Yan Holtz.