README.md

In raredd/forest: Forest plots

forest plots

this is an experimental package and not to be trusted

Installation

# install.packages('devtools')
devtools::install_github('raredd/forest')

Basic usage and supported models/objects

| object | package | |:---------------------|:-----------------------------------------------------------------| | coxph | survival | | coxphf | coxphf | | crr | cmprsk | | crr2 | cmprsk2 | | formula | stats | | glm | stats | | logistf | logistf |

library('survival')
forest(coxph(Surv(time, status) ~ I(age / 10) + factor(sex) + factor(ph.ecog), lung))
box('outer')

More options

lung2 <- within(lung, {
  sex <- factor(sex, 1:2, c('Male', 'Female'))
  ph.ecog <- factor(ph.ecog)
})

lbl <- c('10-year increase', levels(lung2$sex), levels(lung2$ph.ecog))
forest(
  coxph(Surv(time, status) ~ I(age / 10) + sex + ph.ecog, lung2),
  header = c('Age at enrollment', 'Sex', 'ECOG PS'),
  plotArgs = list(
    cex = 2, layout = 'unified', show_conf = TRUE, xlim = c(0, 10),
    labels = lbl, reset_par = FALSE, names = c('', 'N (%)', 'HR (95% CI)', 'p-value')
  )
)
title(xlab = 'Hazard ratio (95% CI)')
box('outer')

Multiple models

models <- list(
  'Model 1' = coxph(Surv(time, status) ~ age + sex + ph.ecog, lung2),
  'Model 2' = coxph(Surv(time, status) ~ age + sex, lung2),
  'Model 3' = coxph(Surv(time, status) ~ age, lung2)
)

forest2(
  models, cex = 2, col.sig = c('grey70', 'green4'),
  panel_size = c(2, 3, 2), xlim = c(0, 10)
)
box('outer')

Panel options

set.seed(1)
x <- forest(
  coxph(Surv(time, status) ~ I(age / 10) + sex + ph.ecog, lung2),
  plot = FALSE
)
y <- replicate(7, rnorm(20), simplify = FALSE)

plot(
  x, cex = 2, panel_size = c(4, 3, 2), xlim = c(-5, 5),
  left_panel = list(
    'Mean y' = sapply(y, function(yy) sprintf('%.3f', mean(yy))),
    'Median y' = sapply(y, function(yy) sprintf('%.3f', median(yy)))
  ),
  center_panel = {
    panel_box(y)
    axis(1, pos = 0.5)
  }
)
box('outer')

library('rawr') ## for tplot
hr_ci <- x$cleanfp_list$numeric[1:3]
plot(
  x, xlim = c(0, 10), reset_par = FALSE,
  center_panel = {
    panel_tplot(
      rev(asplit(hr_ci, 1)), type = 'd', cex = 3,
      pch = c(16, 1, 1), group.pch = FALSE,
      col = c(1, 2, 2), group.col = FALSE
    )
    axis(1, pos = 0.5)
  }
)
legend(
  6, 8.5, legend = c('Point estimate', '95% CI'),
  col = 1:2, pch = c(16, 1), bty = 'n', xpd = NA
)
box('outer')

Coerce raw data to a forest plot

set.seed(1)
x <- c(NA, 1, 2, NA, 1, 2, 3)
dat <- data.frame(
  N = x * 10,
  x = x,
  lower = x - 1,
  upper = x + 1,
  p.value = replace(runif(7), is.na(x), NA)
)
dat

##    N  x lower upper   p.value
## 1 NA NA    NA    NA        NA
## 2 10  1     0     2 0.3721239
## 3 20  2     1     3 0.5728534
## 4 NA NA    NA    NA        NA
## 5 10  1     0     2 0.2016819
## 6 20  2     1     3 0.8983897
## 7 30  3     2     4 0.9446753

x <- as.forest(
  x = dat$x, lower = dat$lower, upper = dat$upper, p.value = dat$p.value,
  labels = ifelse(is.na(dat$x), 'header', paste0('   ', x)),
  N = dat$N, P = dat$N / 100
)
x

##      Term     N (%)     Estimate CI            p-value
## [1,] "header" ""        ""       ""            ""     
## [2,] " 1"     "10 (10)" "1.00"   "0.00 - 2.00" "0.37" 
## [3,] " 2"     "20 (20)" "2.00"   "1.00 - 3.00" "0.57" 
## [4,] "header" ""        ""       ""            ""     
## [5,] " 1"     "10 (10)" "1.00"   "0.00 - 2.00" "0.20" 
## [6,] " 2"     "20 (20)" "2.00"   "1.00 - 3.00" "0.90" 
## [7,] " 3"     "30 (30)" "3.00"   "2.00 - 4.00" "0.94"

plot(x, show_conf = TRUE)
box('outer')

Session info

within.list(sessionInfo(), loadedOnly <- NULL)

## R version 4.1.2 (2021-11-01)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] rawr_1.0.1        survival_3.3-2    knitr_1.38        forest_0.0.0.9000

raredd/forest documentation built on Feb. 19, 2024, 9:22 p.m.