Package 'forestmodel' reference manual

Title:	Forest Plots from Regression Models
Description:	Produces forest plots using 'ggplot2' from models produced by functions such as stats::lm(), stats::glm() and survival::coxph().
Authors:	Nick Kennedy <[email protected]>
Maintainer:	Nick Kennedy <[email protected]>
License:	GPL-2
Version:	0.6.2
Built:	2024-11-29 08:57:39 UTC
Source:	CRAN

Default panels for forest_model

Description

Default panels for forest_model

Usage

default_forest_panels(
  model = NULL,
  factor_separate_line = FALSE,
  measure = NULL,
  trans_char = "I"
)
default_forest_panels(
  model = NULL,
  factor_separate_line = FALSE,
  measure = NULL,
  trans_char = "I"
)

Arguments

`model`	model object to guess label and determine defaults
`factor_separate_line`	changes defaults for widths of variable depending on whether factors have their name on separate line
`measure`	label for main forest plot
`trans_char`	character representation of transform for axes

Value

'list' ready to be passed to 'forest_model'

Calculate default breaks for limits

Description

This function does not work as well as grDevices::axisTicks and so that should be used instead.

Usage

forest_breaks(limits, trans = I)
forest_breaks(limits, trans = I)

Arguments

`limits`	limits of plot
`trans`	transformation that will be used on the limits

Value

a vector with breaks ready to pass to panel_forest_plot

Produce a forest plot based on a regression model

Description

Produce a forest plot based on a regression model

Usage

forest_model(
  model,
  panels = default_forest_panels(model, factor_separate_line = factor_separate_line),
  covariates = NULL,
  exponentiate = NULL,
  funcs = NULL,
  factor_separate_line = FALSE,
  format_options = forest_model_format_options(),
  theme = theme_forest(),
  limits = NULL,
  breaks = NULL,
  return_data = FALSE,
  recalculate_width = TRUE,
  recalculate_height = TRUE,
  model_list = NULL,
  merge_models = FALSE,
  exclude_infinite_cis = TRUE
)
forest_model(
  model,
  panels = default_forest_panels(model, factor_separate_line = factor_separate_line),
  covariates = NULL,
  exponentiate = NULL,
  funcs = NULL,
  factor_separate_line = FALSE,
  format_options = forest_model_format_options(),
  theme = theme_forest(),
  limits = NULL,
  breaks = NULL,
  return_data = FALSE,
  recalculate_width = TRUE,
  recalculate_height = TRUE,
  model_list = NULL,
  merge_models = FALSE,
  exclude_infinite_cis = TRUE
)

Arguments

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

Details

This function takes the model output from one of the common model functions in R (e.g. lm, glm, coxph). If a label attribute was present on any of the columns in the original data (e.g. from the labelled package), this label is used in preference to the column name.

The panels parameter is a list of lists each of which have an element width and, optionally, item, display, display_na, heading, hjust and fontface. item can be "forest" for the forest plot (exactly one required) or "vline" for a vertical line. display indicates which column to display as text. It can be a quoted variable name or a formula. The column display can include the standard ones produced by tidy and in addition variable (the term in the model; for factors this is the bare variable without the level), level (the level of factors), reference (TRUE for the reference level of a factor). For coxph models, there will also be n_events for the number of events in the group with that level of the factor and person_time for the person-time in that group. The function trans is definded to be the transformation between the coefficients and the scales (e.g. exp). Other functions not in base R can be provided as a list with the parameter funcs. display_na allows for an alternative display for NA terms within estimate.

Value

A ggplot ready for display or saving, or (with return_data == TRUE, a list with the parameters to call panel_forest_plot in the element plot_data and the ggplot itself in the element plot)

Examples


library("survival")
library("dplyr")
pretty_lung <- lung %>%
  transmute(time,
    status,
    Age = age,
    Sex = factor(sex, labels = c("Male", "Female")),
    ECOG = factor(lung$ph.ecog),
    `Meal Cal` = meal.cal
  )

print(forest_model(coxph(Surv(time, status) ~ ., pretty_lung)))

# Example with custom panels

panels <- list(
  list(width = 0.03),
  list(width = 0.1, display = ~variable, fontface = "bold", heading = "Variable"),
  list(width = 0.1, display = ~level),
  list(width = 0.05, display = ~n, hjust = 1, heading = "N"),
  list(width = 0.05, display = ~n_events, width = 0.05, hjust = 1, heading = "Events"),
  list(
    width = 0.05,
    display = ~ replace(sprintf("%0.1f", person_time / 365.25), is.na(person_time), ""),
    heading = "Person-\nYears", hjust = 1
  ),
  list(width = 0.03, item = "vline", hjust = 0.5),
  list(
    width = 0.55, item = "forest", hjust = 0.5, heading = "Hazard ratio", linetype = "dashed",
    line_x = 0
  ),
  list(width = 0.03, item = "vline", hjust = 0.5),
  list(width = 0.12, display = ~ ifelse(reference, "Reference", sprintf(
    "%0.2f (%0.2f, %0.2f)",
    trans(estimate), trans(conf.low), trans(conf.high)
  )), display_na = NA),
  list(
    width = 0.05,
    display = ~ ifelse(reference, "", format.pval(p.value, digits = 1, eps = 0.001)),
    display_na = NA, hjust = 1, heading = "p"
  ),
  list(width = 0.03)
)
forest_model(coxph(Surv(time, status) ~ ., pretty_lung), panels)

data_for_lm <- tibble(
  x = rnorm(100, 4),
  y = rnorm(100, 3, 0.5),
  z = rnorm(100, 2, 2),
  outcome = 3 * x - 2 * y + 4 * z + rnorm(100, 0, 0.1)
)

print(forest_model(lm(outcome ~ ., data_for_lm)))

data_for_logistic <- data_for_lm %>% mutate(
  outcome = (0.5 * (x - 4) * (y - 3) * (z - 2) + rnorm(100, 0, 0.05)) > 0.5
)

print(forest_model(glm(outcome ~ ., binomial(), data_for_logistic)))
library("survival")
library("dplyr")
pretty_lung <- lung %>%
  transmute(time,
    status,
    Age = age,
    Sex = factor(sex, labels = c("Male", "Female")),
    ECOG = factor(lung$ph.ecog),
    `Meal Cal` = meal.cal
  )

print(forest_model(coxph(Surv(time, status) ~ ., pretty_lung)))

# Example with custom panels

panels <- list(
  list(width = 0.03),
  list(width = 0.1, display = ~variable, fontface = "bold", heading = "Variable"),
  list(width = 0.1, display = ~level),
  list(width = 0.05, display = ~n, hjust = 1, heading = "N"),
  list(width = 0.05, display = ~n_events, width = 0.05, hjust = 1, heading = "Events"),
  list(
    width = 0.05,
    display = ~ replace(sprintf("%0.1f", person_time / 365.25), is.na(person_time), ""),
    heading = "Person-\nYears", hjust = 1
  ),
  list(width = 0.03, item = "vline", hjust = 0.5),
  list(
    width = 0.55, item = "forest", hjust = 0.5, heading = "Hazard ratio", linetype = "dashed",
    line_x = 0
  ),
  list(width = 0.03, item = "vline", hjust = 0.5),
  list(width = 0.12, display = ~ ifelse(reference, "Reference", sprintf(
    "%0.2f (%0.2f, %0.2f)",
    trans(estimate), trans(conf.low), trans(conf.high)
  )), display_na = NA),
  list(
    width = 0.05,
    display = ~ ifelse(reference, "", format.pval(p.value, digits = 1, eps = 0.001)),
    display_na = NA, hjust = 1, heading = "p"
  ),
  list(width = 0.03)
)
forest_model(coxph(Surv(time, status) ~ ., pretty_lung), panels)

data_for_lm <- tibble(
  x = rnorm(100, 4),
  y = rnorm(100, 3, 0.5),
  z = rnorm(100, 2, 2),
  outcome = 3 * x - 2 * y + 4 * z + rnorm(100, 0, 0.1)
)

print(forest_model(lm(outcome ~ ., data_for_lm)))

data_for_logistic <- data_for_lm %>% mutate(
  outcome = (0.5 * (x - 4) * (y - 3) * (z - 2) + rnorm(100, 0, 0.05)) > 0.5
)

print(forest_model(glm(outcome ~ ., binomial(), data_for_logistic)))

Create format options for `forest_model`

Description

Create format options for forest_model

Usage

forest_model_format_options(
  colour = "black",
  color = NULL,
  shape = 15,
  text_size = 5,
  point_size = 5,
  banded = TRUE
)
forest_model_format_options(
  colour = "black",
  color = NULL,
  shape = 15,
  text_size = 5,
  point_size = 5,
  banded = TRUE
)

Arguments

`colour`	colour of the point estimate and error bars
`color`	alias for colour
`shape`	shape of the point estimate
`text_size`	text size in mm
`point_size`	point size
`banded`	whether to show light grey bands behind alternate rows

Value

list of format options

Create definition of a panel for `forest_model`

Description

Create definition of a panel for forest_model

Usage

forest_panel(
  width,
  item = c("", "forest", "vline"),
  display = NULL,
  display_na = NULL,
  hjust = NULL,
  heading = NULL,
  fontface = NULL,
  linetype = NULL,
  line_x = NULL,
  parse = NULL,
  width_group = NULL
)
forest_panel(
  width,
  item = c("", "forest", "vline"),
  display = NULL,
  display_na = NULL,
  hjust = NULL,
  heading = NULL,
  fontface = NULL,
  linetype = NULL,
  line_x = NULL,
  parse = NULL,
  width_group = NULL
)

Arguments

`width`	relative width of the panel
`item`	specification of which type of item to use; overridden if display is not missing
`display`	bare expression that specifies the variable or expresion to display
`display_na`	what to display if a value is `NA`
`hjust`	horizontal justification
`heading`	heading to be used (defaults to the variable name)
`fontface`	fontface to use
`linetype`	line type to use
`line_x`	position for dashed line in forest plot
`parse`	whether text should be parsed as expressions
`width_group`	grouping used when recalcualting widths of panels

Value

panel definition as a list

Generate panels for forest plots

Description

Generate panels for forest plots

Usage

forest_panels(..., margin = 0.03)
forest_panels(..., margin = 0.03)

Arguments

`...`	panels to variables in data
`margin`	margin to leave at left and right edges

Value

a panels list ready for forest_model or forest_rma

Generate a forest plot from a meta-analysis

Description

Generate a forest plot from a meta-analysis

Usage

forest_rma(
  model,
  panels = NULL,
  study_labels = NULL,
  additional_data = NULL,
  point_size = NULL,
  model_label = NULL,
  show_individual_studies = TRUE,
  show_model = TRUE,
  show_stats = list(`I^2` = rlang::quo(sprintf("%0.1f%%", I2)), p =
    rlang::quo(format.pval(QEp, digits = 4, eps = 1e-04, scientific = 1))),
  trans = I,
  funcs = NULL,
  format_options = forest_model_format_options(),
  theme = theme_forest(),
  limits = NULL,
  breaks = NULL,
  return_data = FALSE,
  recalculate_width = TRUE,
  recalculate_height = TRUE
)
forest_rma(
  model,
  panels = NULL,
  study_labels = NULL,
  additional_data = NULL,
  point_size = NULL,
  model_label = NULL,
  show_individual_studies = TRUE,
  show_model = TRUE,
  show_stats = list(`I^2` = rlang::quo(sprintf("%0.1f%%", I2)), p =
    rlang::quo(format.pval(QEp, digits = 4, eps = 1e-04, scientific = 1))),
  trans = I,
  funcs = NULL,
  format_options = forest_model_format_options(),
  theme = theme_forest(),
  limits = NULL,
  breaks = NULL,
  return_data = FALSE,
  recalculate_width = TRUE,
  recalculate_height = TRUE
)

Arguments

`model`	a single `rma` object or a `list` of them
`panels`	`list` with details of the panels that make up the plot (See Details)
`study_labels`	a character vector of study labels or list of character vectors the same length as `model`
`additional_data`	a `data.frame` of additional data that can be referenced for the data shown in the panels of the forest plot
`point_size`	a numeric vector with the point sizes for the individual studies, or a single value used for all studies, or a list of numeric vectors if more than one model is to be plotted
`model_label`	a single model label or character vector of model labels the same length as `model`
`show_individual_studies`	whether to show the individual studies (the default) or just the summary diamond
`show_model`	a logical value, if 'TRUE', show model result, otherwise only show forest plots for studies
`show_stats`	a `list` of stats to show at the bottom of the forest plot for e.g. heterogeneity
`trans`	an optional transform function used on the numeric data for plotting the axes
`funcs`	optional list of functions required for formatting `panels$display`
`format_options`	formatting options as a list as generated by `forest_model_format_options`
`theme`	theme to apply to the plot
`limits`	limits of the forest plot on the X-axis (taken as the range of the data by default)
`breaks`	breaks to appear on the X-axis (note these will be exponentiated if `exponentiate == TRUE`)
`return_data`	return the data to produce the plot as well as the plot itself
`recalculate_width`	`TRUE` to recalculate panel widths using the current device or the desired plot width in inches
`recalculate_height`	`TRUE` to shrink text size using the current device or the desired plot height in inches

Details

This produces a forest plot using the rma

Value

plot

Examples

if (require("metafor")) {
  data("dat.bcg")
  dat <- escalc(measure = "RR", ai = tpos, bi = tneg, ci = cpos, di = cneg, data = dat.bcg)
  model <- rma(yi, vi, data = dat)

  print(forest_rma(model,
    study_labels = paste(dat.bcg$author, dat.bcg$year),
    trans = exp
  ))

  print(forest_rma(model,
    panels = forest_panels(
      Study = ~study,
      N = ~n, ~vline, `Log Relative Risk` = ~ forest(line_x = 0),
      ~ spacer(space = 0.10),
      ~ sprintf("%0.3f (%0.3f, %0.3f)", estimate, conf.low, conf.high)
    ),
    study_labels = paste(dat.bcg$author, dat.bcg$year),
    trans = exp
  ))
}
if (require("metafor")) {
  data("dat.bcg")
  dat <- escalc(measure = "RR", ai = tpos, bi = tneg, ci = cpos, di = cneg, data = dat.bcg)
  model <- rma(yi, vi, data = dat)

  print(forest_rma(model,
    study_labels = paste(dat.bcg$author, dat.bcg$year),
    trans = exp
  ))

  print(forest_rma(model,
    panels = forest_panels(
      Study = ~study,
      N = ~n, ~vline, `Log Relative Risk` = ~ forest(line_x = 0),
      ~ spacer(space = 0.10),
      ~ sprintf("%0.3f (%0.3f, %0.3f)", estimate, conf.low, conf.high)
    ),
    study_labels = paste(dat.bcg$author, dat.bcg$year),
    trans = exp
  ))
}

Plot a forest plot with panels of text

Description

Plot a forest plot with panels of text

Usage

panel_forest_plot(
  forest_data,
  mapping = aes(estimate, xmin = conf.low, xmax = conf.high),
  panels = default_forest_panels(),
  trans = I,
  funcs = NULL,
  format_options = list(colour = "black", shape = 15, banded = TRUE, text_size = 5,
    point_size = 5),
  theme = theme_forest(),
  limits = NULL,
  breaks = NULL,
  recalculate_width = TRUE,
  recalculate_height = TRUE,
  exclude_infinite_cis = TRUE
)
panel_forest_plot(
  forest_data,
  mapping = aes(estimate, xmin = conf.low, xmax = conf.high),
  panels = default_forest_panels(),
  trans = I,
  funcs = NULL,
  format_options = list(colour = "black", shape = 15, banded = TRUE, text_size = 5,
    point_size = 5),
  theme = theme_forest(),
  limits = NULL,
  breaks = NULL,
  recalculate_width = TRUE,
  recalculate_height = TRUE,
  exclude_infinite_cis = TRUE
)

Arguments

`forest_data`	`data.frame` with the data needed for both the plot and text
`mapping`	mapping aesthetic created using `aes`
`panels`	`list` with details of the panels that make up the plot (See Details)
`trans`	transform for scales
`funcs`	optional list of functions required for formatting `panels$display`
`format_options`	formatting options as a list as generated by `forest_model_format_options`
`theme`	theme to apply to the plot
`limits`	limits of the forest plot on the X-axis (taken as the range of the data by default)
`breaks`	breaks to appear on the X-axis (note these will be exponentiated if `exponentiate == TRUE`)
`recalculate_width`	`TRUE` to recalculate panel widths using the current device or the desired plot width in inches
`recalculate_height`	`TRUE` to shrink text size using the current device or the desired plot height in inches
`exclude_infinite_cis`	whether to exclude points and confidence intervals that go to positive or negative infinity from plotting. They will still be displayed as text. Defaults to `TRUE`, since otherwise plot is malformed

Value

A ggplot ready for display or saving

Default forest theme

Description

Default forest theme

Usage

theme_forest()
theme_forest()

Value

a theme object for use with ggplot2

Package 'forestmodel'

Help Index

Default panels for forest_model

Description

Usage

Arguments

Value

Calculate default breaks for limits

Description

Usage

Arguments

Value

Produce a forest plot based on a regression model

Description

Usage

Arguments

Details

Value

Examples

Create format options for forest_model

Description

Usage

Arguments

Value

Create definition of a panel for forest_model

Description

Usage

Arguments

Value

Generate panels for forest plots

Description

Usage

Arguments

Value

Generate a forest plot from a meta-analysis

Description

Usage

Arguments

Details

Value

Examples

Plot a forest plot with panels of text

Description

Usage

Arguments

Value

Default forest theme

Description

Usage

Value

Create format options for `forest_model`

Create definition of a panel for `forest_model`