forest.umbrella: Forest plots for "umbrella" objects

Description Usage Arguments Details Value References Examples

Description

Draw a forest plot of the factors included in an umbrella review. The basic version of this plot contains three parts:

Usage

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## S3 method for class 'umbrella'
forest(
  x,
  measure = "eG",
  main_title = NA,
  main_value = NA,
  main_x_axis = NA,
  max.value = NULL,
  print.classes = NULL,
  col_sig = c("#252525", "#252525"),
  log_cex_dots = FALSE,
  fix_size_dots = NA,
  xlim = NULL,
  xlim_main_title = 0,
  xlim_value = 2.1,
  xlim_factor = -2.1,
  ylim_correction_value = 0,
  ylim_correction_text = 0,
  cex_title = 1.4,
  cex_text_header = 1,
  cex_text = 0.9,
  cex_value_header = 1,
  cex_value = 0.9,
  cex_x_axis = 1.1,
  cex_x_axis_value = 0.8,
  cex_dots = 1.2,
  col_title = "#1D1D1D",
  col_text_header = "#252525",
  col_text = "#252525",
  col_value_header = "#252525",
  col_value = "#252525",
  col_x_axis = "#252525",
  col_dots = "#252525",
  col_lines = "#252525",
  pos_value = "left-align",
  pos_text = "right-align",
  add_columns = NULL,
  main_add_columns = NA,
  xlim_add_columns = NA,
  x_lim_adj = 0,
  y_lim_adj = 0,
  x_axis_adj = 0,
  ...
)

Arguments

x

an object of class “umbrella”.

measure

type of effect size used in the plot. Default is equivalent Hedges' g ("eG"). Alternatively, equivalent Odds Ratio ("eOR") can be used.

main_title

the title of the plot

main_value

a title for the header of the 'value' column.

main_x_axis

title of the x-axis

max.value

the maximum value that will be plotted on the x-axis. Must be strictly superior to 1 when equivalent odds ratio (eOR) measure is used, and strictly superior to 0 when SMD measure is used. Note that minimum value will be automatically set to the inverse of max.value for eOR measure and to - max.value for SMD measure.

print.classes

a vector of classes. Only factors reaching these classes will be displayed on the plot. These classes must be:

  • "I", "II", "III", "IV" and/or "ns" for the "Ioannidis" classification

  • "High", "Moderate", "Weak" and/or "Very weak" for the "GRADE" classification

  • "I", "II", "III", "IV", and/or "V" for the "Personalized" classification

col_sig

a vector of two colors. Statistically significant factors are displayed using these colors:

  • Protective factors (i.e., with an eOR < 1 or an SMD < 0) are displayed with the first color

  • Risk factors (i.e., with an eOR >= 1 or an SMD >= 0) will be displayed with the second color.

  • Non-significant factors are displayed with the color indicated in the 'col_dots' argument.

log_cex_dots

a logical value indicating whether the logarithm of the size of the dot should be used (should be TRUE or FALSE). When set as TRUE, this argument allows to reduce the disparities in the size of the dots between factors.

fix_size_dots

a unique positive numeric value that is used to fix the size of all dots

xlim

a vector containing the limits of the x-axis (x1, x2) of the plot.

xlim_main_title

position of the title of the plot on the x-axis.

xlim_value

position of the 'value' column on the x-axis.

xlim_factor

position of the 'factor' column on the x-axis.

ylim_correction_value

when the position of columns is modified (e.g., "right-align" versus "center"), the height of the columns can be slighlty modified. This correction value allows to adjust the height of the 'value' column.

ylim_correction_text

when the position of columns is modified (e.g., "right-align" versus "center"), the height of the columns can be slighlty modified. This correction value allows to adjust the height of the 'factor' column and to any new column added to the plot.

cex_title

numeric value indicating the amount by which title text should be scaled relative to the default.

cex_text_header

numeric value indicating the amount by which the text of the header of the 'factor' column and of any column added to the plot should be scaled relative to the default.

cex_text

numeric value indicating the amount by which the text of the 'factor' column and of any column added to the plot should be scaled relative to the default.

cex_value_header

numeric value indicating the amount by which the text of the header of the 'value' column should be scaled relative to the default.

cex_value

numeric value indicating the amount by which the text of the 'value' column should be scaled relative to the default.

cex_x_axis

numeric value indicating the amount by which the text of the x-axis title should be scaled relative to the default.

cex_x_axis_value

numeric value indicating the amount by which the text of the x-axis values should be scaled relative to the default.

cex_dots

numeric value indicating the amount by which dot size should be scaled relative to the default.

col_title

color of the font of the title.

col_text_header

color of the font of the header of the 'factor' column and to any column added to the plot.

col_text

color of the font of the 'factor' column and of any column added to the plot.

col_value_header

color of the header of the 'value' column.

col_value

color of the font of the 'value' column.

col_x_axis

color of the font of the x-axis.

col_dots

color of the dots.

col_lines

color of the lines.

pos_value

type of centering of the column displaying the values. Must be either "left-align", "center", or "right-align".

pos_text

type of centering of the 'factor' column. Must be either "left-align", "center", or "right-align".

add_columns

a vector/dataframe containing the columns that should be added to the plot. The number of rows of the columns added to the plot should be equal to the number of factors.

main_add_columns

a vector containing the name of the header of the new columns added to the plot (default is the name of the columns in the dataset).

xlim_add_columns

position of the new columns added on x-axis. Should be a numeric vector containing the exact same number values as the number of columns added. Mandatory when columns are added to the plot.

x_lim_adj

a numeric value that can be used to adjust the size of the window of the plot on the x-axis.

y_lim_adj

a numeric value that can be used to adjust the size of the window of the plot on the y-axis.

x_axis_adj

a numeric value that can be used to adjust the height of the space between the x-axis and the title of the x-axis.

...

additional arguments that can be passed to the forest.umbrella function

Details

The function allows to have a visualization of the results of an umbrella review. Various parameters, such as the type of effect size displayed, the restriction to some classes or the color of the dots, allows to simplify the visualization.

Value

In addition to the plot, the function returns a list including:

References

Tortella-Feliu, M. and Fullana, M.A., Perez-Vigil, A., Torres, X., Chamorro, J., and Littarelli, S.A., ..., & Radua, J. (2019). Risk Factors for Posttraumatic Stress Disorder: An Umbrella Review of Systematic Reviews and Meta-Analyses. Neuroscience & Biobehavioral Reviews, 107, 154–165.

Examples

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### perform an umbrella review of various datasets
umbs <- union.umbrella(union.umbrella(union.umbrella(union.umbrella(
umbrella(df.OR), umbrella(df.SMD)), umbrella(df.RR)), umbrella(df.IRR)), umbrella(df.HR))

### stratify the evidence according to some Personalized criteria
umbs.crit <- add.evidence(umbs, criteria = "Personalized",
  class_I = c(n_cases = 1000, p_value = 1e-6, esb_p = 0.10, egger_p = 0.10,
  I2 = 0.25, pi = "notnull"),
  class_II = c(n_cases = 1000, p_value = 1e-6, largest_CI = "notnull"),
  class_III = c(n_cases = 1000, p_value = 1e-3),
  class_IV = c(p_value = 5e-2))
sum.umbs <- summary.umbrella(umbs.crit)

### generate a forest plot of each factor included in the umbrella review
forest.umbrella(umbs.crit, max.value = 7,
                main_title = "Plot of the umbrella review")

metaumbrella documentation built on Jan. 7, 2022, 5:08 p.m.