plot.frag.alpha {fragility}

Plot Method for "frag.alpha" Objects

Description

Visualizes the fragility at different statistical significance levels.

Usage

## S3 method for class 'frag.alpha'
plot(x, method, fragility = "FI", percentage = TRUE,
     xlab, ylab, xlim, ylim, cex.pts, col.line, col.pval, col.sig,
     lty.pval, lwd, lwd.pval, pch, pch.na, tid1, tid2, FQ.nma = FALSE, ...)

Arguments

x

an object of class "frag.alpha" produced by the function frag.study.alpha, frag.ma.alpha, or frag.nma.alpha.

method

a character string indicating the method used to calculate the p-value when x is of class "frag.study.alpha" produced by frag.study.alpha. It must be an element of x$methods; the default is the first method in x$methods.

fragility

a character string of either "FI" (fragility index, the default) or "FQ" (fragility quotient), indicating which fragility measure will be presented in the plot.

percentage

a logical value indicating whether the fragility quotient is presented in percentage (TRUE, the default) or not (FALSE). It is only used when the argument fragility = "FQ".

xlab

a label for the x axis.

ylab

a label for the y axis.

xlim

the x limits c(x1, x2) of the plot.

ylim

the y limits c(y1, y2) of the plot.

cex.pts

the size of points in the plot (the default is 0.5).

col.line

the color of the line segments that join the points (the default is "gray50").

col.pval

the color of the vertical line depicting the p-value of the original data (the default is "gray50"). It is only used when the p-value is between the lower and upper limits of the considered significance levels.

col.sig

a vector of the two colors for two directions of significance change. The default includes "forestgreen" (for non-significance altered to significance) and "firebrick" (for significance altered to non-significance).

lty.pval

the type of the vertical line depicting the p-value of the original data. The default is 2 (dashed). It is only used when the p-value is between the lower and upper limits of the considered significance levels.

lwd

the width of the line segments that join the points (the default is 1).

lwd.pval

the width of the vertical line depicting the p-value of the original data. The default is 1. It is only used when the p-value is between the lower and upper limits of the considered significance levels.

pch

the symbol of points in the plot. The default is 16 (filled circle).

pch.na

the symbol of points depicting fragility index/quotient = NA (if any, in cases that significance or non-significance cannot be altered). The default is 1 (unfilled circle).

tid1

the first treatment of the comparison of interest; if not specified, the first comparison in x$tid.f will be used. It is only used when x is of class "frag.nma.alpha" for a network meta-analysis.

tid2

the second treatment of the comparison of interest. Only one comparison can be specified by tid1 and tid2 at one time for plotting. It is only used when x is of class "frag.nma.alpha".

FQ.nma

a logical value indicating whether the fragility quotient in a network meta-analysis is the total sample size associated with the specific treatment comparison (FALSE, the default) or the total sample size in the whole network meta-analysis across all treatment groups (TRUE). It is only used when x is of class "frag.nma.alpha".

...

other arguments that can be passed to plot.default.

Details

A scatter plot is generated, where the x axis presents the different significance levels, and the y axis presents the corresponding fragility indexes or fragility quotients.

Value

None.

References

Lin L (2021). "Factors that impact fragility index and their visualizations." Journal of Evaluation in Clinical Practice, 27(2), 356–64. <doi: 10.1111/jep.13428>

Lin L, Chu H (2022). "Assessing and visualizing fragility of clinical results with binary outcomes in R using the fragility package." PLOS ONE, 17(6), e0268754. <doi: 10.1371/journal.pone.0268754>

See Also

frag.study.alpha, frag.ma.alpha, and frag.nma.alpha for assessing fragility of an individual study, a meta-analysis, and a network meta-analysis at multiple significance levels, respectively.