plotrix: add.ps – R documentation

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add.ps

add p-values from t-tests

Description

Adds p-values comparing the different cells at each x-axis position with a reference cell. Uses a syntax similar to raw.means.plot2.

Usage

add.ps(data, col.id, col.offset, col.x, col.value, fun.aggregate = "mean",
 ref.offset = 1, prefixes,alternative = c("two.sided", "less", "greater"),
 mu = 0, paired = FALSE, var.equal = FALSE, lty = 0, ...)

Arguments

`data`	A data.frame
`col.id`	character vector specifying the id column.
`col.offset`	character vector specifying the offset column.
`col.x`	character vector specifying the x-axis column.
`col.value`	character vector specifying the data column.
`fun.aggregate`	Function or function name used for aggregating the results. Default is "mean".
`ref.offset`	Scalar numeric indicating the reference level to be tested against. The default is 1 corresponding to levels(factor(d[,col.offset]))[1].
`prefixes`	character vector of the indices for the p-values. If missing corresponds to levels(factor(d.new[,col.offset]))[-ref.offset].
`alternative`	same as in t.test
`mu`	same as in t.test
`paired`	same as in t.test
`var.equal`	same as in t.test
`lty`	line type of axis, Default is 0 (i.e., no line).
`...`	further arguments passed to axis.

Details

This function computes t-tests comparing the values at each x-axis position for each condition against the reference condition at and adds the p-values to the axis.

This functions uses the same syntax as raw.means.plot2 and should be used in addition to it. Note that values are ordered according to the col.id so paired = TRUE should be fine.

Value

axis is plotted.

Author(s)

Henrik Singmann

Examples

## Not run: 
#The examples uses the OBrienKaiser dataset from car and needs reshape.
# This extends the examples from raw.means.plot
require(reshape)
require(car)
data(OBrienKaiser)
OBKnew <- cbind(factor(1:nrow(OBrienKaiser)), OBrienKaiser)
colnames(OBKnew)[1] <- "id"
OBK.long <- melt(OBKnew)
OBK.long[, c("measurement", "time")] <-
 t(vapply(strsplit(as.character(OBK.long$variable), "\\."),  "[", c("", "")))

# For this example the position at each x-axis are within-subject comparisons!
raw.means.plot2(OBK.long, "id", "measurement", "gender", "value")
 add.ps(OBK.long, "id", "measurement", "gender", "value", paired = TRUE)
 #reference is "fup"

raw.means.plot2(OBK.long, "id", "measurement", "gender", "value")
add.ps(OBK.long, "id", "measurement", "gender", "value", ref.offset = 2,
 paired = TRUE) #reference is "post"

# Use R's standard (i.e., Welch test)
raw.means.plot2(OBK.long, "id", "treatment", "gender", "value")
add.ps(OBK.long, "id", "treatment", "gender", "value",
 prefixes = c("p(control vs. A)", "p(control vs. B)"))

# Use standard t-test
raw.means.plot2(OBK.long, "id", "treatment", "gender", "value")
add.ps(OBK.long, "id", "treatment", "gender", "value", var.equal = TRUE,
 prefixes = c("p(control vs. A)", "p(control vs. B)"))


## End(Not run)

plotrix

Various Plotting Functions

v3.8-1

GPL (>= 2)

Authors

Jim Lemon, Ben Bolker, Sander Oom, Eduardo Klein, Barry Rowlingson, Hadley Wickham, Anupam Tyagi, Olivier Eterradossi, Gabor Grothendieck, Michael Toews, John Kane, Rolf Turner, Carl Witthoft, Julian Stander, Thomas Petzoldt, Remko Duursma, Elisa Biancotto, Ofir Levy, Christophe Dutang, Peter Solymos, Robby Engelmann, Michael Hecker, Felix Steinbeck, Hans Borchers, Henrik Singmann, Ted Toal, Derek Ogle, Darshan Baral, Ulrike Groemping, Bill Venables

Initial release

2021-01-21