Summarize multiple paired comparisons

Description

Convert a logical vector or a vector of p-values or a difference or distance matrix into a display identifying the pairs for which the differences were not significantly different or for which the difference exceeded a threshold.

Details

Convert a logical vector or a vector of p-values or a difference or distance matrix into either a letter-based display using "multcompLetters" or a graphic roughly like a "T" using "multcompTs" to identify factor levels or similar groupings that are or are not significantly different. Designed for use in conjunction with the output of functions like TukeyHSD, diststats, simint, simtest, csimint, csimtestmultcomp, friedmanmc, kruskalmcpgirmess.

Author(s)

Spencer Graves and Hans-Peter Piepho with help from Sundar Dorai-Raj

Maintainer: Spencer Graves <spencer.graves@prodsyse.com>

References

Piepho, Hans-Peter (2004) "An Algorithm for a Letter-Based Representation of All-Pairwise Comparisons", Journal of Computational and Graphical Statistics, 13(2)456-466.

John R. Donaghue (2004) "Implementing Shaffer's multiple comparison procedure for a large number of groups", pp. 1-23 in Benjamini, Bretz and Sarkar (eds) Recent Developments in Multiple Comparison Procedures (Institute of Mathematical Statistics Lecture Notes-Monograph Series vol. 47)

Examples

dif3 <- c(FALSE, FALSE, TRUE)
names(dif3) <- c("a-b", "a-c", "b-c")
multcompTs(dif3)
multcompLetters(dif3)

library(MASS)
multcompBoxplot(Postwt~Treat, data=anorexia)

Extracts p-values

Description

For a given object it will look for the column named "p adj" or "difference" and extract its value keeping its names

Usage

extract_p(x)

## Default S3 method:
extract_p(x)

## S3 method for class 'TukeyHSD'
extract_p(x)

## S3 method for class 'mc'
extract_p(x)

Arguments

Value

A named vector with p-values or logical values.

Methods (by class)

• extract_p(default):

• extract_p(TukeyHSD): extract p values from a TukeyHSD object

• extract_p(mc):

Author(s)

Luciano Selzer

See Also

multcompLetters multcompTs

Examples

experiment <- data.frame(treatments = gl(11, 20, labels = c("dtl", "ctrl", "treat1", 
              "treat2", "treatA2", "treatB", "treatB2",
              "treatC", "treatD", "treatA1", "treatX")),
              y = c(rnorm(20, 10, 5), rnorm(20, 20, 5), rnorm(20, 22, 5), rnorm(20, 24, 5),
               rnorm(20, 35, 5), rnorm(20, 37, 5), rnorm(20, 40, 5), rnorm(20, 43, 5),
               rnorm(20, 45, 5), rnorm(20, 60, 5), rnorm(20, 60, 5)))
exp_tukey <- TukeyHSD(exp_aov <- aov(y  ~ treatments, data = experiment))

extract_p(exp_tukey)

if(require(pgirmess)){
extract_p(kruskalmc(y ~ treatments, data = experiment))
}

boxplot with multcomp graphics

Description

Create boxplots with multcompTs and / or multcompLetters

Usage

multcompBoxplot(
  formula,
  data,
  horizontal = TRUE,
  compFn = "TukeyHSD",
  sortFn = "mean",
  decreasing = TRUE,
  plotList = list(boxplot = list(fig = c(0, 0.75, 0, 1)), multcompTs = list(fig = c(0.7,
    0.85, 0, 1)), multcompLetters = list(fig = c(0.87, 0.97, 0.03, 0.98), fontsize = 20,
    fontface = "bold"))
)

Arguments

Details

For formula = y~z, if 'sortFn' is a function or the name of a function, 'multcompBoxplot' starts by applying sortFn to the subsets of y corresponding to each level of z, and then sorting those summaries in increasing or decreasing order, per 'decreasing'. If 'sortFn' is NULL or NA, this sort step is skipped.

'multcompBoxplot' then creates 'boxplot' as specified in 'plotList'. Next, 'compFn' is called to generate comparisons to feed to the functions (multcompTs and / or multcompLetters, whose output is then passed to (plot.multcomp) for plotting. Components of the relevant sublists of 'plotList' are made available to par or (for plot.multcompLetters) to gpar.

Value

This function invisibly returns a list with one component for each component of plotList containing the output of the appropriate "plot.multcomp" call plus the output of "compFn".

Author(s)

Spencer Graves

See Also

boxplot multcompTs multcompLetters plot.multcomp TukeyHSD par gpar

Examples

# Example from help("TukeyHSD")
multcompBoxplot(breaks~tension, data=warpbreaks)
# 'sortFn' can be either a function or a function name
# default order is 'decreasing=TRUE'
multcompBoxplot(breaks~tension, data=warpbreaks,
       sortFn=median, decreasing=FALSE)

##################
library(multcomp)
data(recovery)
# Horizontal boxplots with both
# multcomp Ts and Letters on the right
# Using recovery{multcomp} data set
multcompBoxplot(minutes~blanket, recovery)

# Plotting boxes rather than letters and Ts

multcompBoxplot(minutes~blanket, recovery,
                plotList=list(
                    boxplot=list(fig=c(0, 0.75, 0, 1), las=1,
                        cex.axis=1.5),
                    multcompTs=list(fig=c(0.7, 0.85, 0, 1),
                        type='boxes'),
                    multcompLetters=list(
                        fig=c(0.87, 0.97, 0.03, 0.98),
                        type='boxes') ) )

####################

# Vertical boxplots with both
# multcomp Ts and Letters on the top
multcompBoxplot(minutes~blanket, recovery,
                        horizontal=FALSE)

# Horizontal boxplots with 2 different
# displays of the "Ts" on the left
multcompBoxplot(minutes~blanket, recovery,
  plotList=list(
      boxplot=list(fig=c(0.3, 1, 0, 1)),
      multcompTs=list(fig=c(0, 0.15, 0, 1),
        orientation="reverse"),
      multcompTs=list(fig=c(0.15, 0.3, 0, 1),
        type="boxes", orientation="reverse",
        mar=c(5,2, 4, 0)+.1) ) )

library(MASS)
anorx <-
multcompBoxplot(Postwt~Treat, data=anorexia)

## Not run: 
# Confirm than sortFn=NULL or NA
# leaves the order unchanged
library(multcomp)
data(cholesterol)
cholesterol$trt3 <- with(cholesterol, factor(
  as.character(trt), levels=levels(trt)[c(5:4,1:3)]))
multcompBoxplot(response ~ trt3, cholesterol,
           sortFn=NULL)
multcompBoxplot(response ~ trt3, cholesterol,
           sortFn=NA)

## End(Not run)

Letter summary of similarities and differences

Description

Convert a logical vector or a vector of p-values or a correlation or distance matrix into a character-based display in which common characters identify levels or groups that are not significantly different. Designed for use with the output of functions like TukeyHSD, diststats, simint, simtest, csimint, csimtestmultcomp, friedmanmc, kruskalmcpgirmess.

Usage

multcompLetters(
  x,
  compare = "<",
  threshold = 0.05,
  Letters = c(letters, LETTERS, "."),
  reversed = FALSE
)

multcompLetters2(formula, x, data, ...)

multcompLetters3(z, y, x, data, ...)

multcompLetters4(object, comp, ...)

Arguments

Details

Produces a "Letter-Based Representation of All- Pairwise Comparisons" as described by Piepho (2004). (The present algorithm does NOT perform his "sweeping" step.) multcompLettersx are wrapper of multcompLetters that will reorder the levels of the data so that the letters appear in a descending order of the mean. mulcompletters3 is similar to multcompletters2 except that it uses vector names to separate and the later has an formula interface. multcompLetters4 will take a aov or lm object and a comparison test and will produce all the letters for the terms and interactions.

Value

An object of class 'multcompLetters', which is a list with the following components:

multcompLetters4 will return a named list with the terms containing a object of class 'multcompLetters' as produced by multcompLetters.

Functions

• multcompLetters2():

• multcompLetters3(): create a compact letters display and order the letters

• multcompLetters4(): create a compact letters display using a aov object

Author(s)

Spencer Graves, Hans-Peter Piepho and Luciano Selzer

References

Piepho, Hans-Peter (2004) "An Algorithm for a Letter-Based Representation of All-Pairwise Comparisons", Journal of Computational and Graphical Statistics, 13(2)456-466.

See Also

multcompBoxplot plot.multcompLetters print.multcompLetters multcompTs vec2mat

Examples

##
## 1.  a logical vector indicating signficant differences
##
dif3 <- c(FALSE, FALSE, TRUE)
names(dif3) <- c("A-B", "A-C", "B-C")
dif3L <- multcompLetters(dif3)
dif3L
print(dif3L)
print(dif3L, TRUE)

##
## 2.  numeric vector indicating statistical significance
##
dif4 <- c(.01, .02, .03, 1)
names(dif4) <- c("a-b", "a-c", "b-d", "a-d")
(diff4.T <- multcompLetters(dif4))

(dif4.L1 <- multcompLetters(dif4,
       Letters=c("*", ".")))
# "Letters" can be any character strings,
# but they should be recognizable when
# concatenated.

##
## 3.  distance matrix
##
dJudge <- dist(USJudgeRatings)
dJl <- multcompLetters(dJudge, compare='>', threshold = median(dJudge))
# comparison of 43 judges;  compact but undecipherable:
dJl

x <- array(1:9, dim=c(3,3),
   dimnames=list(LETTERS[1:3], NULL) )
d3 <- dist(x)
dxLtrs <- multcompLetters(d3, compare=">", threshold=2)

d3d <- dist(x, diag=TRUE)
dxdLtrs <- multcompLetters(d3d, compare=">", threshold=2)


all.equal(dxLtrs, dxdLtrs)


d3u <- dist(x, upper=TRUE)
dxuLtrs <- multcompLetters(d3d, compare=">", threshold=2)


all.equal(dxLtrs, dxuLtrs)


##
## 4.  cor matrix
##
set.seed(4)
x100 <- matrix(rnorm(100), ncol=5,
               dimnames=list(NULL, LETTERS[1:5]) )
cx <- cor(x100)
cxLtrs <- multcompLetters(abs(cx), threshold=.3)


##
##5. reversed
##

dif3 <- c(FALSE, FALSE, TRUE)
names(dif3) <- c("A-B", "A-C", "B-C")
dif3L <- multcompLetters(dif3)
dif3L.R <- multcompLetters(dif3, rev = TRUE)
dif3L
dif3L.R


##
##6. multcompletters2 usage

experiment <- data.frame(treatments = gl(11, 20, labels = c("dtl", "ctrl", "treat1", 
              "treat2", "treatA2", "treatB", "treatB2",
              "treatC", "treatD", "treatA1", "treatX")),
              y = c(rnorm(20, 10, 5), rnorm(20, 20, 5), rnorm(20, 22, 5), rnorm(20, 24, 5),
               rnorm(20, 35, 5), rnorm(20, 37, 5), rnorm(20, 40, 5), rnorm(20, 43, 5),
               rnorm(20, 45, 5), rnorm(20, 60, 5), rnorm(20, 60, 5)))
exp_tukey <- TukeyHSD(exp_aov <- aov(y  ~ treatments, data = experiment))
exp_letters1 <- multcompLetters(exp_tukey$treatments[,4])
exp_letters1
#Notice lowest mean treatments gets a "e"
#Ordered letters
multcompLetters2(y ~ treatments, exp_tukey$treatments[,"p adj"], experiment)
multcompLetters2(y ~ treatments, exp_tukey$treatments[,"p adj"], experiment, reversed = TRUE)

##7. multcompletters3 usage

multcompLetters3("treatments", "y", exp_tukey$treatments[,"p adj"], experiment)

##8. multcompletters4 usage


multcompLetters4(exp_aov, exp_tukey)

"T" depiction of undifferentiated classes

Description

Convert a logical vector or a vector of p-values or a correlation or distance matrix into a matrix with an associated visual display to show whether the differences between items exceed a threshold. Designed for use with the output of functions like TukeyHSD, diststats, simint, simtest, csimint, csimtestmultcomp, friedmanmc, kruskalmcpgirmess.

Usage

multcompTs(x, compare = "<", threshold = 0.05, sep = ".")

Arguments

Details

Produces a matrix of class "multcompTs", describing the "undifferentiated classes" that identify the other factor levels or items that are not distinct or not significantly different from the "base" of the "T"; if two or more levels have the same pattern of significant differences, the two are combined into one "T" with two "bases". The resulting T's are similar to the "undifferentiated classes" discussed by Donaghue (2004).

Value

An object of class "multcompTs", which is a matrix of values -1, 0, 1, with one row for each level compared and one column for each "T", read as follows: 1 = base of the "T" represented by that column, 0 = level(s) not significantly different, and (-1) = levels(s) significantly different. If two or more levels have the same pattern of significant and insignificant differences, they are combined into a single column that can be represented by a "T" with multiple bases. The column name will be a character string concatenating all row names with "1" in that column separated by the "sep" character. Thus, the matrix should have as many 1's as it has rows. Also, the lower triangular portion should have as many "-1's" as there are "TRUE" (e.g., significant) differences among the comparisons.

Author(s)

Spencer Graves and Hans-Peter Piepho

References

John R. Donaghue (2004) "Implementing Shaffer's multiple comparison procedure for a large number of groups", pp. 1-23 in Benjamini, Bretz and Sarkar (eds) Recent Developments in Multiple Comparison Procedures (Institute of Mathematical Statistics Lecture Notes-Monograph Series vol. 47)

Spencer Graves and Hans-Peter Piepho (2006) "Simple Visualizations of Paired Comparisons", vignette("VisualizingPairedComparisons", package = "multcompView")

See Also

multcompBoxplot multcompLetters plot.multcompTs vec2mat dist

Examples

##
## 0.  Conference presentation comparing Ts and Letters
##
dir(system.file('doc', package='multcompView'),
    pattern='\\.pdf$', full.name=TRUE)

##
## 1.  logical vector indicating different pairs
##
dif3 <- c(FALSE, FALSE, TRUE)
names(dif3) <- c("a-b", "a-c", "b-c")
multcompTs(dif3)

##
## 2.  numeric vector indicating statistical significance
##
dif4 <- c(.01, .02, .03, 1)
names(dif4) <- c("a-b", "a-c", "b-d", "a-d")
(diff4.T <- multcompTs(dif4))
plot(diff4.T)

##
## 3.  Distance matrix
##
dJudge <- dist(USJudgeRatings)
dJt <- multcompTs(dJudge, compare='>', threshold = median(dJudge))
# comparison of 43 judges;  compact but undecipherable:
plot(dJt, cex.axis=.5)

x <- array(1:9, dim=c(3,3),
   dimnames=list(LETTERS[1:3], NULL) )
d3 <- dist(x)
dxTs <- multcompTs(d3, compare=">", threshold=2)
plot(dxTs)

d3d <- dist(x, diag=TRUE)
dxdTs <- multcompTs(d3d, compare=">", threshold=2)


all.equal(dxTs, dxdTs)


d3u <- dist(x, upper=TRUE)
dxuTs <- multcompTs(d3d, compare=">", threshold=2)


all.equal(dxTs, dxuTs)


##
## 4.  cor matrix
##
set.seed(4)
x100 <- matrix(rnorm(100), ncol=5,
               dimnames=list(NULL, LETTERS[1:5]) )
cx <- cor(x100)
cxTs <- multcompTs(abs(cx), threshold=.3)
plot(cxTs)

plot multcomp graphics

Description

Plot graphic(s) for multcompTs or multcompLetters objects

Usage

## S3 method for class 'multcompLetters'
plot(
  x,
  horizontal = FALSE,
  col = 1:6,
  type = c("Letters", "boxes"),
  add = FALSE,
  at,
  width,
  fig = c(0, 1, 0, 1),
  label.levels = if (add) NA else 0.05,
  label.groups = NA,
  ...
)

Arguments

Details

The requested graphic is either plotted by itself or added to an existing plot as specified by the arguments. The placement can be controlled by 'fig' and 'at'.

The fontsize and fontface of a plot of a multcompLetters object with 'type = "Letters"' can be adjusted as describe on the gpar help page.

Value

A list with two components:

Author(s)

Spencer Graves

See Also

multcompTs multcompLetters multcompBoxplot gpar

Examples

##
## plot(multcompTs(...))
##
dif4 <- c(.1, .02, .03, 1)
names(dif4) <- c("A-B", "A-C", "B-C", "A-D")
(mcT4 <- multcompTs(dif4))
# Standard plot, base of "Ts" point left
mcT4.1 <- plot(mcT4, label.groups=0.05)
# Redo using "at" = list 
plot(mcT4, label.groups=0.05, at=mcT4.1)
# Same plot with group labels closer to the figure
plot(mcT4, label.groups=0.02)

# Base of "Ts" point right 
plot(mcT4, label.groups=TRUE, orientation="r")
# Base of "Ts" point down 
plot(mcT4, horizontal=TRUE, label.groups=0.05)
# Base of "Ts" point up
plot(mcT4, horizontal=TRUE, label.groups=0.05,
     orientation="r")

# Same 4 plots but with boxes & triangles, not Ts
plot(mcT4, label.groups=0.05, type="b")
plot(mcT4, label.groups=0.05, orientation="r",
     type="b")
plot(mcT4, horizontal=TRUE, label.groups=0.05,
     type="b")
plot(mcT4, horizontal=TRUE, label.groups=0.05,
     orientation="r", type="b")

##
## plot(multcompLetters(...))
##
# ... using dif4 from above
(mcL4 <- multcompLetters(dif4, Letters=LETTERS))
# Standard plot
## Not run: 
# Requires (grid)
mcL4.1 <- plot(mcL4, label.groups=0.05)
# Redo using "at" = list 
plot(mcL4, label.groups=0.05, at=mcL4.1)

# With bold face and larger font 
plot(mcL4, label.groups=0.05,
     fontsize=28, fontface="bold")

# Horizontal rather than vertical 
plot(mcL4, horizontal=TRUE, label.groups=0.05)

## End(Not run)

# Same as boxes rather than letters 
plot(mcL4, label.groups=0.05, type="b")
plot(mcL4, horizontal=TRUE, label.groups=0.05,
     type="b")

plot multcomp graphics

Description

Plot graphic(s) for multcompTs or multcompLetters objects

Usage

## S3 method for class 'multcompTs'
plot(
  x,
  horizontal = FALSE,
  col = 1:6,
  type = c("Ts", "boxes"),
  orientation = c("standard", "reverse"),
  add = FALSE,
  at,
  width,
  fig = c(0, 1, 0, 1),
  lwd = 3,
  label.levels = if (add) NA else 0.05,
  label.groups = NA,
  T.base = 0.4,
  ...
)

Arguments

Details

The requested graphic is either plotted by itself or added to an existing plot as specified by the arguments. The placement can be controlled by 'fig' and 'at'.

The fontsize and fontface of a plot of a multcompLetters object with 'type = "Letters"' can be adjusted as describe on the gpar help page.

Value

A list with two components:

Author(s)

Spencer Graves

See Also

multcompTs multcompLetters multcompBoxplot gpar

Examples

##
## plot(multcompTs(...))
##
dif4 <- c(.1, .02, .03, 1)
names(dif4) <- c("A-B", "A-C", "B-C", "A-D")
(mcT4 <- multcompTs(dif4))
# Standard plot, base of "Ts" point left
mcT4.1 <- plot(mcT4, label.groups=0.05)
# Redo using "at" = list 
plot(mcT4, label.groups=0.05, at=mcT4.1)
# Same plot with group labels closer to the figure
plot(mcT4, label.groups=0.02)

# Base of "Ts" point right 
plot(mcT4, label.groups=TRUE, orientation="r")
# Base of "Ts" point down 
plot(mcT4, horizontal=TRUE, label.groups=0.05)
# Base of "Ts" point up
plot(mcT4, horizontal=TRUE, label.groups=0.05,
     orientation="r")

# Same 4 plots but with boxes & triangles, not Ts
plot(mcT4, label.groups=0.05, type="b")
plot(mcT4, label.groups=0.05, orientation="r",
     type="b")
plot(mcT4, horizontal=TRUE, label.groups=0.05,
     type="b")
plot(mcT4, horizontal=TRUE, label.groups=0.05,
     orientation="r", type="b")

##
## plot(multcompLetters(...))
##
# ... using dif4 from above
(mcL4 <- multcompLetters(dif4, Letters=LETTERS))
# Standard plot
## Not run: 
# Requires (grid)
mcL4.1 <- plot(mcL4, label.groups=0.05)
# Redo using "at" = list 
plot(mcL4, label.groups=0.05, at=mcL4.1)

# With bold face and larger font 
plot(mcL4, label.groups=0.05,
     fontsize=28, fontface="bold")

# Horizontal rather than vertical 
plot(mcL4, horizontal=TRUE, label.groups=0.05)

## End(Not run)

# Same as boxes rather than letters 
plot(mcL4, label.groups=0.05, type="b")
plot(mcL4, horizontal=TRUE, label.groups=0.05,
     type="b")

plot multcomp displays

Description

Helper functions for plot.multcompTs and plot.multcompLetters. These not intended to be called directly and are hidden in a namespace. You can use 'getAnywhere' to see them.

Usage

plotBoxes(
  obj,
  at,
  width,
  horizontal,
  col,
  add,
  label.levels,
  label.groups,
  orientation = "",
  ...
)

Arguments

Details

The requested graphic is either plotted by itself or added to an existing plot as specified by the arguments.

"plotTs" and "plotBoxes" use traditional R graphics and will not be discussed further here.

"plotLetters" uses 'grid' graphics, because it seems to provide more support for controlling the side-by-side placement of "Letters" of possibly different colors and widths. The "Letters" display will be positioned in the "plot region" defined by fig and mar, assuming the entire device region is 37 lines both wide and tall. Thus, the plot region is diff(fig[1:2])*37 lines wide and diff(fig(1:2])*37 lines high. If, for example, fig = c(0.9, 1, 0, 1), this makes the plot region 3.7 lines wide. With the default mar=c(5, 4, 4, 2)+0.1 lines, the "width" of the plot region is therefore 3.7 - (4.1+2.1) = (-2.5) lines. "plotLetters" initially ignores this contradictory negative width, and centers the plot at the midpoint of h0 = fig[1]+mar[2]/37, h1 = fig[2]-mar[4]/37, v0 = fig[3]+mar[1]/37, and v1 = fig[4]-mar[3]/37. The "Letters" for the different levels compared are rescaled from at[, "center"] to fit inside At.rng = if(horizontal) c(h0, h1) else c(v0, v1). With "n" levels compared and at.rng = range(at[, "center"]), at[, "center"] is expanded to (at.rng+/-0.5) and rescaled to match At.rng; if(diff(At.rng)<=0), an error message is issued.

Meanwhile, the "Letters" are centered at the midpoint of W.rng = if(horizontal) c(v0, v1) else v(h0, h1) [the opposite of At.rng]; the argument "width" used by plotTs and plotBoxes is not used (and not even accepted) by plotLetters. If(label.levels), these are positioned in the midpoint of the right margin in the "W" direction.

Value

"Done"

Author(s)

Spencer Graves

See Also

plot.multcompTs plot.multcompLetters gpar

Examples

# Designed to be called from plot.multcompTs
# or plot.multcompLetters, NOT directly by users.  

plot multcomp displays

Description

Helper functions for plot.multcompTs and plot.multcompLetters. These not intended to be called directly and are hidden in a namespace. You can use 'getAnywhere' to see them.

Usage

plotLetters(
  obj,
  at,
  horizontal,
  col,
  add,
  label.levels,
  font.family = "mono",
  fig = par("fig"),
  mar = par("mar"),
  ...
)

Arguments

Details

The requested graphic is either plotted by itself or added to an existing plot as specified by the arguments.

"plotTs" and "plotBoxes" use traditional R graphics and will not be discussed further here.

"plotLetters" uses 'grid' graphics, because it seems to provide more support for controlling the side-by-side placement of "Letters" of possibly different colors and widths. The "Letters" display will be positioned in the "plot region" defined by fig and mar, assuming the entire device region is 37 lines both wide and tall. Thus, the plot region is diff(fig[1:2])*37 lines wide and diff(fig(1:2])*37 lines high. If, for example, fig = c(0.9, 1, 0, 1), this makes the plot region 3.7 lines wide. With the default mar=c(5, 4, 4, 2)+0.1 lines, the "width" of the plot region is therefore 3.7 - (4.1+2.1) = (-2.5) lines. "plotLetters" initially ignores this contradictory negative width, and centers the plot at the midpoint of h0 = fig[1]+mar[2]/37, h1 = fig[2]-mar[4]/37, v0 = fig[3]+mar[1]/37, and v1 = fig[4]-mar[3]/37. The "Letters" for the different levels compared are rescaled from at[, "center"] to fit inside At.rng = if(horizontal) c(h0, h1) else c(v0, v1). With "n" levels compared and at.rng = range(at[, "center"]), at[, "center"] is expanded to (at.rng+/-0.5) and rescaled to match At.rng; if(diff(At.rng)<=0), an error message is issued.

Meanwhile, the "Letters" are centered at the midpoint of W.rng = if(horizontal) c(v0, v1) else v(h0, h1) [the opposite of At.rng]; the argument "width" used by plotTs and plotBoxes is not used (and not even accepted) by plotLetters. If(label.levels), these are positioned in the midpoint of the right margin in the "W" direction.

Value

"Done"

Author(s)

Spencer Graves

See Also

plot.multcompTs plot.multcompLetters gpar

Examples

# Designed to be called from plot.multcompTs
# or plot.multcompLetters, NOT directly by users.  

plot multcomp displays

Description

Helper functions for plot.multcompTs and plot.multcompLetters. These not intended to be called directly and are hidden in a namespace. You can use 'getAnywhere' to see them.

Usage

plotTs(
  obj,
  at,
  width,
  horizontal,
  col,
  add,
  lwd,
  label.levels,
  label.groups,
  T.base,
  orientation = "",
  ...
)

Arguments

Details

The requested graphic is either plotted by itself or added to an existing plot as specified by the arguments.

"plotTs" and "plotBoxes" use traditional R graphics and will not be discussed further here.

"plotLetters" uses 'grid' graphics, because it seems to provide more support for controlling the side-by-side placement of "Letters" of possibly different colors and widths. The "Letters" display will be positioned in the "plot region" defined by fig and mar, assuming the entire device region is 37 lines both wide and tall. Thus, the plot region is diff(fig[1:2])*37 lines wide and diff(fig(1:2])*37 lines high. If, for example, fig = c(0.9, 1, 0, 1), this makes the plot region 3.7 lines wide. With the default mar=c(5, 4, 4, 2)+0.1 lines, the "width" of the plot region is therefore 3.7 - (4.1+2.1) = (-2.5) lines. "plotLetters" initially ignores this contradictory negative width, and centers the plot at the midpoint of h0 = fig[1]+mar[2]/37, h1 = fig[2]-mar[4]/37, v0 = fig[3]+mar[1]/37, and v1 = fig[4]-mar[3]/37. The "Letters" for the different levels compared are rescaled from at[, "center"] to fit inside At.rng = if(horizontal) c(h0, h1) else c(v0, v1). With "n" levels compared and at.rng = range(at[, "center"]), at[, "center"] is expanded to (at.rng+/-0.5) and rescaled to match At.rng; if(diff(At.rng)<=0), an error message is issued.

Meanwhile, the "Letters" are centered at the midpoint of W.rng = if(horizontal) c(v0, v1) else v(h0, h1) [the opposite of At.rng]; the argument "width" used by plotTs and plotBoxes is not used (and not even accepted) by plotLetters. If(label.levels), these are positioned in the midpoint of the right margin in the "W" direction.

Value

"Done"

Author(s)

Spencer Graves

See Also

plot.multcompTs plot.multcompLetters gpar

Examples

# Designed to be called from plot.multcompTs
# or plot.multcompLetters, NOT directly by users.  

print a multcompLetters object

Description

print method for an object of class 'multcompLetters'.

Usage

## S3 method for class 'multcompLetters'
print(x, all = FALSE, ...)

Arguments

Details

Prints only the Letters component of the 'multcompLetters' list unless all=TRUE.

Value

the named, character vector representation of the 'multcompLetters' evaluation of the distance relationships

Author(s)

Spencer Graves

See Also

multcompLetters

Examples

dif3 <- c(FALSE, FALSE, TRUE)
names(dif3) <- c("A-B", "A-C", "B-C")
dif3L <- multcompLetters(dif3)
dif3L
print(dif3L)
print(dif3L, TRUE)

Convert a vector with hyphenated names into a matrix.

Description

Convert a vector with hypehnated names into a symmetric matrix with names

Usage

vec2mat(x, sep = "-")

Arguments

Details

x must have names each of which contains exactly one hyphen; if not, vec2mat issues an error message. If the same comparison is present multiple times, the last value is used; no check is made for duplicates.

Value

A symmetric matrix of the same class as the input with names obtained from unique(strsplit(names(x))). All nonspecified elements will be 1 if class(x) is numeric, FALSE if logical and "" if character. Used by the functions 'multcompLetters' and 'multcompTs'.

Author(s)

Spencer Graves

See Also

multcompLetters multcompTs

Examples

dif3 <- c(FALSE, FALSE, TRUE)
names(dif3) <- c("a-b", "a-c", "b-c")
vec2mat(dif3)

dif3. <- 1:3
names(dif3.) <- c("a-b", "a-c", "b-c")
vec2mat(dif3.)

dif.ch <- c("this",'is','it')
names(dif.ch) <- c("a-b", "a-c", "b-c")
vec2mat(dif.ch)

vec2mat(array(1, dim=c(2,2)))
 

Convert a vector of hyphenated names into a character matrix.

Description

Convert a vector of hyphenated names into a character matrix with 2 columns containing the names split in each row.

Usage

vec2mat2(x, sep = "-")

Arguments

Details

If each element of x does not contain exactly 1 "sep" character, an error is issued.

Value

A character matrix with rownames = x and with the character string preceding the "sep" character in the first column and the character string following the "sep" character in the second column.

Author(s)

Spencer Graves

See Also

vec2mat multcompLetters

Examples

vec2mat2(c("a-b", "a-c", "b-c"))

vec2mat2(c("a-b", "b-a"))