G'day Patrick,
On Mon, 05 May 2008 08:15:29 +0200
Patrick Giraudoux <patrick.giraudoux at univ-fcomte.fr> wrote:
Berwin A Turlach a ?crit :
But I have compiled R on my boxes myself. How did you install R?
From source or by using the prepackaged Ubuntu deb files?
From the pre-packaged Ubuntu, updated to 6.7.0 recently ? Do you
think it may come from this ?
Could be possible, but I would find it hard to believe. But it raises
the question which pre-packaged packages have you all installed. Your
package pgirmess seems to have quite a few dependencies (which I had
to install first on my machine before I could run R CMD check). But
that could be a red herring too, since the problem seems to be that the
command PermTest is not found while the code in the examples are run.
There has been a threat on something similar in R-devel on August
2007... but I cannot understand the meaning.
Did you look at the file in pgirmess.Rcheck that I mentioned?
You'll find a copy of pgirmess-Ex.R, but I cannot get what is the
meaning of this file...
Also,
did you try to load the version of the library in pgrimess.Rcheck in a
R session and check if you find the PermTest function in that case?
Yes indeed. I found PermTest in the R folder and in the R-ex folder of
the pgirmess folder in the pgirmess.Rcheck folder.
With these problems, I am a bit of a trial-and-error person, so if I
cannot reproduce the error, I cannot find out what the problem is....
Cheers,
Berwin
Thanks anyway for the hints. It may help.
### * <HEADER>
###
attach(NULL, name = "CheckExEnv")
assign("nameEx",
local({
s <- "__{must remake R-ex/*.R}__"
function(new) {
if(!missing(new)) s <<- new else s
}
}),
pos = "CheckExEnv")
## Add some hooks to label plot pages for base and grid graphics
assign("base_plot_hook",
function() {
pp <- par(c("mfg","mfcol","oma","mar"))
if(all(pp$mfg[1:2] == c(1, pp$mfcol[2]))) {
outer <- (oma4 <- pp$oma[4]) > 0; mar4 <- pp$mar[4]
mtext(sprintf("help(\"%s\")", nameEx()), side = 4,
line = if(outer)max(1, oma4 - 1) else min(1, mar4 - 1),
outer = outer, adj = 1, cex = .8, col = "orchid", las=3)
}
},
pos = "CheckExEnv")
assign("grid_plot_hook",
function() {
grid::pushViewport(grid::viewport(width=grid::unit(1, "npc") -
grid::unit(1, "lines"), x=0, just="left"))
grid::grid.text(sprintf("help(\"%s\")", nameEx()),
x=grid::unit(1, "npc") + grid::unit(0.5,
"lines"),
y=grid::unit(0.8, "npc"), rot=90,
gp=grid::gpar(col="orchid"))
},
pos = "CheckExEnv")
setHook("plot.new", get("base_plot_hook", pos = "CheckExEnv"))
setHook("persp", get("base_plot_hook", pos = "CheckExEnv"))
setHook("grid.newpage", get("grid_plot_hook", pos = "CheckExEnv"))
assign("cleanEx",
function(env = .GlobalEnv) {
rm(list = ls(envir = env, all.names = TRUE), envir = env)
RNGkind("default", "default")
set.seed(1)
options(warn = 1)
.CheckExEnv <- as.environment("CheckExEnv")
delayedAssign("T", stop("T used instead of TRUE"),
assign.env = .CheckExEnv)
delayedAssign("F", stop("F used instead of FALSE"),
assign.env = .CheckExEnv)
sch <- search()
newitems <- sch[! sch %in% .oldSearch]
for(item in rev(newitems))
eval(substitute(detach(item), list(item=item)))
missitems <- .oldSearch[! .oldSearch %in% sch]
if(length(missitems))
warning("items ", paste(missitems, collapse=", "),
" have been removed from the search path")
},
pos = "CheckExEnv")
assign("ptime", proc.time(), pos = "CheckExEnv")
## at least one package changes these via ps.options(), so do this
## before loading the package.
## Use postscript as incomplete files may be viewable, unlike PDF.
## Choose a size that is close to on-screen devices, fix paper
ps.options(width = 7, height = 7, paper = "a4", reset = TRUE)
grDevices::postscript("pgirmess-Ex.ps")
assign("par.postscript", graphics::par(no.readonly = TRUE), pos =
"CheckExEnv")
options(contrasts = c(unordered = "contr.treatment", ordered =
"contr.poly"))
options(warn = 1)
library('pgirmess')
assign(".oldSearch", search(), pos = 'CheckExEnv')
assign(".oldNS", loadedNamespaces(), pos = 'CheckExEnv')
cleanEx(); nameEx("PermTest")
### * PermTest
flush(stderr()); flush(stdout())
### Name: PermTest
### Title: Permutation test for lm, lme and glm (binomial and Poisson)
### objects
### Aliases: PermTest PermTest.lm PermTest.lme PermTest.glm print.PermTest
### Keywords: htest
### ** Examples
library(MASS)
mylm<-lm(Postwt~Prewt,data=anorexia)
PermTest(mylm,B=250)
## Dobson (1990) Page 93: Randomized Controlled Trial :
counts <- c(18,17,15,20,10,20,25,13,12)
outcome <- gl(3,1,9)
treatment <- gl(3,3)
glm.D93 <- glm(counts ~ outcome + treatment, family=poisson)
PermTest(glm.D93,B=250)
library(nlme)
fm2 <- lme(distance ~ age + Sex, data = Orthodont, random = ~ 1)
PermTest(fm2,B=250)
cleanEx(); nameEx("Segments")
### * Segments
flush(stderr()); flush(stdout())
### Name: Segments
### Title: Draw line segments between pairs of points.
### Aliases: Segments
### Keywords: hplot
### ** Examples
mydata<-cbind(rnorm(20),rnorm(20),rnorm(20),rnorm(20))
plot(range(rbind(mydata[,1],mydata[,3])),range(rbind(mydata[,2],mydata[,4])),type="n",xlab="",ylab="")
Segments(mydata,col=rainbow(20))
myvec<-rnorm(4)
plot(myvec[c(1,3)],myvec[c(2,4)],type="n",xlab="",ylab="")
Segments(myvec)
myvec<-rnorm(16)
plot(myvec,myvec,type="n",xlab="",ylab="")
Segments(myvec)
cleanEx(); nameEx("TukeyHSDs")
### * TukeyHSDs
flush(stderr()); flush(stdout())
### Name: TukeyHSDs
### Title: Simplify the list of a TukeyHSD object keeping the significant
### differences only.
### Aliases: TukeyHSDs
### Keywords: htest
### ** Examples
summary(fm1 <- aov(breaks ~ wool + tension, data = warpbreaks))
myobject<-TukeyHSD(fm1, "tension", ordered = TRUE)
myobject
TukeyHSDs(myobject)
cleanEx(); nameEx("ci")
### * ci
flush(stderr()); flush(stdout())
### Name: CI
### Title: Confidence interval of percentages
### Aliases: CI
### Keywords: htest
### ** Examples
x<-c(2,10,7,8,7) # eg: number of positive cases
y<-c(56,22,7,20,5)# eg: number of negative cases
CI(x,y)
x<-c(2,10,7,8,7) # eg: number of positive cases
y<-c(4,11,7,16,10)# eg: total number of cases
CI(x,y,totrials=TRUE)
cleanEx(); nameEx("classnum")
### * classnum
flush(stderr()); flush(stdout())
### Name: classnum
### Title: Gives an index vector of the class category of each value of a
### numerical vector
### Aliases: classnum print.clnum
### Keywords: misc
### ** Examples
x<-rnorm(30)
classnum(x)
classnum(x,breaks="fd")
classnum(x, breaks=c(-1,0,1))
classnum(x,breaks=5)
cleanEx(); nameEx("cormat")
### * cormat
flush(stderr()); flush(stdout())
### Name: cormat
### Title: Gives a correlation matrix and the probability of Ho for each
### correlation
### Aliases: cormat
### Keywords: htest
### ** Examples
cormat(longley)
cormat(longley,sep=TRUE)
cleanEx(); nameEx("correlog")
### * correlog
flush(stderr()); flush(stdout())
### Name: correlog
### Title: Computes Moran's or Geary's coefficients on distance classes
### Aliases: correlog plot.correlog print.correlog
### Keywords: spatial
### ** Examples
library(spdep)
data(oldcol)
attach(COL.OLD)
coords<-cbind(X,Y)
res<-correlog(coords,CRIME)
plot(res)
res<-correlog(coords,CRIME,method="Geary")
plot(res)
cleanEx(); nameEx("deg2dec")
### * deg2dec
flush(stderr()); flush(stdout())
### Name: deg2dec
### Title: Convert degree minutes coordinates into decimal degrees (1.60 =
### 2)
### Aliases: deg2dec
### Keywords: manip
### ** Examples
deg2dec(c(1,1.3,1.6))
cleanEx(); nameEx("diag2edge")
### * diag2edge
flush(stderr()); flush(stdout())
### Name: diag2edge
### Title: Computes the edge of a square from its diagonal
### Aliases: diag2edge
### Keywords: dplot spatial
### ** Examples
# diagonal sloping up
coord<-matrix(c(20,20,90,90),nr=2,byrow=TRUE)
plot(coord,type="n",xlim=c(0,100),ylim=c(0,110),asp=1)
lines(coord,lty=2)
# square edge
lines(diag2edge(coord),col="red")
# diagonal sloping down
coord<-matrix(c(20,90,90,20),nr=2,byrow=TRUE)
plot(coord,type="n",xlim=c(0,100),ylim=c(0,110),asp=1)
lines(coord,lty=2)
# square edge
lines(diag2edge(coord),col="red")
# diagonal vertical
coord<-matrix(c(20,90,20,20),nr=2,byrow=TRUE)
plot(coord,type="n",xlim=c(0,100),ylim=c(0,110),asp=1)
lines(coord,lty=2)
# square edge
lines(diag2edge(coord),col="red")
cleanEx(); nameEx("difshannonbio")
### * difshannonbio
flush(stderr()); flush(stdout())
### Name: difshannonbio
### Title: Empirical confidence interval of the bootstrap of the difference
### between two Shannon indices
### Aliases: difshannonbio
### Keywords: misc
### ** Examples
data(preybiom)
attach(preybiom)
jackal<-preybiom[site=="Y" & sp=="C",5:6]
genet<-preybiom[site=="Y" & sp=="G",5:6]
difshannonbio(jackal,genet,R=150)
cleanEx(); nameEx("dirProj")
### * dirProj
flush(stderr()); flush(stdout())
### Name: dirProj
### Title: Computes new coordinates given bearings and distances.
### Aliases: dirProj
### Keywords: spatial
### ** Examples
df<-data.frame(x1=0,y1=0,alpha=runif(3,0,380),d=runif(3,0,1))
df
plot(-1:1,-1:1,type="n")
points(0,0,pch=19)
points(dirProj(df))
text(dirProj(df)[,1],dirProj(df)[,2],1:3,pos=4)
cleanEx(); nameEx("dirSeg")
### * dirSeg
flush(stderr()); flush(stdout())
### Encoding: latin1
### Name: dirSeg
### Title: Computes segment directions.
### Aliases: dirSeg
### Keywords: spatial
### ** Examples
x2<-rnorm(10)
y2<-rnorm(10)
mydata<-cbind(0,0,x2,y2)
dirs<-dirSeg(mydata)
dirs
plot(range(mydata[,c(1,3)]),range(mydata[,c(2,4)]),type="n")
Segments(mydata)
text(mydata[,3],mydata[,4],paste(round(dirs,0),"?"),cex=0.7)
cleanEx(); nameEx("distNode")
### * distNode
flush(stderr()); flush(stdout())
### Name: distNode
### Title: Computes the distances between each nodes of a polyline.
### Aliases: distNode
### Keywords: spatial
### ** Examples
x<-c(10,56,100)
y<-c(23,32,150)
distNode(cbind(x,y))
cleanEx(); nameEx("distPolylines")
### * distPolylines
flush(stderr()); flush(stdout())
### Name: distPolylines
### Title: Computes the length of each lines of an output (polylines) of
### 'read.shape' from maptools.
### Aliases: distPolylines
### Keywords: spatial
### ** Examples
# see example of Norwegian rivers in library maptools: ?Map2lines
library(maptools)
try4 <- read.shape(system.file("shapes/fylk-val.shp",
package="maptools")[1])
distPolylines(try4)
cleanEx(); nameEx("distSeg")
### * distSeg
flush(stderr()); flush(stdout())
### Name: distSeg
### Title: Computes distances between the top coordinates of segments.
### Aliases: distSeg
### Keywords: spatial
### ** Examples
x1<-rnorm(20)
y1<-rnorm(20)
x2<-rnorm(20)
y2<-rnorm(20)
mydata<-cbind(x1,y1,x2,y2)
distSeg(mydata)
cleanEx(); nameEx("distTot")
### * distTot
flush(stderr()); flush(stdout())
### Name: distTot
### Title: Computes the total length of a polyline.
### Aliases: distTot
### Keywords: spatial
### ** Examples
x<-c(10,56,100)
y<-c(23,32,150)
distTot(cbind(x,y))
cleanEx(); nameEx("distTotshp")
### * distTotshp
flush(stderr()); flush(stdout())
### Name: distTotshp
### Title: Computes the total length of the lines of an output of
### 'read.shape' from maptools.
### Aliases: distTotshp
### Keywords: spatial
### ** Examples
# see example of Norwegian rivers in library maptools: ?Map2lines
library(maptools)
try4 <- read.shape(system.file("shapes/fylk-val.shp",
package="maptools")[1])
distTotshp(try4)
cleanEx(); nameEx("expandpol")
### * expandpol
flush(stderr()); flush(stdout())
### Name: expandpoly
### Title: Homothetia (size expansion) of a polygon
### Aliases: expandpoly
### Keywords: manip
### ** Examples
x<-c(-5,-4.5,0,10,5)
y<-c(-10,0,5,5,-8)
poly<-cbind(x,y)
plot(-10:20,-20:10,type="n")
polygon(poly)
polygon(expandpoly(poly,1.5),border="red")
polygon(expandpoly(poly,0.5),border="blue")
cleanEx(); nameEx("friedmanmc")
### * friedmanmc
flush(stderr()); flush(stdout())
### Name: friedmanmc
### Title: Multiple comparisons after Friedman test
### Aliases: friedmanmc
### Keywords: htest
### ** Examples
data(siegelp179)
attach(siegelp179)
friedman.test(score,treatment,block)
friedmanmc(score,treatment,block)
friedmanmc(score,treatment,block,probs=0.01)
mymatrix<-matrix(score,nc=3)
friedman.test(mymatrix)
friedmanmc(mymatrix)
cleanEx(); nameEx("kruskalmc")
### * kruskalmc
flush(stderr()); flush(stdout())
### Name: kruskalmc
### Title: Multiple comparison test after Kruskal-Wallis
### Aliases: kruskalmc
### Keywords: htest
### ** Examples
resp<-c(0.44,0.44,0.54,0.32,0.21,0.28,0.7,0.77,0.48,0.64,0.71,0.75,0.8,0.76,0.34,0.80,0.73,0.8)
categ<-as.factor(rep(c("A","B","C"),times=1,each=6))
kruskalmc(resp, categ)
kruskalmc(resp, categ, probs=0.01)
kruskalmc(resp, categ, cont="one-tailed")
kruskalmc(resp, categ, cont="two-tailed")
cleanEx(); nameEx("ks.gof")
### * ks.gof
flush(stderr()); flush(stdout())
### Name: ks.gof
### Title: Kolmogorof-Smirnov goodness of fit test to normal distribution
### Aliases: ks.gof
### Keywords: htest
### ** Examples
x<-rnorm(50)
ks.gof(x)
cleanEx(); nameEx("pairsrp")
### * pairsrp
flush(stderr()); flush(stdout())
### Name: pairsrp
### Title: Produces a matrix of scatterplot, regression coefficient and
### p(Ho)
### Aliases: pairsrp
### Keywords: hplot
### ** Examples
data(iris)
pairsrp(iris[,1:4],meth="pears",pansmo=TRUE,abv=TRUE)
cleanEx(); nameEx("pave")
### * pave
flush(stderr()); flush(stdout())
### Name: pave
### Title: Provide square polygons or their node coordinates along a
### segment
### Aliases: pave
### Keywords: dplot spatial
### ** Examples
# segment sloping up
coord<-matrix(c(20,20,90,90),nr=2,byrow=TRUE)
plot(coord,type="n",xlim=c(0,100),ylim=c(0,110),asp=1)
lines(coord)
# point grids
gr<-pave(coord,20,4,output="points") # y decreasing
points(gr)
gr<-pave(coord,20,4,output="points",ydown=FALSE) # y increasing
points(gr,col="blue")
# square polygon grids
gr<-pave(coord,20,4) # y decreasing
for (i in 1:length(gr)) polygon(gr[[i]])
gr<-pave(coord,20,4,ydown=FALSE) # y increasing
for (i in 1:length(gr)) polygon(gr[[i]],border="blue")
# segment sloping down
coord<-matrix(c(20,90,90,20),nr=2,byrow=TRUE)
plot(coord,type="n",xlim=c(0,100),ylim=c(0,110),asp=1)
lines(coord)
# point grids
gr<-pave(coord,20,4,output="points") # y decreasing
points(gr)
gr<-pave(coord,20,4,output="points",ydown=FALSE) # y increasing
points(gr,col="blue")
# fixed edge
plot(coord,type="n",xlim=c(0,100),ylim=c(0,110),asp=1)
lines(coord)
gr<-pave(coord,20,4,fix.edge=4,output="points")
points(gr,col="blue")
plot(coord,type="n",xlim=c(0,100),ylim=c(0,110),asp=1)
lines(coord)
gr<-pave(coord,20,4,fix.edge=5.5,output="points")
points(gr,col="red")
# square polygon grids
coord<-matrix(c(20,90,90,20),nr=2,byrow=TRUE)
plot(coord,type="n",xlim=c(0,100),ylim=c(0,110),asp=1)
lines(coord,lwd=2)
gr<-pave(coord,20,4)# y decreasing
for (i in 1:length(gr)) polygon(gr[[i]])
gr<-pave(coord,20,4,ydown=FALSE) # y increasing
for (i in 1:length(gr)) polygon(gr[[i]],border="blue")
## Not run:
##D # Writing a polygon shapefile
##D gr<-pave(coord,20,4,output="spdf") # y decreasing
##D library(maptools)
##D writePolyShape(gr, "myshapefilename")
## End(Not run)
cleanEx(); nameEx("pclig")
### * pclig
flush(stderr()); flush(stdout())
### Name: pclig
### Title: Compute the percentage of each cell of a matrix or data.frame by
### row
### Aliases: pclig
### Keywords: array
### ** Examples
x<-c(2,10,7,8,7)
y<-c(56,22,7,20,5)
pclig(cbind(x,y))
cleanEx(); nameEx("permcont")
### * permcont
flush(stderr()); flush(stdout())
### Name: permcont
### Title: Random permutation of a contingency table n row x 2 columns
### Aliases: permcont
### Keywords: distribution
### ** Examples
tab<-cbind(n1=c(10,12,8,7,5),n2=c(4,5,8,10,12))
tab
permcont(tab)
cleanEx(); nameEx("piankabio")
### * piankabio
flush(stderr()); flush(stdout())
### Name: piankabio
### Title: Computes the Pianka's index of niche overlap
### Aliases: piankabio
### Keywords: misc
### ** Examples
data(preybiom)
attach(preybiom)
jackal<-preybiom[site=="Y" & sp=="C",5:6]
genet<-preybiom[site=="Y" & sp=="G",5:6]
piankabio(jackal,genet)
cleanEx(); nameEx("piankabioboot")
### * piankabioboot
flush(stderr()); flush(stdout())
### Name: piankabioboot
### Title: Bootstrap Pianka's index
### Aliases: piankabioboot
### Keywords: htest
### ** Examples
data(preybiom)
attach(preybiom)
jackal<-preybiom[site=="Y" & sp=="C",5:6]
genet<-preybiom[site=="Y" & sp=="G",5:6]
piankabioboot(jackal,genet,B=100)
cleanEx(); nameEx("plot.variogenv")
### * plot.variogenv
flush(stderr()); flush(stdout())
### Name: plot.variogenv
### Title: Plots empirical variogram and its envelop
### Aliases: plot.variogenv
### Keywords: spatial
### ** Examples
library(gstat)
data(meuse)
myvar<-variogenv(log(zinc)~1, loc=~x+y, meuse)
plot(myvar)
cleanEx(); nameEx("polycirc")
### * polycirc
flush(stderr()); flush(stdout())
### Name: polycirc
### Title: Computes the polygon coordinates of a circle
### Aliases: polycirc
### Keywords: manip
### ** Examples
plot(1:10,1:10,type="n",asp=1)
polygon(polycirc(5),col="blue")
polygon(polycirc(2,c(5,5)), col="red")
cleanEx(); nameEx("polycirc2")
### * polycirc2
flush(stderr()); flush(stdout())
### Name: polycirc2
### Title: Computes the polygon coordinates of a circle sector
### Aliases: polycirc2
### Keywords: dplot
### ** Examples
plot(c(-1,+1),c(-1,+1),type="n",asp=1)
polygon(polycirc2(),col="red")
polygon(polycirc2(init=pi,angle=pi/4),col="green")
polygon(polycirc2(init=1.5*pi,angle=pi/4),col="violet")
polygon(polycirc2(radius=0.5,center=c(0.5,1)),col="blue")
polycirc2(init=pi,angle=pi/4)
cleanEx(); nameEx("postxt")
### * postxt
flush(stderr()); flush(stdout())
### Name: postxt
### Title: Computes coordinates defined from their relative position on x
### and y in the plotting region
### Aliases: postxt
### Keywords: dplot
### ** Examples
plot(rnorm(30),rnorm(30),type="n")
text(postxt("ul"),"here",pos=4)
text(postxt("ur"),"here again",pos=2)
text(postxt("bc"),"again and again")
cleanEx(); nameEx("print.mc")
### * print.mc
flush(stderr()); flush(stdout())
### Name: print.mc
### Title: print method for objects of class 'mc'
### Aliases: print.mc
### Keywords: print
### ** Examples
resp<-c(0.44,0.44,0.54,0.32,0.21,0.28,0.7,0.77,0.48,0.64,0.71,0.75,0.8,0.76,0.34,0.80,0.73,0.8)
categ<-as.factor(rep(c("A","B","C"),times=1,each=6))
kruskalmc(resp, categ)
cleanEx(); nameEx("rmls")
### * rmls
flush(stderr()); flush(stdout())
### Name: rmls
### Title: Select objects in the parent frame and remove them.
### Aliases: rmls
### Keywords: utilities
### ** Examples
toremove<-NULL
ls()
## Not run:
##D rmls()# select the object 'toremove' and click OK
##D
## End(Not run)
ls()
cleanEx(); nameEx("selMod")
### * selMod
flush(stderr()); flush(stdout())
### Name: selMod
### Title: Model selection according to information theoretic methods
### Aliases: selMod selMod.lm selMod.glm selMod.list
### Keywords: models
### ** Examples
library(MASS)
anorex.1 <- lm(Postwt ~ Prewt*Treat, data = anorexia)
selMod(anorex.1)
anorex.2 <- glm(Postwt ~ Prewt*Treat, family=gaussian,data = anorexia)
selMod(anorex.2)
anorex.3<-lm(Postwt ~ Prewt+Treat, data = anorexia)
mycomp<-selMod(list(anorex.1,anorex.2,anorex.3))
mycomp
attributes(mycomp)$models
cleanEx(); nameEx("shannon")
### * shannon
flush(stderr()); flush(stdout())
### Name: shannon
### Title: Computes Shannon's and equitability indices
### Aliases: shannon
### Keywords: misc
### ** Examples
x<-c(0.1,0.5,0.2,0.1,0.1)
sum(x)
shannon(x)
x<-rpois(10,6)
shannon(x, proba=FALSE)
cleanEx(); nameEx("shannonbio")
### * shannonbio
flush(stderr()); flush(stdout())
### Name: shannonbio
### Title: Computes Shannon's and equitability indices from a data frame of
### dietary analysis (n, biomass,...)
### Aliases: shannonbio
### Keywords: misc
### ** Examples
data(preybiom)
shannonbio(preybiom[,5:6])
cleanEx(); nameEx("shannonbioboot")
### * shannonbioboot
flush(stderr()); flush(stdout())
### Name: shannonbioboot
### Title: Boostrap Shannon's and equitability indices
### Aliases: shannonbioboot
### Keywords: htest
### ** Examples
data(preybiom)
myboot<-shannonbioboot(preybiom[,5:6],B=100)
boot.ci(myboot, index=1,type=c("norm","basic","perc")) # confidence
intervals for H'
boot.ci(myboot, index=2,type=c("norm","basic","perc")) # confidence
intervals for J'
cleanEx(); nameEx("siegelp179")
### * siegelp179
flush(stderr()); flush(stdout())
### Name: siegelp179
### Title: Data on rats training
### Aliases: siegelp179
### Keywords: datasets
### ** Examples
data(siegelp179)
cleanEx(); nameEx("tabcont2categ")
### * tabcont2categ
flush(stderr()); flush(stdout())
### Name: tabcont2categ
### Title: Convert a contingency table (data.frame) into a presence/absence
### table of categories
### Aliases: tabcont2categ
### Keywords: array
### ** Examples
mydata<-as.data.frame(matrix(rpois(9,5),nr=3,nc=3))
names(mydata)<-LETTERS[1:3]
row.names(mydata)<-letters[1:3]
tabcont2categ(mydata)
cleanEx(); nameEx("trans2pix")
### * trans2pix
flush(stderr()); flush(stdout())
### Name: trans2pix
### Title: Convert a transect coordinate file with some landmarks into a
### matrix with intermediate coordinates.
### Aliases: trans2pix
### Keywords: utilities
### ** Examples
x<-c(10,NA, NA, NA,56,NA,NA,100)
y<-c(23,NA, NA, NA,32,NA,NA,150)
cols=c("red","blue","blue","blue","red","blue","blue","red")
plot(x,y,col=cols,pch=19)
plot(trans2pix(cbind(x,y)),col=cols,pch=19)
cleanEx(); nameEx("trans2seg")
### * trans2seg
flush(stderr()); flush(stdout())
### Name: trans2seg
### Title: Convert a transect coordinate file into a matrix with segment
### coordinates.
### Aliases: trans2seg
### Keywords: utilities
### ** Examples
x<-c(10,NA, NA, NA,56,NA,NA,100)
y<-c(23,NA, NA, NA,32,NA,NA,150)
cols=c("red","blue","blue","blue","red","blue","blue","red")
plot(x,y,col=cols,pch=19)
mysegs<-trans2seg(cbind(x,y))
segments(mysegs[,1],mysegs[,2],mysegs[,3],mysegs[,4])
cleanEx(); nameEx("val4symb")
### * val4symb
flush(stderr()); flush(stdout())
### Name: val4symb
### Title: Centres a numerical vector on a parameter position and provides
### absolute values and colors according to negative and positive values
### Aliases: val4symb
### Keywords: color dplot
### ** Examples
x<-rnorm(30)
y<-rnorm(30)
z<-val4symb(rnorm(30))
symbols(x,y,circle=z$size,inches=0.2,bg=z$col)
z<-val4symb(scale(rnorm(30)))
symbols(x,y,circle=z$size,inches=0.2,bg=z$col)
z<-val4symb(rnorm(30),col=c("green","violet"))
symbols(x,y,circle=z$size,inches=0.2,bg=z$col)
z<-val4symb(rnorm(30),trim=0.025)
symbols(x,y,circle=z$size,inches=0.2,bg=z$col)
z<-val4symb(rnorm(30),median)
symbols(x,y,circle=z$size,inches=0.2,bg=z$col)
myfun<-function(x) 20 # passes an arbitrary constant
z<-val4symb(1:30,myfun)
symbols(x,y,circle=z$size,inches=0.2,bg=z$col)
cleanEx(); nameEx("valat")
### * valat
flush(stderr()); flush(stdout())
### Name: valat
### Title: Expected values of a contingency table under the null hypothesis
### Aliases: valat
### Keywords: array
### ** Examples
x <- matrix(c(12, 5, 7, 7), nc = 2)
x
valat(x)
cleanEx(); nameEx("valchisq")
### * valchisq
flush(stderr()); flush(stdout())
### Name: valchisq
### Title: Values of the partial chi-square in each cell of a contingency
### table
### Aliases: valchisq
### Keywords: array
### ** Examples
x <- matrix(c(12, 5, 7, 7), nc = 2)
x
valchisq(x)
cleanEx(); nameEx("variogenv")
### * variogenv
flush(stderr()); flush(stdout())
### Name: variogenv
### Title: Envelops for empirical variograms based on permutations
### Aliases: variogenv
### Keywords: spatial
### ** Examples
library(gstat)
data(meuse)
myvar<-variogenv(log(zinc)~1, loc=~x+y, meuse)
myvar
plot(myvar)
cleanEx(); nameEx("write.arcGrid")
### * write.arcGrid
flush(stderr()); flush(stdout())
### Name: write.arcGrid
### Title: Writes an ArcInfo ASCII grid from a matrix or data frame, with
### x, y, z values.
### Aliases: write.arcGrid
### Keywords: utilities
### ** Examples
library(splancs)
data(bodmin)
mykernel<-kernel2d(as.points(bodmin), bodmin$poly, h0=2, nx=100, ny=100)
attributes(mykernel$z)<-NULL
mykernel$z[is.na(mykernel$z)]<--9999
mydata<-cbind(expand.grid(mykernel$x,mykernel$y),mykernel$z)
write.arcGrid(mydata,file="mytextgrid",NODATA=-9999)
cleanEx(); nameEx("write.cl2grass")
### * write.cl2grass
flush(stderr()); flush(stdout())
### Name: write.cl2grass
### Title: Convert the output of contourLines into a ascii GRASS vector
### file (lines).
### Aliases: write.cl2grass
### Keywords: utilities
### ** Examples
x<-1:nrow(volcano)
y<-1:ncol(volcano)
contour(x, y, volcano)
mycontours<-contourLines(x, y, volcano)
write.cl2grass(mycontours, "volcanocont")
# check the new files "volacnocont.txt" and "volacnocontlev.txt"in the
working directory
cleanEx(); nameEx("write.delim")
### * write.delim
flush(stderr()); flush(stdout())
### Name: write.delim
### Title: Write a data.frame
### Aliases: write.delim
### Keywords: utilities
### ** Examples
data(preybiom)
write.delim(preybiom[1:10,]) # output to the console
write.delim(preybiom[1:10,],file="Myfile.txt") # write a file in the
working directory
cleanEx(); nameEx("write.kernel2points")
### * write.kernel2points
flush(stderr()); flush(stdout())
### Name: write.kernel2points
### Title: Write a text file of X,Y coordinates and Z value from the output
### of 'kernel2d' (library splancs)
### Aliases: write.kernel2points
### Keywords: utilities
### ** Examples
library(splancs)
data(bodmin)
mykernel<-kernel2d(as.points(bodmin), bodmin$poly, h0=2, nx=100, ny=100)
write.kernel2points(mykernel, "mypoints")
cleanEx(); nameEx("write.pts2grass")
### * write.pts2grass
flush(stderr()); flush(stdout())
### Name: write.pts2grass
### Title: Convert a matrix of points coordinates (x,y) into an ascii GRASS
### vector file (lines).
### Aliases: write.pts2grass
### Keywords: utilities
### ** Examples
x<-rnorm(30)
y<-rnorm(30)
write.pts2grass(cbind(x,y),"myfile.txt")
# check the new file "myfile.txt"in the working directory
### * <FOOTER>
###
cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
grDevices::dev.off()
###
### Local variables: ***
### mode: outline-minor ***
### outline-regexp: "\\(> \\)?### [*]+" ***
### End: ***
quit('no')
G'day Patrick,
since you seem to be hell-bent on having r-devel in this discussion, I
guess I might CC this there too. :)
On Mon, 05 May 2008 08:50:04 +0200
Patrick Giraudoux <patrick.giraudoux at univ-fcomte.fr> wrote:
There has been a threat on something similar in R-devel on August
2007... but I cannot understand the meaning.
It might be a good idea to provide a link to that discussion. Perhaps
others can understand the meaning and judge the relevance to this
thread.
Did you look at the file in pgirmess.Rcheck that I mentioned?
You'll find a copy of pgirmess-Ex.R, but I cannot get what is the
meaning of this file...
This file collects all the code in the example sections of your
documentation file, and puts some necessary code in front, in between
the examples and at the end. This file is then sourced to run all the
examples and the output can be found in pgrimess-Ex.Rout. And it was
this file that I suggested you look at to see if it provides further
clues about what goes wrong.
Also, did you try to load the version of the library in
pgrimess.Rcheck in a R session and check if you find the PermTest
function in that case?
Yes indeed. I found PermTest in the R folder and in the R-ex folder
of the pgirmess folder in the pgirmess.Rcheck folder.
I am surprised to hear this. R-ex holds all the code from the example
sections in the Rd files, so it is no surprise that you will find a
file PermTest.R in the R-ex folder, it just contains the code from the
example section of PermTest.Rd, at last on my machine. It definitely
does not contain the definition of the funcion. And on my machine,
after running `R CMD check' on the tar.gz file, the R folder in
pgirmess.Rcheck/pgirmess contains the files pgirmess, pgirmess.rdb and
pgirmess.rdx, but no files with R code. So how did you find PermTest
in the R folder? Is lazy-loading somehow switched off in your version
of `R CMD check'?
With these problems, I am a bit of a trial-and-error person, so if I
cannot reproduce the error, I cannot find out what the problem
is....
Thanks anyway for the hints. It may help.
I would suggest the following:
1) remove the directore pgirmess.Rcheck
2) run `R CMD check pgirmess' and see if the error occurs again
3) look at pgirmess.Rcheck/pgirmess/R. Does it contain the three files
that I mentioned or the original source files. If the latter,
check whether PermTest.R is in that directory and whether it really
contains the commands that define that function. If the former, start
an R session and issue the following commands:
R> env <- new.env()
R> lazyLoad("/path/to/pgirmess.Rcheck/pgirmess/R/pgirmess", envir=env)
R> ls(envir=env)
Make sure to replace the /path/to part above with the correct path. Do
you see the PermTest function listed?
This should establish whether the file that contains the PermTest
function is part of the sources that you believe make up your package
source. At the moment, I am leaning towards agreeing with Brian that
the most likely reason for your problem is that the PermTest function
got lost from your sources and is not installed.
Best wishes,
Berwin
I would suggest the following:
1) remove the directore pgirmess.Rcheck
2) run `R CMD check pgirmess' and see if the error occurs again
3) look at pgirmess.Rcheck/pgirmess/R. Does it contain the three files
that I mentioned or the original source files. If the latter,
check whether PermTest.R is in that directory and whether it really
contains the commands that define that function. If the former, start
an R session and issue the following commands:
R> env <- new.env()
R> lazyLoad("/path/to/pgirmess.Rcheck/pgirmess/R/pgirmess", envir=env)
R> ls(envir=env)
Make sure to replace the /path/to part above with the correct path. Do
you see the PermTest function listed?
This should establish whether the file that contains the PermTest
function is part of the sources that you believe make up your package
source. At the moment, I am leaning towards agreeing with Brian that
the most likely reason for your problem is that the PermTest function
got lost from your sources and is not installed.
So I did actually removing everything (on Prof. Ripley's advise) and
restarting from the version downloaded from CRAN (the one I sent
yesterday to Kurt Hornik !!!)... And he does work !!!! Arrrrgh.... and
all those sort of things...
A least now I know the trouble does not come from Ubuntu but likely from
the way I copied files created under Windows to Linux. Maybe more than a
clue...
Sorry to have taken time from you both for so few (I was really messing
on the wrong tracks) and heartly thanks,
Patrick