Patrick Giraudoux
2008-May-05 05:02 UTC
[Rd] troubles with R CMD check and examples under Ubuntu gutsy
Dear listers, I was used to package pgirmess under Windows with everything OK, but, for the first time, I had a trial this afternoon on Ubuntu 7.10 gutsy (I have a double boot computer and work more and more under unix) and R 2.7.0. Everything went OK except this: sudo R CMD check pgirmess ..... * checking examples ... ERROR Running examples in 'pgirmess-Ex.R' failed. The error most likely occurred in: > ### * 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) Error: could not find function "PermTest" Execution halted If I run R CMD check --no-examples pgirmess, everything comes OK. Seems again that this check makes problem. I googled a bit on R-devel but did not find any understandable post on that... Any idea about what happens ? (please consider if I can write some lines and build a package, I am *not* an advanced fellow in matter of packaging... and just know something about running the commands 'R CMD check' and R CMD build...) Thanks in advance, Patrick
Prof Brian Ripley
2008-May-05 05:34 UTC
[Rd] troubles with R CMD check and examples under Ubuntu gutsy
It seems likely that the contents of 'pgirmess' under Linux are incomplete. There's a recent version of pgirmess on CRAN, and that works under Linux. I suggest you try that (start with the tarball, perhaps). On Mon, 5 May 2008, Patrick Giraudoux wrote:> Dear listers, > > I was used to package pgirmess under Windows with everything OK, but, for the > first time, I had a trial this afternoon on Ubuntu 7.10 gutsy (I have a > double boot computer and work more and more under unix) and R 2.7.0. > Everything went OK except this: > > sudo R CMD check pgirmessDo you really want to be doing this under root? I see no reason to do so -- just make sure you have a writeable current directory for your account.> ..... > > * checking examples ... ERROR > Running examples in 'pgirmess-Ex.R' failed. > The error most likely occurred in: > >> ### * 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) > Error: could not find function "PermTest" > Execution halted > > > If I run R CMD check --no-examples pgirmess, everything comes OK. Seems again > that this check makes problem. I googled a bit on R-devel but did not find > any understandable post on that... > > Any idea about what happens ? (please consider if I can write some lines and > build a package, I am *not* an advanced fellow in matter of packaging... and > just know something about running the commands 'R CMD check' and R CMD > build...) > > Thanks in advance, > > Patrick > >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595
Patrick Giraudoux
2008-May-05 06:15 UTC
[Rd] troubles with R CMD check and examples under Ubuntu gutsy
Berwin A Turlach a ?crit :> G'day Patrick > > On Mon, 05 May 2008 07:02:23 +0200 > Patrick Giraudoux <patrick.giraudoux at univ-fcomte.fr> wrote: > > >> I was used to package pgirmess under Windows with everything OK, but, >> for the first time, I had a trial this afternoon on Ubuntu 7.10 gutsy >> (I have a double boot computer and work more and more under unix) and >> R 2.7.0. >> > > FWIW, on my Ubuntu 8.04 heron machine, with pgirmess_1.3.6.tar.gz from > CRAN, I can run `R CMD check pgirmess_1.3.6.tar.gz' without problems. > > Are you talking about that version, or a current development version? > > 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 ?>> sudo R CMD check pgirmess >> > > Why do you run this command as root? I would avoid something like > this. Is the directory in which pgirmess is in not writeable for your > usual user-id? Perhaps the problem is that the root account is not > correctly set up to use R (but I would find that hard to believe). > >No, sorry it was just my mistake. After the failure as standard user, I was wondering if packaging should be done as super-user... but things come similar. Patrick
Patrick Giraudoux
2008-May-05 06:50 UTC
[Rd] troubles with R CMD check and examples under Ubuntu gutsy
Berwin A Turlach a ?crit :> 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')