Re: [R] No ~ in JGR
CG Pettersson said the following on 2005-05-25 14:25: R2.1.0 JGR 1.2 W2k Hello all! I´ve just installed JGR on my both R-equipped computers and am very pleased with the look and functionality. Except in one, very important, way. I can´t figure out how to get the ~ sign from the keyboard to the console. Copying it from old code works fine. Using the traditional GUI works as usual. I have a Swedish keyboard layout, where ~ shares key with ¨ and ^, all reguiring a space after the hit to produce the sign on the screen. The other signs from the key works, but AltGr + ~ followed by space just gives a blank. What do I do wrong? Probably nothing, or we're both doing something wrong. I'm experiencing the same thing, and the asked the JGR developers about it some time ago. See the thread that starts with http://mailman.rz.uni-augsburg.de/pipermail/stats-rosuda-devel/2005q1/30.html Henric __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Soil texture triangle in R?
Hi Jim,
Your email was classified as spam, so I missed it previously.
Unfortunately you did not send a cc to the R-help list. I send a cc to
the mailing list now, so all code gets archived.
Thanks for the improvements on your function! It seems that drawing the
ternary graph and the points with the generic plot functions works well.
Makes the function less dependent on other packages!
Will merge the two functions into one and post it back to the mailing
list! Then the graph might be ready for the graph gallery!
Thanks,
Sander.
Jim Lemon wrote:
> Sander Oom wrote:
>> Hi Jim,
>>
>> This looks impressive! It gives me the 'background' graph. However,
>> I'm not sure how I can use this function to plot my soil texture
>> values! Can you explain?
>>
>> I would like to be able to plot my soil texture samples in the same
>> graph as the one your function plots.
>>
> Yes, that's just the background figure for which you attached the link.
> I was unsure of how you were going to use this, that is, do you just
> place a symbol for each soil sample? Aha! Just read your latest email
> and I think that's what you want.
>
> Let's say you have one or more soil samples with the proportions of
> clay, sand and silt.
>
> sample1<-c(0.1,0.4,0.5)
> sample2<-c(0.2,0.5,0.3)
> soil.samples<-rbind(sample1,sample2)
> colnames(soil.samples)<-c("clay","sand","silt")
>
> This more complicated function allows you to overlay colored points
> representing soil samples on either an empty triangle, a gridded
> triangle or a triangle with soil type names. It also has an optional
> legend.
>
> par(ask=TRUE)
> soil.triangle(soil.samples)
> soil.triangle(soil.samples,show.grid=TRUE)
> soil.triangle(soil.samples,soil.names=TRUE,legend=TRUE)
> par(ask=FALSE)
>
> Jim
>
>
>
> soil.triangle<-function(soilprop,pch=NULL,col=NULL,soil.names=FALSE,
> show.grid=FALSE,show.legend=FALSE) {
> if(missing(soilprop))
> stop("Usage:
soil.triangle(soilprop,pch=NULL,col=NULL,soil.names=FALSE,show.grid=FALSE)")
> if(!is.matrix(soilprop))
> stop("soilprop must be a matrix with at least three columns and one
row.")
> if(any(soilprop > 1) || any(soilprop < 0))
> stop("All soil proportions must be between zero and one.")
> if(any(abs(rowSums(soilprop)-1) > 0.01))
> warning("At least one set of soil proportions does not equal one.")
> oldpar<-par(no.readonly=TRUE)
> plot(0:1,type="n",axes=FALSE,xlim=c(0,1.1),ylim=c(0,1),
> main="Soil Triangle",xlab="",ylab="")
> # first draw the triangle
> x1<-c(0,0,0.5)
> sin60<-sin(pi/3)
> x2<-c(1,0.5,1)
> y1<-c(0,0,sin60)
> y2<-c(0,sin60,0)
> segments(x1,y1,x2,y2)
> # now the bottom internal ticks
> bx1<-seq(0.1,0.9,by=0.1)
> bx2<-bx1-0.01
> by1<-rep(0,9)
> by2<-rep(0.02*sin60,9)
> segments(bx1,by1,bx2,by2)
> text(bx1,by1-0.03,as.character(rev(seq(10,90,by=10
> # now the left internal ticks
> ly1<-bx1*sin60
> lx1<-bx1*0.5
> lx2<-lx1+0.02
> ly2<-ly1
> segments(lx1,ly1,lx2,ly2)
> text(lx1-0.03,ly1,as.character(seq(10,90,by=10)))
> # right internal ticks
> rx1<-rev(lx1+0.5-0.01)
> rx2<-rx1+0.01
> ry1<-ly1-0.02*sin60
> ry2<-ly2
> segments(rx1,ry1,rx2,ry2)
> if(show.grid) {
> segments(bx2,by2,lx1,ly1,lty=3)
> segments(lx2,ly2,rx2,ry2,lty=3)
> segments(rev(rx1),rev(ry1),bx1,by1,lty=3)
> }
> text(rx2+0.03,ry1+0.025,as.character(rev(seq(10,90,by=10
> text(0.5,0.9,"100% clay")
> par(xpd=TRUE)
> text(-0.1,0,"100% sand")
> text(1.1,0,"100% loam")
> text(0.07,0.43,"percent clay")
> text(0.93,0.43,"percent silt")
> text(0.5,-0.1,"percent sand")
> if(soil.names) {
> # boundary of clay with extensions
> x1<-c(0.275,0.35,0.6)
> x2<-c(0.4,0.79,0.7)
> y1<-c(0.55*sin60,0.41*sin60,0.41*sin60)
> y2<-c(0.285*sin60,0.41*sin60,0.6*sin60)
> segments(x1,y1,x2,y2)
> # lower bound of clay loam & silty divider
> x1<-c(0.4,0.68)
> x2<-c(0.86,0.6)
> y1<-c(0.285*sin60,0.285*sin60)
> y2<-c(0.285*sin60,0.41*sin60)
> segments(x1,y1,x2,y2)
> x1<-c(0.185,0.1,0.37)
> x2<-c(0.36,0.37,0.4)
> y1<-c(0.37*sin60,0.2*sin60,0.2*sin60)
> y2<-c(0.37*sin60,0.2*sin60,0.285*sin60)
> segments(x1,y1,x2,y2)
> # sand corner
> x1<-c(0.05,0.075)
> x2<-c(0.12,0.3)
> y1<-c(0.1*sin60,0.15*sin60)
> y2<-c(0,0)
> segments(x1,y1,x2,y2)
> x1<-c(0.37,0.42,0.5,0.8,0.86)
> x2<-c(0.42,0.54,0.65,0.86,0.94)
> y1<-c(0.2*sin60,0.08*sin60,0,0,0.12*sin60)
> y2<-c(0.08*sin60,0.08*sin60,0.285*sin60,0.12*sin60,0.12*sin60)
> segments(x1,y1,x2,y2)
> text(0.5,0.57,"Clay")
> text(0.7,0.49*sin60,"Silty")
> text(0.7,0.44*sin60,"clay")
> text(0.73,0.37*sin60,"Silty clay")
> text(0.73,0.33*sin60,"loam")
> text(0.5,0.35*sin60,"Clay loam")
> text(0.27,0.43*sin60,"Sandy")
> text(0.27,0.39*sin60,"clay")
> text(0.27,0.3*sin60,"Sandy clay")
> text(0.27,0.26*sin60,"loam")
> text(0.25,0.13*sin60,"Sandy loam")
> text(0.13,0.075*sin60,"Loamy")
> text(0.15,0.035*sin60,"sand")
> text(0.0
Re: [R] Soil texture triangle in R?
Apologies, removed a crucial line by accident! Here the working version
of the function, with added control over the colours used.
Enjoy!
plot.soiltexture <- function(x,pch,col,colgrid,coltext) {
## triangle plots:
## triangle.plot {ade4}
## triplot{klaR}
## ternaryplot {vcd}
require(vcd)
ternaryplot(x,
grid=FALSE,
dimnames.position = "none",
pch=pch, col=col,
scale=1, main=NULL,
prop.size=FALSE
)
oldpar <- par(no.readonly=TRUE)
ticlength <- 0.01
sin60<-sin(pi/3)
## now the bottom internal ticks
x1<-seq(0.1,0.9,by=0.1)
x2<-x1
y1<-rep(0,9)
y2<-rep(ticlength,9)
segments(x1,y1,x2,y2)
text(x1,y1-0.03,as.character(rev(seq(10,90,by=10 #, cex=0.8)
## now the left internal ticks
y1<-x1*sin60
x1<-x1*0.5
x2<-x1+ticlength*sin60
y2<-y1-ticlength*0.5
segments(x1,y1,x2,y2)
text(x1-0.03,y1+0.015,as.character(seq(10,90,by=10)))
## now the right internal ticks
x1<-rev(x1+0.5-ticlength*sin60)
x2<-x1+ticlength*sin60
segments(x1,y2,x2,y1)
text(x2+0.03,y1+0.015,as.character(rev(seq(10,90,by=10
## the labels at the corners
par(xpd=TRUE)
# text(0.5,0.9,"100% clay")
# text(-0.1,0,"100% sand")
# text(1.1,0,"100% loam")
## the axis labels
text(0.09,0.43,"% Clay")
text(0.90,0.43,"% Silt")
text(0.5,-0.1,"% Sand")
# boundary of clay with extensions
x1<-c(0.275,0.355,0.6)
x2<-c(0.415,0.8,0.7)
y1<-c(0.55*sin60,0.4*sin60,0.4*sin60)
y2<-c(0.285*sin60,0.4*sin60,0.6*sin60)
segments(x1,y1,x2,y2, col=colgrid)
text(0.5,0.57,"Clay", col=coltext)
# lower bound of clay loam & silty divider
x1<-c(0.415,0.66)
x2<-c(0.856,0.6)
y1<-c(0.285*sin60,0.285*sin60)
y2<-c(0.285*sin60,0.40*sin60)
segments(x1,y1,x2,y2, col=colgrid)
text(0.7,0.49*sin60,"Silty", col=coltext)
text(0.7,0.44*sin60,"clay", col=coltext)
text(0.72,0.36*sin60,"Silty clay", col=coltext)
text(0.73,0.32*sin60,"loam", col=coltext)
text(0.5,0.35*sin60,"Clay loam", col=coltext)
x1<-c(0.185,0.1,0.37)
x2<-c(0.37,0.37,0.415)
y1<-c(0.37*sin60,0.2*sin60,0.2*sin60)
y2<-c(0.37*sin60,0.2*sin60,0.285*sin60)
segments(x1,y1,x2,y2, col=colgrid)
text(0.28,0.43*sin60,"Sandy", col=coltext)
text(0.27,0.39*sin60,"clay", col=coltext)
text(0.27,0.3*sin60,"Sandy clay", col=coltext)
text(0.27,0.26*sin60,"loam", col=coltext)
# sand corner
x1<-c(0.05,0.075)
x2<-c(0.15,0.3)
y1<-c(0.1*sin60,0.15*sin60)
y2<-c(0,0)
segments(x1,y1,x2,y2, col=colgrid)
text(0.25,0.13*sin60,"Sandy loam", col=coltext)
text(0.14,0.07*sin60,"Loamy", col=coltext)
text(0.18,0.03*sin60,"sand", col=coltext)
text(0.06,0.021,"Sand", col=coltext)
x1<-c(0.37,0.435,0.5,0.8,0.86)
x2<-c(0.435,0.537,0.64,0.86,0.94)
y1<-c(0.2*sin60,0.08*sin60,0,0,0.12*sin60)
y2<-c(0.08*sin60,0.08*sin60,0.285*sin60,0.12*sin60,0.12*sin60)
segments(x1,y1,x2,y2, col=colgrid)
text(0.49,0.18*sin60,"Loam", col=coltext)
text(0.72,0.15*sin60,"Silt loam", col=coltext)
text(0.9,0.06*sin60,"Silt", col=coltext)
par(oldpar)
}
tmp <- array(dim=c(10,3))
tmp[,2] <- abs(rnorm(10)*20)
tmp[,3] <- abs(rnorm(10)*10)
tmp[,1] <- 100-tmp[,2]-tmp[,3]
col <- rep("black",10)
pch <- rep(1, 10)
plot.soiltexture(tmp,pch,col=NULL,colgrid="black", coltext="black")
plot.soiltexture(tmp,pch,col="black",colgrid="grey", coltext="white")
Sander Oom wrote:
Cleaned up the class divisions and created a full function.
Still to do:
- rotate axis labels;
- correct the partial covering of the bottom tick labels;
- rotate ticks in order to simplify viewing the graph.
See:
http://soil.scijournals.org/content/vol65/issue4/images/large/1038f2.jpeg
Wonder whether triangle.plot{ade4} will give more flexibility!?
Anyway, hopefully the result so far is useful for other people.
Cheers,
Sander.
plot.soiltexture <- function(x,pch,col) {
## triangle plots:
## triangle.plot {ade4}
## triplot{klaR}
## ternaryplot {vcd}
require(vcd)
require(Zelig)
ternaryplot(x,
grid=FALSE,
dimnames.position = "none",
pch=pch, col=col,
scale=1, main=NULL,
prop.size=FALSE
)
oldpar <- par(no.readonly=TRUE)
ticlength <- 0.01
## now the bottom internal ticks
x1<-seq(0.1,0.9,by=0.1)
x2<-x1
y1<-rep(0,9)
y2<-rep(ticlength,9)
segments(x1,y1,x2,y2)
text(x1,y1-0.03,as.character(rev(seq(10,90,by=10 #, cex=0.8)
## now the left internal ticks
y1<-x1*sin60
x1<-x1*0.5
x2<-x1+ticlength*sin60
y2<-y1-ticlength*0.5
segments(x1,y1,x2,y2)
text(x1-0.03,y1+0.015,as.character(seq(10,90,by=10)))
## now the right internal ticks
x1<-rev(x1+0.5-ticlength*sin60)
x2<-x1+ticlength*sin60
segments(x1,y2,x2,y1)
text(x2+0.03,y1+0.015,as.character(rev(seq(10,90,by=10
## the labels at the corners
par(xpd=TRUE)
# text(0.5,0.9,"100% clay")
# text(-0.1,0,"100% sand")
# text(1.1,0,"100% loam")
## the axis labels
text(0.09,0.43,"% Clay")
text(0.90,0.43,"% Silt")
text(0.5,-0.1,"% Sand")
# boundary of clay with extensions
x1<-c(0.275,0.355,0.6)
x2<-c(0
[R] read.spss trouble
Hello!
I'm not sure if this is an german list, so I will post in english.
I'm using R on my gentoo linux and now I got an spss .sav file. I found
that r has a function like read.spss("file.sav") but when I try this I
get the Error: couldn't find function "read.spss". Can anyone tell me
what's going wrong?
Thanks for your help,
Martin
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Re: [R] images and maps in R
On Fri, 27 May 2005, Don MacQueen wrote:
> This is is not difficult from the online help for the map() function.
> Here is an example.
>
> map('state', region = c('new york', 'new jersey', 'penn'),fill=TRUE,col=1:4)
>
> There is also an example there in how to add text to the map.
>
> Another way uses the maptools package.
>
> require(maptools)
> ?plot.Map
>
> and then follow the examples given in the help page for plot.Map().
Both for map() in the maps package and plot.Map() and plot.polylist() in
the maptools package, there are three things to sort out. Firstly, are the
map polygons the same, and in the same order as the data you want to map?
Next, which palette of colours do you want to use (the RColorBrewer
palettes are well-chosen)? And finally, which breakpoints will you use
for the class intervals to divide the data into colours?
If the breakpoints are brks:
cols <- brewer.pal(length(brks)-1, "your choice of palette)
col_choices <- findInterval(data, brks, all.inside=TRUE)
and your data are the same length and in the same order as the polygons,
thematic maps are not too difficult.
>
> At 2:42 PM -0700 5/27/05, yyan liu wrote:
> >Hi:
> > I have a question arising from my project.
> > A sample of the data is below. The first row stands
> >for the names of state in USA. The second row stand
> >for some numeric value in that state. Some of them are
> >NA. I can use the commands "data(stateMapEnv)" and
> >"map('state', fill = F)" in library "maps" to make a
> >plot of USA states. What I want to do is: 1. put the
> >corresponding state name on the Map 2. give different
> >state different colors which is related to their
> >value. For example, "red" for values ranging from
> >0-30, "green" for values from 80-90, etc. 3. if
> >possible, put the value of each state within the state
> >on the map. here, take the numeric value as some text.
> >
> >Thank you very much!
> >
> >AB AK AL AR AZ CT CA
> >91 80 NA NA 17 33 20
> >
> >__
> >R-help@stat.math.ethz.ch mailing list
> >https://stat.ethz.ch/mailman/listinfo/r-help
> >PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
>
>
--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen,
Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: [EMAIL PROTECTED]
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Re: [R] read.spss trouble
Hi Martin,
Martin Klaffenboeck wrote:
Hello!
I'm not sure if this is an german list, so I will post in english.
It's an English list.
I'm using R on my gentoo linux and now I got an spss .sav file. I found
that r has a function like read.spss("file.sav") but when I try this I
get the Error: couldn't find function "read.spss". Can anyone tell me
what's going wrong?
It's in the package "foreign". Try:
library(foreign)
HTH,
Kevin
--
Ko-Kang Kevin Wang
PhD Student
Centre for Mathematics and its Applications
Building 27, Room 1004
Mathematical Sciences Institute (MSI)
Australian National University
Canberra, ACT 0200
Australia
Homepage: http://wwwmaths.anu.edu.au/~wangk/
Ph (W): +61-2-6125-2431
Ph (H): +61-2-6125-7407
Ph (M): +61-40-451-8301
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Re: [R] read.spss trouble
On Sat, 2005-05-28 at 13:23 +, Martin Klaffenboeck wrote:
> Hello!
>
> I'm not sure if this is an german list, so I will post in english.
The official language is English.
> I'm using R on my gentoo linux and now I got an spss .sav file. I found
> that r has a function like read.spss("file.sav") but when I try this I
> get the Error: couldn't find function "read.spss". Can anyone tell me
> what's going wrong?
read.spss() is part of the "foreign" package, which is installed as part
of the base R installation, but it is not loaded by default.
Thus, you need to use:
library(foreign)
read.spss(...)
See ?library and page 74 in "An Introduction to R".
HTH,
Marc Schwartz
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Re: [R] read.spss trouble
Martin,
If you have trouble finding page 74 of Introduction to R, you can get
the information that Marc suggested you read by doing the following. At
the R prompt enter
help.start()
Then when you see the web page "Statistical Data Analysis R", click on
the SEARCH ENGINE & KEYWORDS link. In the search box enter SPSS.
John
John Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
Baltimore VA Medical Center GRECC and
University of Maryland School of Medicine Claude Pepper OAIC
University of Maryland School of Medicine
Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
410-605-7119
- NOTE NEW EMAIL ADDRESS:
[EMAIL PROTECTED]
>>> Marc Schwartz <[EMAIL PROTECTED]> 5/28/2005 9:35:52 AM >>>
On Sat, 2005-05-28 at 13:23 +, Martin Klaffenboeck wrote:
> Hello!
>
> I'm not sure if this is an german list, so I will post in english.
The official language is English.
> I'm using R on my gentoo linux and now I got an spss .sav file. I
found
> that r has a function like read.spss("file.sav") but when I try this
I
> get the Error: couldn't find function "read.spss". Can anyone tell
me
> what's going wrong?
read.spss() is part of the "foreign" package, which is installed as
part
of the base R installation, but it is not loaded by default.
Thus, you need to use:
library(foreign)
read.spss(...)
See ?library and page 74 in "An Introduction to R".
HTH,
Marc Schwartz
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Re: [R] Errors in Variables
I'm interested in this "2D line fitting" too! I've been looking, without success, in the list of R packages. It might be possible to implement quite easily some of the formalism that you can find in Numerical Recipes (Fortran 77, 2nd ed.), paragraph 15.3. As a matter of fact, I did this in R but only for a model of the form y ~ x (with a given covariance matrix between x and y). I can send you the R code (preliminary version: I wrote it yesterday), if you want. Another interesting reference might be Am. J. Phys. 60, p. 66 (1992). But, again, you would have to implement things by yourself. All the best, EOL -- Dr. Eric-Olivier LE BIGOT (EOL)CNRS Associate Researcher ~~~o~oo~o~~~ Kastler Brossel Laboratory (LKB) http://www.lkb.ens.fr Université P. & M. Curie and Ecole Normale Supérieure, Case 74 4 place Jussieu 75252 Paris CEDEX 05 France ~~~o~oo~o~~~ office : 01 44 27 73 67 fax: 01 44 27 38 45 ECR room: 01 44 27 47 12 x-ray room: 01 44 27 63 00 home: 01 73 74 61 87 For int'l calls: 33 + number without leading 0 On Wed, 25 May 2005, Jacob van Wyk wrote: I hope somebody can help. A student of mine is doing a study on Measurement Error models (errors-in-variables, total least squares, etc.). I have an old reference to a "multi archive" that contains leiv3: Programs for best line fitting with errors in both coordinates. (The date is October 1989, by B.D. Ripley et al.) I have done a search for something similar in R withour success. Has this been implemented in a R-package, possibly under some sort of assumptions about variances. I would lke my student to apply some regression techniques to data that fit this profile. Any help is much appreciated. (If I have not done my search more carefully - my apologies.) Thanks Jacob Jacob L van Wyk Department of Mathematics and Statistics University of Johannesburg APK P O Box 524 Auckland Park 2006 South Africa Tel: +27-11-489-3080 Fax: +27-11-489-2832 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Forcing ticks in plot for hclust object outside the limits
Hello!
I have the following problem.
I would like to plot the hclust object "hcd" (bellow, at the end of the
mail) with ticks at seq(0.05,0.25,by=0.05). I tried using the code
plot(hcd)
and
plot(hcd,axes=FALSE)
axis(2,seq(0.05,0.25,by=0.05))
In both cases, the resoult is the same, ticks at 0.05 and 0.25 are not
printed. I tried changing the ylim argumet in plot, however I got a warning
"parameter "ylim" couldn't be set in high-level plot() function".
I would like to force those two ticks. Can this be done with axis or plot,
or should I use "lines"?
Thanks in advance for any suggestions!
Aleš Žiberna
"hcd" <-
structure(list(merge = structure(as.integer(c(-4, -5, -1, -7,
-6, -10, -3, -12, -8, -2, 8, 1, -9, -11, 2, 3, -13, 4, 6, 5,
7, 9, 10, 11)), .Dim = as.integer(c(12, 2))), height = c(0.0906288626438465,
0.10278145998519, 0.114885217561497, 0.127812745765521, 0.13237798522,
0.168594637784091, 0.177187802444346, 0.209803430657638, 0.210361529934791,
0.218946973173863, 0.234000873708654, 0.235702383243089), order =
as.integer(c(4,
9, 12, 6, 13, 2, 8, 3, 10, 7, 1, 5, 11)), labels = NULL, method = "single",
call = quote(hclust(d = d, method = "single")), dist.method = NULL),
.Names = c("merge",
"height", "order", "labels", "method", "call", "dist.method"), class =
"hclust")
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[R] Lag selection
Dear All , Is it possible to find and select the best lags for time series in R? ( Lag Selection Problem ) Could you please introduce a package or function for this ? Thanks a lot __ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Forcing ticks in plot for hclust object outside the limits
Aleš Žiberna wrote:
Hello!
I have the following problem.
I would like to plot the hclust object "hcd" (bellow, at the end of the
mail) with ticks at seq(0.05,0.25,by=0.05). I tried using the code
plot(hcd)
and
plot(hcd,axes=FALSE)
axis(2,seq(0.05,0.25,by=0.05))
In both cases, the resoult is the same, ticks at 0.05 and 0.25 are not
printed. I tried changing the ylim argumet in plot, however I got a
warning "parameter "ylim" couldn't be set in high-level plot() function".
I would like to force those two ticks. Can this be done with axis or
plot, or should I use "lines"?
Not easy with the plot method for a hclust object, because 0.05 and 0.25
are getting clipped, because they are out od the "usr" coordinated of
the plot.
Of course you could hack plot.hclust (in Namespace stats) by modifying
.../R/library/src/stats/R/hclust.R as follows (in order to provide a
proper ylim argument):
diff hclust.R-orig hclust.R
91c91,92
< sub = NULL, xlab = NULL, ylab = "Height", ...)
---
> sub = NULL, xlab = NULL, ylab = "Height",
> ylim = NULL, ...)
116c117,120
< .Internal(dend.window(n, merge, height, hang, labels, ...))
---
> height2 <- height
> if(!is.null(ylim))
> height2 <- c(range(ylim), rep(ylim[1], length(height) - 2))
> .Internal(dend.window(n, merge, height2, hang, labels, ...))
Note that this quick hack is a *dirty* solution.
Uwe Ligges
Thanks in advance for any suggestions!
Aleš Žiberna
"hcd" <-
structure(list(merge = structure(as.integer(c(-4, -5, -1, -7,
-6, -10, -3, -12, -8, -2, 8, 1, -9, -11, 2, 3, -13, 4, 6, 5,
7, 9, 10, 11)), .Dim = as.integer(c(12, 2))), height =
c(0.0906288626438465,
0.10278145998519, 0.114885217561497, 0.127812745765521, 0.13237798522,
0.168594637784091, 0.177187802444346, 0.209803430657638, 0.210361529934791,
0.218946973173863, 0.234000873708654, 0.235702383243089), order =
as.integer(c(4,
9, 12, 6, 13, 2, 8, 3, 10, 7, 1, 5, 11)), labels = NULL, method = "single",
call = quote(hclust(d = d, method = "single")), dist.method = NULL),
.Names = c("merge",
"height", "order", "labels", "method", "call", "dist.method"), class =
"hclust")
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[R] how to make legends on histograms
I have a histogram with histograms for several datasets superimposed. How can I add a legend that indicates which dataset uses which linetype? Thanks Andreas -- -- Dr. med. Andreas Zankl Division de Pediatrie Moleculaire Clinique Infantile 02/50 CHUV Avenue Pierre Decker 2 CH-1011 Lausanne Suisse Tel.: +41-21-3143778 Fax: +41-21-3143546 Email: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Soil texture triangle in R?
Dear R users,
Please find attached a new plot function, plot.soiltexture, to plot soil
texture data on a triangular plot with an optional backdrop of the USDA
soil texture classification, written by Jim Lemon and me.
I tried to write the function and documentation confirm the R
conventions. However, this is a new experience for me, so any comments
and suggestions are welcome!
I tried to find a suitable package for the plot function, but none are
obvious.
I have approached Todd Skaggs to ask permission to include sample data
from the paper:
Skaggs, T.H., L.M. Arya, P.J. Shouse, and B.P. Mohanty. 2001. Estimating
particle-size distribution from limited soil texture data. Soil Sci.
Soc. Am. J., 65:1038-1044.
http://soil.scijournals.org/cgi/content/full/65/4/1038
Things still to do:
- rotate axis labels;
- rotate axis tick labels
- provide option to plot ticks inside or outside plot area.
Thus making it look like:
http://soils.usda.gov/technical/manual/images/fig3-16_large.jpg
or
http://soil.scijournals.org/content/vol65/issue4/images/large/1038f2.jpeg
Enjoy,
Sander.
# Description
#
# Plots soil texture data on an equilateral triangle. Provides the option to
# draw the USDA soil texture classification as a backdrop.
#
# Usage
#
# plot.soiltexture <- function(soiltexture, main=NULL, pch=1, col="black",
# soil.names=TRUE, soil.lines=TRUE, show.points=TRUE,
# show.clabels=FALSE, show.grid=FALSE, show.legend=FALSE,
# col.names="grey", col.lines="grey", bg.pch="white",
# col.grid="grey", lty.grid=3)
#
# Arguments
#
# soiltexture a matrix with three columns (see details)
# main title of the plot; defaults to NULL
# pch variable or vector containing point symbols; defaults to 1
# col variable or vector containing point colour; defaults to black
# soil.namesa logical value indicating whether the soil texture class names
are printed; defaults to TRUE
# soil.linesa logical value indicating whether the soil texture class
division lines are plotted; defaults to TRUE
# show.points a logical value indicating whether the soil sample points are
plotted; defaults to TRUE
# show.clabels a logical value indicating whether the corner labels for 100%
sand, silt and clay are printed; defaults to FALSE
# show.grid a logical value indicating whether the fixed grid is plotted;
defaults to FALSE
# show.legend a logical value indicating whether the legendis plotted;
defaults to FALSE
# col.names colour of the soil texture class names; defaults to grey
# col.lines colour of the soil texture class division lines; defaults to
grey
# bg.pchcolour of the points symbols when pch 21:25 are used; defaults
to white
# col.grid colour of the fixed grid; defaults to grey
# lty.grid line style for the fixed grid; defaults to 3
#
# Details
#
# The object soiltexture must be a matrix with at least three columns and one
row.
# Columns should contain data for Sand, Silt, and Clay, in that order! Sand,
Silt,
# and Clay should be expressed in proportions between 0 and 1.
#
# The soil sample points' coordinates are calculated using simple trigonometry.
# Thus, the coordinates of a point P(Sand,Silt,Clay), where Sand + Silt + Clay
= 1,
# are: P(1-Sand+(Sand-(1-Silt))*0.5, Clay*sin(pi/3))
#
# Author(s)
#
# Jim Lemon
# Sander Oom
#
# References
#
# Soil Survey Division Staff. 1993. Soil survey manual. Soil Conservation
Service.
# U.S. Department of Agriculture Handbook 18.
#
# Examples
#
# # some triangular data
# library(MASS)
# tmp<-(Skye/100)
# # colnames choosen to be consistent with MASS-fig4.4
# colnames(tmp) <- c("Clay","Sand","Silt")
# soiltexture <- cbind(tmp$Sand,tmp$Silt,tmp$Clay)
# # the USDA backdrop in black
# plot.soiltexture(NULL, show.points=FALSE, col.names="black",
col.lines="black")
# # the USDA backdrop and a fixed grid in grey
# plot.soiltexture(NULL, show.points=FALSE, show.grid=TRUE)
# # soil sample points with backdrop in grey
# plot.soiltexture(soiltexture)
plot.soiltexture <- function(soiltexture, main="Soil Texture Plot", pch=1,
col="black",
soil.names=TRUE, soil.lines=TRUE,
show.points=TRUE, show.clabels=FALSE, show.grid=FALSE, show.legend=FALSE,
col.names="grey", col.lines="grey", bg.pch="white",
col.grid="grey", lty.grid=3) {
if(show.points) {
## error checking
if(missing(soiltexture))
stop("Usage: plot.soiltexture(soiltexture, pch=NULL, col=NULL,
soil.names=FALSE, show.grid=FALSE)")
if(!is.matrix(soiltexture))
stop("Object soiltexture must be a matrix with at least three columns
(for Sand, Silt, and Clay) and one row.")
if(any(soiltexture > 1) || any(soiltexture < 0))
stop("All soil texture proportions must be between zero and one.")
if(any(abs(rowSums(soiltexture)-1) > 0.01))
warning("At least one set of soil texture proportions does not equal
one.")
}
oldpar<-par(no.readonly=TRUE)
sin60<-sin(pi/3)
par(xpd=TRUE)
# create empt
Re: [R] how to make legends on histograms
Andreas Zankl wrote: I have a histogram with histograms for several datasets superimposed. How can I add a legend that indicates which dataset uses which linetype? Thanks Andreas ?legend ?locator -- Kjetil Halvorsen. Peace is the most effective weapon of mass construction. -- Mahdi Elmandjra -- No virus found in this outgoing message. Checked by AVG Anti-Virus. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Errors in Variables
I'm sorry, I have not followed this thread, but I wonder if you have considered library(sem), "structural equations modeling"? "Errors in variables" problems are the canonical special case. Also, have you done a search of "www.r-project.org" -> search -> "R site search" for terms like "errors in variables regression"? This just led me to "ODRpack", which is NOT a CRAN package but is apparently available after a Google search. If it were my problem, I'd first try to figure out "sem"; if that seemed too difficult, I might then look at "ODRpack". Also, have you read the posting guide! http://www.R-project.org/posting-guide.html? This suggests, among other things, that you provide a toy example that a potential respondant could easily copy from your email, test a few modifications, and prase a reply in a minute or so. This also helps clarify your question so any respondants are more likely to suggest something that is actually useful to you. Moreover, many people have reported that they were able to answer their own question in the course of preparing a question for this list using the posting guide. hope this helps. spencer graves Eric-Olivier Le Bigot wrote: I'm interested in this "2D line fitting" too! I've been looking, without success, in the list of R packages. It might be possible to implement quite easily some of the formalism that you can find in Numerical Recipes (Fortran 77, 2nd ed.), paragraph 15.3. As a matter of fact, I did this in R but only for a model of the form y ~ x (with a given covariance matrix between x and y). I can send you the R code (preliminary version: I wrote it yesterday), if you want. Another interesting reference might be Am. J. Phys. 60, p. 66 (1992). But, again, you would have to implement things by yourself. All the best, EOL -- Dr. Eric-Olivier LE BIGOT (EOL)CNRS Associate Researcher ~~~o~oo~o~~~ Kastler Brossel Laboratory (LKB) http://www.lkb.ens.fr Université P. & M. Curie and Ecole Normale Supérieure, Case 74 4 place Jussieu 75252 Paris CEDEX 05 France ~~~o~oo~o~~~ office : 01 44 27 73 67 fax: 01 44 27 38 45 ECR room: 01 44 27 47 12 x-ray room: 01 44 27 63 00 home: 01 73 74 61 87 For int'l calls: 33 + number without leading 0 On Wed, 25 May 2005, Jacob van Wyk wrote: I hope somebody can help. A student of mine is doing a study on Measurement Error models (errors-in-variables, total least squares, etc.). I have an old reference to a "multi archive" that contains leiv3: Programs for best line fitting with errors in both coordinates. (The date is October 1989, by B.D. Ripley et al.) I have done a search for something similar in R withour success. Has this been implemented in a R-package, possibly under some sort of assumptions about variances. I would lke my student to apply some regression techniques to data that fit this profile. Any help is much appreciated. (If I have not done my search more carefully - my apologies.) Thanks Jacob Jacob L van Wyk Department of Mathematics and Statistics University of Johannesburg APK P O Box 524 Auckland Park 2006 South Africa Tel: +27-11-489-3080 Fax: +27-11-489-2832 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Lag selection
What kind of problem? For one variable or more? What have you tried? For only a single time series, the standard approach that I learned from Box and Jenkins, Time Series Analysis, Forecasting and Control, starts by preparing both acf and pacf, both of which are functions in R. If the acf shows only 1, 2 or 3 significant spikes, it suggests a moving average only model of the indicated order. If the pacf shows only 1, 2, or 3 significant spikes, that suggests an autogregression only model. If the acf shows very high autoregressions of all orders with very slow decay, it suggests at least one difference. If both acf and pacf show reasonable, possibly oscillating decay with no clear cut-off, then I'd first try an ARMA(1,1), then look at the residuals and expand the model as needed. Finally, have you read the posting guide! http://www.R-project.org/posting-guide.html? This suggests, among other things, that you provide a toy example that a potential respondant could easily copy from your email, test a few modifications, and prase a reply in a minute or so. This also helps clarify your question so any respondants are more likely to suggest something that is actually useful to you. Moreover, many people have reported that they were able to answer their own question in the course of preparing a question for this list using the posting guide. hope this helps. spencer graves Amir Safari wrote: Dear All , Is it possible to find and select the best lags for time series in R? ( Lag Selection Problem ) Could you please introduce a package or function for this ? Thanks a lot __ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
