[R] limit to complex plots?
Hello all. I am trying to create one figure, divided into 6 graphs/plots each with an inset sub-figure. I can use to layout command to generate one figure with one inset sub-figure, but cannot seem to do it for multiple figures on one page. I've tried a test with the following code: layout(matrix(c(1,2,3,4), nrow=2, byrow=TRUE)) plot(rnorm(10), rnorm(10)) plot(rnorm(10), rnorm(10)) plot(rnorm(30), rnorm(30)) plot(rnotm(40), rnorm(40)) layout.show(4) #this works and gives me my one page with 4 figures on it layout(matrix(c(0,0,0,0,0,1,0,2,0,0,0,0,0,3,0,4), nrow=4, byrow=TRUE)) par(new=TRUE) plot(rnorm(10), rnorm(10)) par(new=TRUE) plot(rnorm(20), rnorm(20)) par(new=TRUE) plot(rnorm(30), rnorm(30)) par(new=TRUE) plot(rnorm(40), rnorm(40)) # this is the part that doesn't. I've tried only one 'par(new=TRUE)' command before ALL the plot commands and as written above. The best I can get is 3 sub-figures #2,3 and 4, in positions 1,2 and 3. Has anyone figured this out? thanks, Suzanne Blatt __ Introducing the New Netscape Internet Service. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Memory clear problem
Hello. I think this is a simple problem. I have R running a program which generates variables that it 'remembers'. The trouble is that I've modified the file that it's generating these variables from but doesn't seem to realize that. When I type 'trees' - I get the same data set produced. I tried shutting R down and not saving the workspace, but when I open 'er up again and type 'trees', there is that same data set. I saw a memory clear command somewhere in one of the help files but I'll be danged if I can locate it now. Please tell me this is a simple problem with a nice(one-line) solution. Thanks, Suzanne __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] cca in vegan
Hello all, I'm hoping this is a simple problem. I'm trying to do cca of my data. I have my plant data and environmental data as 2 separate files. I have 3 years of data, stacked vertically, within these files. I want to conduct the cca for each year and am trying to create separate year files using the following: cnts94 - cnts[1:27,] env94 - env[1:27,] when I run cca(cnts94, env94) I get the following error message: Error in cca.default(cnts94, env94): All row and column sums must be 0 in the community matrix There are no missing data points in the data set. If I run the whole data set: cca(cnts, env) it works, and I can plot and do all the associated stuff. Why not work if I specify a smaller data set? Am I specifying it wrong? Thanks, Suzanne __ New! Unlimited Netscape Internet Service. Only $9.95 a month -- Sign up today at http://isp.netscape.com/register __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] mpl and ppp
Hello. I'm trying to use mpl to compare one spatial pattern with soil variables. I have generated a surface trend for the soil variables and predicted their values for the x,y of my trees - that's fine. I have generated a 'ppp' for my tree data, but when I try to put the 2 together in mpl, I get the following error message: Error in as.ppp(X): Can't interpret X as a point pattern which is odd because when I,in R, ask it to examine my object it reads: marked planar point pattern: 55 points multitype, with levels = 1 2 3 4 5 6 window: polygonal boundary enclosing rectangle: [4943.5, 5023.4] x [4965.2, 5083.7] which, as far as I can tell is a ppp. Can anybody shed some light as to why R would not like it? Is it the polygonal boundary? Thanks, Suzanne __ New! Unlimited Access from the Netscape Internet Service. Beta test the new Netscape Internet Service for only $1.00 per month until 3/1/04. Sign up today at http://isp.netscape.com/register Act now to get a personalized email address! Netscape. Just the Net You Need. __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Barplots
Hello, Can anyone tell me how to label individual bars on a barplot? I want to put an * or letter ABOVE the bar to denote statistical significance. Is this possible and how? Thanks, Suzanne __ McAfee VirusScan Online from the Netscape Network. Comprehensive protection for your entire computer. Get your free trial today! http://channels.netscape.com/ns/computing/mcafee/index.jsp?promo=393397 Get AOL Instant Messenger 5.1 free of charge. Download Now! __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Barplots
Hello,
Thanks for the suggestion below. I did one of my figures and it worked perfectly. I
tried it on my second figure and got double-labelling on the first bar. I used the
same code to create both figures, and the same code to label. I've attached the code
for one of the plots (there were 3/figure) if anyone has a chance to figure out why.
Thanks,
Suzanne
Philipp Pagel [EMAIL PROTECTED] wrote:
Hi!
On Fri, Nov 07, 2003 at 10:46:27AM -0500, Suzanne E. Blatt wrote:
Can anyone tell me how to label individual bars on a barplot? I want
to put an * or letter ABOVE the bar to denote statistical
significance. Is this possible and how?
You can use text() to put arbitrary strings in your plot. So you only
need to add some offset to your y-values and work out the x-positions:
y - c(10,12,15,8)
lab - c('*','**','***','*')
barplot(y, ylim=c(0,20), space=0.5)
x - (0:3*0.5)+1:4
text(x, y+1, lab, adj=0.5)
cu
Philipp
--
Dr. Philipp PagelTel. +49-89-3187-3675
Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585
GSF - National Research Center for Environment and Health
Ingolstaedter Landstrasse 1
85764 Neuherberg, Germany
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Re: [R] Barplots (THANK YOU!!)
Thanks! That did it!! Suzanne Philipp Pagel [EMAIL PROTECTED] wrote: On Fri, Nov 07, 2003 at 03:16:13PM -0500, Suzanne E. Blatt wrote: Thanks for the suggestion below. I did one of my figures and it worked perfectly. I tried it on my second figure and got double-labelling on the first bar. I used the same code to create both figures, and the same code to label. Well, maybe you should use the x values returned by barplot (your variable blocks) instead of computing x-positions yourself as I originally suggested. cu Philipp -- Dr. Philipp PagelTel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg, Germany __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help __ McAfee VirusScan Online from the Netscape Network. Comprehensive protection for your entire computer. Get your free trial today! http://channels.netscape.com/ns/computing/mcafee/index.jsp?promo=393397 Get AOL Instant Messenger 5.1 free of charge. Download Now! __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
Re: [R] Deciphering an error message
Hello again,
Below is the code I am using which generates the error message.
Any comments greatly appreciated,
S.
#
# Function to create a PPP object for all the points in a particular
# include. Mark the points with their species name (or a number
# indicating it)
#
# Usage:
# x - getBigPPP(year, include, species, number=FALSE)
#
# Where:
# x = ppp object with coordinates and bounds for indicated species
# and plots.
# year = year(s) to include data for. Either a single number or a
#vector of numbers
# include = name(s) of plots to include data from. Either a single
# character expression or a vector of characters.
# species = name(s) of species to include data for. Either a single
# species name or a vector of characters.
# number = flag indicating whether species names or numbers are used
# as marks in ppp object. Species names are default. To
# use numbers, set number=TRUE. This argument is not needed
# unless numbers are desired.
#
# Example:
# source(spat1.R) # source file to install functions
# getBigPPP(1992, G1, apple) # print PPP object (summary of)
## for apple in G1 in 1992. Marks
## will be species name 'apple'
# x - getBigPPP(1992, c(P1,P2,P3), c(apple,hawthorn), number=TRUE)
## x is defined as PPP object with
## coordinates and plot information
## for apple and hawthorn species
## in plots P1, P2, and P3, with
## marks set to numbers.
# plot(x)# plot locations of species, with
## different marks for each one, and
## plot boundaries.
#
getBigPPP - function(year=NULL, include=NULL, species=NULL, number=FALSE,
spColNam=Species) {
# message about usage
if(is.null(year) || is.null(include)) {
return(ERROR !)
}
# create species selection if it is now null
spCol - t(trees[spColNam])
# print(spCol)
if(is.null(species)) {
species - as.character(unique(spCol))
}
# create the bounds for this object
bounds - plotBounds(include)
# selection based on include and year
select - (trees$Plot %in% include) (trees$Year %in% year)
(spCol %in% species) (!is.na(trees$Northing))
(!is.na(trees$Easting)) (trees$Present == 1)
# mark with numbers or with species name
if(!number) {
return(ppp(x=trees$Easting[select], y=trees$Northing[select],
marks=as.factor(spCol[select]), poly=bounds))
}
specs - unique(spCol[select])
marks - apply(as.matrix(spCol[select]), 1, function(x) {
which(specs == x)[1]
})
return(ppp(x=trees$Easting[select], y=trees$Northing[select],
marks=as.factor(marks), poly=bounds))
}
--
Uwe Ligges [EMAIL PROTECTED] wrote:
Suzanne E. Blatt wrote:
Hello,
I'm working in spatstat and having difficulty with the ppp objects. I can get a
ppp object for one set of data, but with the same code applied to a second data set
(all I am changing is the field identifier), I get the following error message:
Error in switch(w$type, rectangle={: internal error: some total scores are neither
0 nor 1
What is a ppp object?
Which function has been applied and generated that error message?
The error message tells you some values a ought to sum up to 0 or 1 but
they don't. I (and perhaps others as well) cannot help when you don't
specify some relevant information.
Uwe Ligges
Any thoughts on what this means and how to correct it would be most appreciated.
Thanks,
Suzanne
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[R] Deciphering an error message
Hello,
I'm working in spatstat and having difficulty with the ppp objects. I can get a ppp
object for one set of data, but with the same code applied to a second data set (all I
am changing is the field identifier), I get the following error message:
Error in switch(w$type, rectangle={: internal error: some total scores are neither 0
nor 1
Any thoughts on what this means and how to correct it would be most appreciated.
Thanks,
Suzanne
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[R] Nested anovas
Hello, Is anyone out there doing nested anovas? I'm familiar with the notation to designate the nesting in SAS but can't seem to find any for R. How can I specify the nesting levels? Thanks, Suzanne __ McAfee VirusScan Online from the Netscape Network. Comprehensive protection for your entire computer. Get your free trial today! http://channels.netscape.com/ns/computing/mcafee/index.jsp?promo=393397 Get AOL Instant Messenger 5.1 free of charge. Download Now! __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
[R] Fonts in expression(paste)
Hello. I'm trying to change the fonts of my text. If I have 'expression(paste)' included (to get scientific symbols), the font= doesn't take effect. Is there a way around this? Thanks, Suzanne __ The NEW Netscape 7.0 browser is now available. Upgrade now! http://channels.netscape.com/ns/browsers/download.jsp __ [EMAIL PROTECTED] mailing list http://www.stat.math.ethz.ch/mailman/listinfo/r-help
