Re: [R] cum sums
In fact, I erred by summing both the year and the value, so i would recommend Peter's (much less messy) solution. Jim On 03/10/2014 02:57 PM, Peter Alspach wrote: Tena koe Philip An alternative to Jim's solution which seems to work and you may, or may not, find less messy: df- read.table(text=id yr val a 1950 1 b 1950 10 a 1951 2 b 1952 3 c 1952 4 a 1954 5 b 1954 2 c 1954 3,header=TRUE) df1- df[order(df$id, df$yr),] df1$valCS- unlist(by(df1$val, df1$id, cumsum)) df1 If you need to get back to the original order you can sort by row.names. HTH Peter Alspach __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Normalized Maximum Likelihood (NML) criterion
Dear R-help, i am working on some research and want to do some comparison among information criterion (e.g. AIC,BIC,..) and want to include (NML); i found AICcmodavg , infotheo -for mutual information- and 'SpatialExtremes however i couldn't find any R-package that provide (NML) calculus; any idea? best regards; Amer. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to obtain a mean by more than one other variable
Hi, If `dat` is the dataset: with(dat,ave(ABUNDHA,SITE,REP,FUN=mean)) #[1] 0.46 0.46 0.14 0.03 0.22 0.67 0.01 I am not sure how you got 0.45 when REP's are not the same. A.K. On Sunday, March 9, 2014 11:29 PM, Erynn Call erynn.c...@maine.edu wrote: I'm trying to create a new variable (meanABUNDHA) by obtaining a mean value *by* other variables. I surveyed birds (multiple species) at multiple sites and have multiple surveys within a REP (i.e. in example data below, SURVEY 55 and 57 are in REP 11). I need the mean ABUNDHA (pooling SURVEY) for each BIRD species by REP and by SITE. Below, I would average 0.77 and 0.15 for MALL in REP 11 at SITE 1 to get 0.46 meanABUNDHA. An example of my data are as follows, including the new variable I hope to create meanABUNDHA: SITE REP SURVEY BIRD ABUNDHA meanABUNDHA 1 11 57 MALL 0.77 0.46 1 11 55 MALL 0.15 0.46 1 12 58 MALL 0.14 0.14 1 2 58 BAEA 0.03 0.03 3 4 64 AMCR 0.22 0.45 3 5 65 AMCR 0.67 0.45 7 11 56 MALL 0.01 0.01 I'm not sure how to incorporate more than one by=? data.all4[,mean(ABUNDHA),by= REP] #Add new column containing the by-REP mean of ABUNDHA data.all5-data.all4[,ABUNDHAmean:=mean(ABUNDHA),by=REP] Thank you for any guidance!! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help resolving issues with generating a chi-squared density plot from scratch
I am far too lazy to go through all your rather complicated code, but my
basic impression is that you are re-inventing quite a few wheels.
Just to get a plot of the density function you can simply do, e.g.:
plot(function(x){dchisq(x,1)},0,qchisq(0.999,1))
I can't see why you are fooling about with the ylim values; just let the
plot() function choose ylim.
As to why you can't get things to work when df=1 ... well don't try to
set the upper y limit equal to infinity! You have a finite plotting
region, after all.
I have no idea what you mean by The y-axis is numbered only
relatively; this makes no sense at all. What *do* you want? The
y-axis labelling that you get will be/is the appropriate labelling.
The arrows will go where you tell them to go, so if they are going
diagonal you are telling them to go diagonal.
cheers,
Rolf Turner
On 10/03/14 13:30, Levi Robinson wrote:
I wrote the code to graph a chi-squared density function, shade the
percentile, and point to the CV, but it has a few issues I can't seem to
resolve
1. It won't work at all for DF = 1 due to ylim going to infinity, but I
haven't been able to resolve this still after hours of trying.
2) The y-axis is numbered only relatively; I'd prefer they were the actual
prob densities, but again, I fiddled with a few things, but it just
wouldn't get me what I wanted.
3) For low degrees of freedom and higher percentiles, the arrow pointing to
CV seems to end up going diagonal instead of straight down
Here's the code below and here's the URL for R fiddle for the code which
might make it easier to fix:
http://www.r-fiddle.org/#/fiddle?id=ChFi0dyJversion=4
chi.dens = function(x = NULL, df = NULL, cv = NULL) {
# x = percentile/quantile
# df = degrees of freedom
# cv = critical value
if(x1 ||x0) stop(Percentile must be between 0 and 1) #
Error-handling
qend = qchisq(x, df)
perc = x
qt0=qchisq(0.5, df) # Defining for arrows later
dy0=dchisq(0.45, df) # Defining for arrows later
xrange = qchisq (0.999, df)
x = seq(0, xrange)
y = dchisq(x, df)
yheight = max(dchisq(x, df))
# Creating plot
plot(x,y,type = l, ylim=c(0,yheight),axes=FALSE)
title( Chi-squared Density Curve with)
mtext(bquote(paste(DF = , .(df), and Percentile = , .(perc))),
side = 3, line = 0) # Input information
# Shading left tail-region
qt = signif(qend,5)
x0=seq(0, qt)
y0=dchisq(x0, df)
polygon(c(0, x0, qt), c(0, y0, 0), col = lightblue)
xtks=signif(seq(0,xrange,length=10),3)
axis(1, pos=0, at=xtks, labels=xtks)
y.unit=max(dchisq(x, df))/5
y.pos=seq(0,5*y.unit, length=5)
y.lab=c(0, 1, 2, 3, 4) # Y axis numbers only reflect relative
densities to each other.
axis(2,pos=0, at=y.pos, labels=y.lab)# set up y-axis
# Normal CV less than the 99.9 Percentile:
if(qt = xrange){
if(length(cv)==0) text(0.75*xrange,3*y.unit, bquote(paste(CV = ,
.(qend))), cex=1.2, col = red,adj=0.5)
#
if(length(perc)==1) text(0.35*xrange,3*y.unit, paste(Area = ,
perc), cex=1.2, col=darkblue, adj=0.5)
if(perc0.5){
arrows(0.35*xrange, 2.5*y.unit, qt0, 0.3*dy0, length=0.1,
angle=20) # pointing to the shaded region
}
if(perc=0.5){
arrows(0.35*xrange, 2.5*y.unit, qt/2, 0.3*dy0, length=0.1,
angle=20) # pointing to the shaded region
}
arrows(0.75*xrange, 2.5*y.unit, qt, 0, length=0.1, angle=20)
points(qt,0,pch=17, col=red)
}
# When CV is greater than the 99.9 Percentile:
if(qt xrange){
print(CV may be too far to the right to be shown on graph due to the
high percentile)
if(length(cv)==0) text(0.75*xrange,3*y.unit, bquote(paste(CV = ,
.(qend))), cex=1.2, col = red,adj=0.5)
if(length(perc)==1) text(0.35*xrange,3*y.unit, paste(Area = ,
perc), cex=1.2, col=darkblue, adj=0.5)
if(perc0.5){
arrows(0.35*xrange, 2.5*y.unit, qt0, 0.3*dy0, length=0.1,
angle=20) # pointing to the shaded region
}
if(perc=0.5){
arrows(0.35*xrange, 2.5*y.unit, qt/2, 0.3*dy0, length=0.1,
angle=20) # pointing to the shaded region
}
arrows(0.75*xrange, 2.5*y.unit, qt, 0, length=0.1, angle=20)
points(qt,0,pch=17, col=red)
}
}
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] Graph densification in large networks
Hi all, I have dynamic large 2-mode networks (1st mode ~50k nodes, 2nd mode ~500k nodes, timepoints ~100). I want to identify the number of new nodes and new edges per timepoint in folded 1-mode networks. In other words, I want to do measure graph densification as proposed by Leskovec et al. (http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.262.3092rep=rep1type=pdf) What package should I use? Best wishes Haiko Haiko Lietz GESIS - Leibniz Institute for the Social Sciences Department of Computational Social Science Unter Sachsenhausen 6-8, D-50667 Köln Tel: + 49 (0) 221 / 476 94 -223 eMail: haiko.li...@gesis.orgmailto:haiko.li...@gesis.org Web: http://www.gesis.orghttp://www.gesis.org/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R Help
I have just installed R 3.0.3 on Windows 7. I open up the GUI and type setwd(c:/users/jon) and press return. Nothing happens, Ive tried manuals, forums etc ... An ex-student needs help using this program. I spent 7 years as an IT consultant before becoming a maths teacher so Im better than average with IT and I cant get it to do anything at all. What's up? Any help greatly appreciated. Jon [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Help
Hello, And what are you expecting the command setwd to do? Regards, Pascal On Mon, Mar 10, 2014 at 5:59 PM, Jon Nash jon.n...@hvhs.school.nz wrote: I have just installed R 3.0.3 on Windows 7. I open up the GUI and type setwd(c:/users/jon) and press return. Nothing happens, Ive tried manuals, forums etc ... An ex-student needs help using this program. I spent 7 years as an IT consultant before becoming a maths teacher so Im better than average with IT and I cant get it to do anything at all. What's up? Any help greatly appreciated. Jon [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Pascal Oettli Project Scientist JAMSTEC Yokohama, Japan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Help
Hello, The function setwd returns the previous working directory invisibly so nothing happens might mean that there is no apparent feedback. You can see if it changed the wd with getwd(). Hope this helps, Rui Barradas Em 10-03-2014 10:58, Pascal Oettli escreveu: Hello, And what are you expecting the command setwd to do? Regards, Pascal On Mon, Mar 10, 2014 at 5:59 PM, Jon Nash jon.n...@hvhs.school.nz wrote: I have just installed R 3.0.3 on Windows 7. I open up the GUI and type setwd(c:/users/jon) and press return. Nothing happens, Ive tried manuals, forums etc ... An ex-student needs help using this program. I spent 7 years as an IT consultant before becoming a maths teacher so Im better than average with IT and I cant get it to do anything at all. What's up? Any help greatly appreciated. Jon [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] package environment versus namespace environment
On 14-03-09 1:59 PM, Benjamin Tyner wrote: Duncan, Thanks for the explanation and commentary. Starting to make more sense...so, long story short, it seems the first thing one should check is whether base imports utils: packageDescription(base) Package: base Version: 3.0.1 Priority: base Title: The R Base Package Author: R Core Team and contributors worldwide Maintainer: R Core Team r-c...@r-project.org Description: Base R functions License: Part of R 3.0.1 Built: R 3.0.1; ; 2013-10-16 10:50:56 UTC; unix -- File: /usr/lib/R/library/base/Meta/package.rds I'll interpret the lack of an Imports: line to mean that base does not import any packages. So then the next thing to check is the enclosing environment: parent.env(.BaseNamespaceEnv) environment: R_GlobalEnv Ah-ha! Unlike the base package environment, the base namespace environment has its enclosing environment already on the search path, so eventually leads back to utils. (This is the piece of the puzzle prompting my original question about ... machinery that allows ...) So hypothetically, if I had attached utils ahead of .GlobalEnv on the search path, then functions in the base namespace would no longer be able to see objects in utils? (I realize the answer may be vacuous, since library() does not honor pos=1). I suspect in that alternate universe the base namespace would still be parented by the first entry in the search list. Duncan Murdoch Regards, Ben On 03/09/2014 09:09 AM, Duncan Murdoch wrote: On 14-03-08 6:42 PM, Benjamin Tyner wrote: Duncan, Thank you for the informative link. So, do the loaded namespaces have an ordering akin to the package search path that determines that functions in the base namespace can see objects in the utils namespace? (I noticed that loadedNamespaces() just comes back in alphabetical order.) No. The article that Henrik cited gives a reasonable description up until near the end, where (in my opinion) it makes things unnecessarily complicated. I'd recommend that you stop reading around where he tries to explain the dotted lines. In particular, ignore the second version of the Map of the World; the first one is accurate, the second is just misleading. In answer to your question: Gupta's article misses the possibility of packages that are loaded but not in the search path. In the notation of the first part of that article, loading a namespace just puts it in the middle two columns (i.e. creates the namespace and imports environments) without putting it in the search list. That happens when you import or load a package without attaching it. The search path imposes an ordering, things that aren't in it aren't ordered. Duncan Murdoch Regards Ben On 03/07/2014 11:46 AM, Duncan Murdoch wrote: On 07/03/2014 10:16 AM, Benjamin Tyner wrote: Hello, I realize that a function in environment: base (for example, function head1 below) is unable to see (without resorting to ::, anyway) objects in utils (for example, head below), since package:base is after package:utils on the search path. However, I'm wondering what is the machinery that allows a function in environment: namespace:base (for example, function head2 below) to be able to see head just fine, without needing to resort to ::. See Luke Tierney's article in R News, Name space management for R. Luke Tierney, R News, 3(1):2-6, June 2003 http://cran.r-project.org/doc/Rnews/Rnews_2003-1.pdf There's a link to it from the R help system. Run help.start(), then look at Technical papers in the Miscellaneous Material section. I believe most of what it says is still current; the only thing I can see at a glance that is no longer correct is that in those days namespaces were optional in packages. Now all packages have namespaces. Duncan Murdoch I'm also wondering more generally, why there is a need (practically speaking) for a distinction between the environment associated with a package and the environment associated with the namespace. $ export R_PROFILE=/home/btyner/Rprofile.site $ cat /home/btyner/Rprofile.site sys.source(/home/btyner/head1.R, envir = baseenv()) sys.source(/home/btyner/head2.R, envir = .BaseNamespaceEnv) $ cat /home/btyner/head1.R head1 - function(x) head(x) $ cat /home/btyner/head2.R head2 - function(x) head(x) $ Rscript -e head1(letters) Error in head1(letters) : could not find function head Execution halted $ Rscript -e head2(letters) [1] a b c d e f $ Rscript -e sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached
[R] catering for rescaling
My barplot has nicely left justified horizontal labels, the names of people. Written using text() . I use par(user)[1] - OFFSET to get the placed nicely. Now of course if i manually rescale/zoom the plot the labels get redrawn at the 'wrong' location, including off the left of the plot. I assume this is because the x-position is based off the size of a unit in the plot, which changes when i rescale. Can i get some pointers on how to adjust for this? Thanks. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] cum sums
Another option is library(plyr) ddply(df, id, transform, valCS = cumsum(val)) Best, Ista On Mon, Mar 10, 2014 at 12:27 AM, Jim Lemon j...@bitwrit.com.au wrote: In fact, I erred by summing both the year and the value, so i would recommend Peter's (much less messy) solution. Jim On 03/10/2014 02:57 PM, Peter Alspach wrote: Tena koe Philip An alternative to Jim's solution which seems to work and you may, or may not, find less messy: df- read.table(text=id yr val a 1950 1 b 1950 10 a 1951 2 b 1952 3 c 1952 4 a 1954 5 b 1954 2 c 1954 3,header=TRUE) df1- df[order(df$id, df$yr),] df1$valCS- unlist(by(df1$val, df1$id, cumsum)) df1 If you need to get back to the original order you can sort by row.names. HTH Peter Alspach __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] format for as.Date and inserting missing rows in a data frame
Thank you to Arun and Petr for the give hints, veru useful. In order to get the date output in the required format, these are the commands that works: dat1$Date - as.Date(paste(dat1$Y_init, dat1$M_init, dat1$D_init, sep= ), format=%Y %m %d) dat1$Date1 - strptime(as.character(dat1$Date), %Y-%m-%d) dat1$Date1txt - format(dat1$Date1, %Y%m%d) Stefano Da: arun [smartpink...@yahoo.com] Inviato: martedì 4 marzo 2014 17.06 A: r-help@r-project.org Cc: Stefano Sofia Oggetto: Re: [R] format for as.Date and inserting missing rows in a data frame Hi, May be this helps: dat - read.table(text=Raingouge_number Station_number Year Month Day Rainfall 2004 2230 1951 1 1 2.60 2004 2230 1951 1 2 0.40 2004 2230 1951 1 3 0.00 2004 2230 1951 1 4 0.00 2004 2230 1951 1 5 0.20 2004 2230 1951 1 6 0.00 2004 2230 1951 1 7 0.00 2004 2230 1951 1 9 0.00 2004 2230 1951 1 10 0.00 2004 2230 1951 1 11 0.20,sep=,header=TRUE) dat - within(dat,Date - as.Date(paste(Year,Month,Day),format=%Y %m %d)) dat2 - data.frame(Date=seq(dat$Date[1],dat$Date[length(dat$Date)],by=day)) res - merge(dat,dat2,all=TRUE) res$Rainfall[is.na(res$Rainfall)] - -999 res A.K. On Tuesday, March 4, 2014 5:58 AM, Stefano Sofia stefano.so...@regione.marche.it wrote: Dear R users, I have a very long data frame (50 years, more than 1.5 million rows) of daily rainfall data from about 80 raingouges. The data frame that I have been given looks like Raingouge_number Station_number Year Month Day Rainfall 2004 2230 1951 1 1 2.60 2004 2230 1951 1 2 0.40 2004 2230 1951 1 3 0.00 2004 2230 1951 1 4 0.00 2004 2230 1951 1 5 0.20 2004 2230 1951 1 6 0.00 2004 2230 1951 1 7 0.00 2004 2230 1951 1 8 0.00 2004 2230 1951 1 9 0.00 2004 2230 1951 1 10 0.00 ... There could be some missing days. I have two questions. 1st question: In order to handle eventual missing days I think that I have to transform three separate numbers (Year, Month and Day) to Date. Is there a format in as.Date suitable for this transformation or before all I have to set all the months and days to two digits, remove spaces and then apply as.Date with format %Y%m%d? 2nd question In case of missing day, the corresponding row will be missing and then I have to insert this new row and put -999.9 as Rainfall. Is there an easy way to do that? Thank you for your help Stefano AVVISO IMPORTANTE: Questo messaggio di posta elettronica può contenere informazioni confidenziali, pertanto è destinato solo a persone autorizzate alla ricezione. I messaggi di posta elettronica per i client di Regione Marche possono contenere informazioni confidenziali e con privilegi legali. Se non si è il destinatario specificato, non leggere, copiare, inoltrare o archiviare questo messaggio. Se si è ricevuto questo messaggio per errore, inoltrarlo al mittente ed eliminarlo completamente dal sistema del proprio computer. Ai sensi dell’art. 6 della DGR n. 1394/2008 si segnala che, in caso di necessità ed urgenza, la risposta al presente messaggio di posta elettronica può essere visionata da persone estranee al destinatario. IMPORTANT NOTICE: This e-mail message is intended to be received only by persons entitled to receive the confidential information it may contain. E-mail messages to clients of Regione Marche may contain information that is confidential and legally privileged. Please do not read, copy, forward, or store this message unless you are an intended recipient of it. If you have received this message in error, please forward it to the sender and delete it completely from your computer system. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help resolving issues with generating a chi-squared density plot from scratch
If you set range of x in [0, something ] for for a function that goes to
infinity for x=0, then what do you expect?
On Mar 10, 2014, at 7:30 AM, Levi Robinson robin...@gmail.com wrote:
I wrote the code to graph a chi-squared density function, shade the
percentile, and point to the CV, but it has a few issues I can't seem to
resolve
1. It won't work at all for DF = 1 due to ylim going to infinity, but I
haven't been able to resolve this still after hours of trying.
2) The y-axis is numbered only relatively; I'd prefer they were the actual
prob densities, but again, I fiddled with a few things, but it just
wouldn't get me what I wanted.
3) For low degrees of freedom and higher percentiles, the arrow pointing to
CV seems to end up going diagonal instead of straight down
Here's the code below and here's the URL for R fiddle for the code which
might make it easier to fix:
http://www.r-fiddle.org/#/fiddle?id=ChFi0dyJversion=4
chi.dens = function(x = NULL, df = NULL, cv = NULL) {
# x = percentile/quantile
# df = degrees of freedom
# cv = critical value
if(x1 ||x0) stop(Percentile must be between 0 and 1) #
Error-handling
qend = qchisq(x, df)
perc = x
qt0=qchisq(0.5, df) # Defining for arrows later
dy0=dchisq(0.45, df) # Defining for arrows later
xrange = qchisq (0.999, df)
x = seq(0, xrange)
y = dchisq(x, df)
yheight = max(dchisq(x, df))
# Creating plot
plot(x,y,type = l, ylim=c(0,yheight),axes=FALSE)
title( Chi-squared Density Curve with)
mtext(bquote(paste(DF = , .(df), and Percentile = , .(perc))),
side = 3, line = 0) # Input information
# Shading left tail-region
qt = signif(qend,5)
x0=seq(0, qt)
y0=dchisq(x0, df)
polygon(c(0, x0, qt), c(0, y0, 0), col = lightblue)
xtks=signif(seq(0,xrange,length=10),3)
axis(1, pos=0, at=xtks, labels=xtks)
y.unit=max(dchisq(x, df))/5
y.pos=seq(0,5*y.unit, length=5)
y.lab=c(0, 1, 2, 3, 4) # Y axis numbers only reflect relative
densities to each other.
axis(2,pos=0, at=y.pos, labels=y.lab)# set up y-axis
# Normal CV less than the 99.9 Percentile:
if(qt = xrange){
if(length(cv)==0) text(0.75*xrange,3*y.unit, bquote(paste(CV = ,
.(qend))), cex=1.2, col = red,adj=0.5)
#
if(length(perc)==1) text(0.35*xrange,3*y.unit, paste(Area = ,
perc), cex=1.2, col=darkblue, adj=0.5)
if(perc0.5){
arrows(0.35*xrange, 2.5*y.unit, qt0, 0.3*dy0, length=0.1,
angle=20) # pointing to the shaded region
}
if(perc=0.5){
arrows(0.35*xrange, 2.5*y.unit, qt/2, 0.3*dy0, length=0.1,
angle=20) # pointing to the shaded region
}
arrows(0.75*xrange, 2.5*y.unit, qt, 0, length=0.1, angle=20)
points(qt,0,pch=17, col=red)
}
# When CV is greater than the 99.9 Percentile:
if(qt xrange){
print(CV may be too far to the right to be shown on graph due to the
high percentile)
if(length(cv)==0) text(0.75*xrange,3*y.unit, bquote(paste(CV = ,
.(qend))), cex=1.2, col = red,adj=0.5)
if(length(perc)==1) text(0.35*xrange,3*y.unit, paste(Area = ,
perc), cex=1.2, col=darkblue, adj=0.5)
if(perc0.5){
arrows(0.35*xrange, 2.5*y.unit, qt0, 0.3*dy0, length=0.1,
angle=20) # pointing to the shaded region
}
if(perc=0.5){
arrows(0.35*xrange, 2.5*y.unit, qt/2, 0.3*dy0, length=0.1,
angle=20) # pointing to the shaded region
}
arrows(0.75*xrange, 2.5*y.unit, qt, 0, length=0.1, angle=20)
points(qt,0,pch=17, col=red)
}
}
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Re: [R] catering for rescaling
If you use axis instead of text the positions should get set in user coordinates. -- David On Mar 10, 2014, at 6:34 PM, Geoffrey lordgeoff...@optusnet.com.au wrote: My barplot has nicely left justified horizontal labels, the names of people. Written using text() . I use par(user)[1] - OFFSET to get the placed nicely. Now of course if i manually rescale/zoom the plot the labels get redrawn at the 'wrong' location, including off the left of the plot. I assume this is because the x-position is based off the size of a unit in the plot, which changes when i rescale. Can i get some pointers on how to adjust for this? Thanks. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Graph densification in large networks
I didn't remember Leskovec et al.'s work correctly. They don't compute the number of new nodes and new edges per unit time but just the number of nodes and edges. This makes it a lot easier. But nevertheless, if I wanted to compute the number of new edges - what package would I use for large (and not necessarily sparse) graphs? Haiko -Ursprüngliche Nachricht- Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im Auftrag von Lietz, Haiko Gesendet: Montag, 10. März 2014 10:34 An: r-help@r-project.org Betreff: [R] Graph densification in large networks Hi all, I have dynamic large 2-mode networks (1st mode ~50k nodes, 2nd mode ~500k nodes, timepoints ~100). I want to identify the number of new nodes and new edges per timepoint in folded 1-mode networks. In other words, I want to do measure graph densification as proposed by Leskovec et al. (http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.262.3092rep=rep1type=pdf) What package should I use? Best wishes Haiko Haiko Lietz GESIS - Leibniz Institute for the Social Sciences Department of Computational Social Science Unter Sachsenhausen 6-8, D-50667 Köln Tel: + 49 (0) 221 / 476 94 -223 eMail: haiko.li...@gesis.orgmailto:haiko.li...@gesis.org Web: http://www.gesis.orghttp://www.gesis.org/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] F10.1 and i3 format in R
Dear list members, I have to export (through 'write.table') a dataframe where two columns must be respectively F10.1 (floating with 10 digits, 1 of which for the decimal position) and i3 (integer of length 3). I looked at the 'format' options, but I couldn't see what I need. I also looked for some examples, with no success. Is it possible to do it within R without external work? Thank you for your help Stefano AVVISO IMPORTANTE: Questo messaggio di posta elettronica può contenere informazioni confidenziali, pertanto è destinato solo a persone autorizzate alla ricezione. I messaggi di posta elettronica per i client di Regione Marche possono contenere informazioni confidenziali e con privilegi legali. Se non si è il destinatario specificato, non leggere, copiare, inoltrare o archiviare questo messaggio. Se si è ricevuto questo messaggio per errore, inoltrarlo al mittente ed eliminarlo completamente dal sistema del proprio computer. Ai sensi dellâart. 6 della DGR n. 1394/2008 si segnala che, in caso di necessità ed urgenza, la risposta al presente messaggio di posta elettronica può essere visionata da persone estranee al destinatario. IMPORTANT NOTICE: This e-mail message is intended to be received only by persons entitled to receive the confidential information it may contain. E-mail messages to clients of Regione Marche may contain information that is confidential and legally privileged. Please do not read, copy, forward, or store this message unless you are an intended recipient of it. If you have received this message in error, please forward it to the sender and delete it completely from your computer system. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] F10.1 and i3 format in R
On 10/03/2014 9:22 AM, Stefano Sofia wrote: Dear list members, I have to export (through 'write.table') Why restrict yourself to write.table? a dataframe where two columns must be respectively F10.1 (floating with 10 digits, 1 of which for the That's not the usual meaning for F10.1: normally the 10 char width includes the decimal point, not just the digits. decimal position) and i3 (integer of length 3). I looked at the 'format' options, but I couldn't see what I need. I'd suggest converting the numbers to character vectors in the right format, then writing those out (perhaps with write.table, but not necessarily). sprintf() uses C-like format strings, where %10.1f is close to F10.1, and %3d is close to i3. You could convert all of the numbers at once and use writeLines, e.g. writeLines(somefile, sprintf(%10.1f%3d, f, i)) will pack two numbers per line with no extra spaces between. Duncan Murdoch I also looked for some examples, with no success. Is it possible to do it within R without external work? Thank you for your help Stefano AVVISO IMPORTANTE: Questo messaggio di posta elettronica può contenere informazioni confidenziali, pertanto è destinato solo a persone autorizzate alla ricezione. I messaggi di posta elettronica per i client di Regione Marche possono contenere informazioni confidenziali e con privilegi legali. Se non si è il destinatario specificato, non leggere, copiare, inoltrare o archiviare questo messaggio. Se si è ricevuto questo messaggio per errore, inoltrarlo al mittente ed eliminarlo completamente dal sistema del proprio computer. Ai sensi dell’art. 6 della DGR n. 1394/2008 si segnala che, in caso di necessità ed urgenza, la risposta al presente messaggio di posta elettronica può essere visionata da persone estranee al destinatario. IMPORTANT NOTICE: This e-mail message is intended to be received only by persons entitled to receive the confidential information it may contain. E-mail messages to clients of Regione Marche may contain information that is confidential and legally privileged. Please do not read, copy, forward, or store this message unless you are an intended recipient of it. If you have received this message in error, please forward it to the sender and delete it completely from your computer system. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] F10.1 and i3 format in R
Hello, Take a look at ?sprintf. sprintf(%9.1f, 12.3) sprintf( %3d, 123) Hope this helps, Rui Barradas Em 10-03-2014 13:22, Stefano Sofia escreveu: Dear list members, I have to export (through 'write.table') a dataframe where two columns must be respectively F10.1 (floating with 10 digits, 1 of which for the decimal position) and i3 (integer of length 3). I looked at the 'format' options, but I couldn't see what I need. I also looked for some examples, with no success. Is it possible to do it within R without external work? Thank you for your help Stefano AVVISO IMPORTANTE: Questo messaggio di posta elettronica può contenere informazioni confidenziali, pertanto è destinato solo a persone autorizzate alla ricezione. I messaggi di posta elettronica per i client di Regione Marche possono contenere informazioni confidenziali e con privilegi legali. Se non si è il destinatario specificato, non leggere, copiare, inoltrare o archiviare questo messaggio. Se si è ricevuto questo messaggio per errore, inoltrarlo al mittente ed eliminarlo completamente dal sistema del proprio computer. Ai sensi dell’art. 6 della DGR n. 1394/2008 si segnala che, in caso di necessità ed urgenza, la risposta al presente messaggio di posta elettronica può essere visionata da persone estranee al destinatario. IMPORTANT NOTICE: This e-mail message is intended to be received only by persons entitled to receive the confidential information it may contain. E-mail messages to clients of Regione Marche may contain information that is confidential and legally privileged. Please do not read, copy, forward, or store this message unless you are an intended recipient of it. If you have received this message in error, please forward it to the sender and delete it completely from your computer system. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Graph densification in large networks
Hello, Take a look at package igraph. Hope this helps, Rui Barradas Em 10-03-2014 12:30, Lietz, Haiko escreveu: I didn't remember Leskovec et al.'s work correctly. They don't compute the number of new nodes and new edges per unit time but just the number of nodes and edges. This makes it a lot easier. But nevertheless, if I wanted to compute the number of new edges - what package would I use for large (and not necessarily sparse) graphs? Haiko -Ursprüngliche Nachricht- Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im Auftrag von Lietz, Haiko Gesendet: Montag, 10. März 2014 10:34 An: r-help@r-project.org Betreff: [R] Graph densification in large networks Hi all, I have dynamic large 2-mode networks (1st mode ~50k nodes, 2nd mode ~500k nodes, timepoints ~100). I want to identify the number of new nodes and new edges per timepoint in folded 1-mode networks. In other words, I want to do measure graph densification as proposed by Leskovec et al. (http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.262.3092rep=rep1type=pdf) What package should I use? Best wishes Haiko Haiko Lietz GESIS - Leibniz Institute for the Social Sciences Department of Computational Social Science Unter Sachsenhausen 6-8, D-50667 Köln Tel: + 49 (0) 221 / 476 94 -223 eMail: haiko.li...@gesis.orgmailto:haiko.li...@gesis.org Web: http://www.gesis.orghttp://www.gesis.org/ [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Help
I open up the GUI and type setwd(c:/users/jon) and press return. Nothing happens Does nothing happens mean that R does not even print , prompting you to enter more input? Did you get such a prompt before typing setwd(...)? What does typing 5:2 cause R to do? Bill Dunlap TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Jon Nash Sent: Monday, March 10, 2014 1:59 AM To: r-help@r-project.org Subject: [R] R Help I have just installed R 3.0.3 on Windows 7. I open up the GUI and type setwd(c:/users/jon) and press return. Nothing happens, Ive tried manuals, forums etc ... An ex-student needs help using this program. I spent 7 years as an IT consultant before becoming a maths teacher so Im better than average with IT and I cant get it to do anything at all. What's up? Any help greatly appreciated. Jon [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] 3.1.0 on April 10
We intend to release R 3.1.0 on April 10. Prerelease versions will appear starting March 13 (for the source version, binaries may come a little later). See developer.r-project.org for details. -- Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com ___ r-annou...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-announce __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Raster projection shift Biomod
Hi all, I am running Biomod with Albers Equal Area Conic Projection for Africa. Within Biomod all seems to work: I can generate a plot with the raster data and the presence and absence points plotted on top. However, when I go to export this to a *.csv file and create a shapefile from the point data in ArcMap, the randomly generated absence point data no longer overlies the continent in the correct location. With a very obvious shift (north-west) over Madagascar The original presence points are in the correct location, but the values for the raster data extracted per point are also incorrect. It seems that at some point the projection is not recognised, but I can't work out which part of the process seems to fail. The projection details for the raster layer were specified through the ArcCatalog projection chooser. If this projection is not supported, what projection is everything getting pushed to? Thanks for any help or suggestions in the right direction. Jenny The Royal Botanic Gardens, Kew is a non-departmental public body with exempt charitable status, whose principal place of business is at Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom. The information contained in this email and any attachments is intended solely for the addressee(s) and may contain confidential or legally privileged information. If you have received this message in error, please return it immediately and permanently delete it. Do not use, copy or disclose the information contained in this email or in any attachment. Any views expressed in this email do not necessarily reflect the opinions of RBG Kew. Any files attached to this email have been inspected with virus detection software by RBG Kew before transmission, however you should carry out your own virus checks before opening any attachments. RBG Kew accepts no liability for any loss or damage which may be caused by software viruses. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Help
You probably want to read the Introduction to R that comes with R
(menu: HelpManuals (in PDF)Introduction to R).
If you have an function, f, and you type just 'f', then R prints the function,
just as it does for any other object.
z - function(x)
+ {
+ if (missing(x)) missing x else x + 100
+ }
z
function (x)
{
if (missing(x)) missing x else x + 100
}
If you want to evaluate a function you must supply the arguments in
parentheses (even if there are no arguments you need the parentheses).
z(10:12)
[1] 110 111 112
z()
[1] missing x
Bill Dunlap
TIBCO Software
wdunlap tibco.com
From: Jon Nash [mailto:jon.n...@hvhs.school.nz]
Sent: Monday, March 10, 2014 11:14 AM
To: William Dunlap
Subject: Re: [R] R Help
Hi Bill,
I start with a prompt
I type the command in the syntax that appears to be correct
I immediately get a prompt back
I type getwd and get no indication of any directory at all just the following:
getwd
function ()
.Internal(getwd())
bytecode: 0x0cb0df80
environment: namespace:base
Jon
On 11 March 2014 03:42, William Dunlap
wdun...@tibco.commailto:wdun...@tibco.com wrote:
I open up the GUI and type setwd(c:/users/jon) and press return. Nothing
happens
Does nothing happens mean that R does not even print , prompting you
to enter more input?
Did you get such a prompt before typing setwd(...)?
What does typing
5:2
cause R to do?
Bill Dunlap
TIBCO Software
wdunlap tibco.comhttp://tibco.com
-Original Message-
From: r-help-boun...@r-project.orgmailto:r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.orgmailto:r-help-boun...@r-project.org] On
Behalf
Of Jon Nash
Sent: Monday, March 10, 2014 1:59 AM
To: r-help@r-project.orgmailto:r-help@r-project.org
Subject: [R] R Help
I have just installed R 3.0.3 on Windows 7.
I open up the GUI and type setwd(c:/users/jon) and press return. Nothing
happens, Ive tried manuals, forums etc ...
An ex-student needs help using this program. I spent 7 years as an IT
consultant before becoming a maths teacher so Im better than average with
IT and I cant get it to do anything at all. What's up? Any help greatly
appreciated.
Jon
[[alternative HTML version deleted]]
__
R-help@r-project.orgmailto:R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] strucchange w dummy variables
Hello, I am having trouble with the output from the strucchange package for a dummy variable regression. Why do I still get an intercept term in the output of lm03, below? library(lmtest) library(strucchange) data(GermanM1) #regular dummy regression with intercept lm01 - lm(m ~ as.factor(season), data=GermanM1) coeftest(lm01) #regular dummy regression without intercept lm02 - lm(m ~ as.factor(season) - 01, data=GermanM1) coeftest(lm02) #segmented regression for which I would like no intercept, yet the output includes an intercept, why? lm03 - lm(m ~ breakfactor(breakpoints(m ~ as.factor(season) - 01, data=GermanM1)) / as.factor(season) - 01, data=GermanM1) coeftest(lm03) Thank you. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] strucchange w dummy variables
On Mon, 10 Mar 2014, Geoffrey Smith wrote: Hello, I am having trouble with the output from the strucchange package for a dummy variable regression. Why do I still get an intercept term in the output of lm03, below? library(lmtest) library(strucchange) data(GermanM1) #regular dummy regression with intercept lm01 - lm(m ~ as.factor(season), data=GermanM1) coeftest(lm01) #regular dummy regression without intercept lm02 - lm(m ~ as.factor(season) - 01, data=GermanM1) coeftest(lm02) #segmented regression for which I would like no intercept, yet the output includes an intercept, why? lm03 - lm(m ~ breakfactor(breakpoints(m ~ as.factor(season) - 01, data=GermanM1)) / as.factor(season) - 01, data=GermanM1) coeftest(lm03) This has nothing to do with strucchange. In general, regressions of type y ~ f1/f2 behave like this. In y ~ f1/f2 you get the treatment contrasts of both f1 and f2. If you do y ~ f1/f2 - 1 then no treatment contrasts are applied for f1 but still for f2. But strucchange provides dedicated tools to do what you want to do. You can simply use the coef() and coeftest() methods for breakpoints objects: bp - breakpoints(m ~ season - 1, data = GermanM1) coef(bp) coeftest(bp) which should be what you are looking for. Thank you. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Shortest connected path in a matrix
This might be done using GIS tools, where finding shortest paths between locations is a common task. But I can't help with details. -Don -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925-423-1062 On 3/5/14 9:44 AM, McCloskey, Bryan bmcclos...@usgs.gov wrote: Here is some example data (hopefully the monospace formatting is preserved): a b c d e - - - - - 1 | F | T | F | T | F | - - - - - 2 | T | F | T | F | T | - - - - - 3 | T | T | F | F | F | - - - - - 4 | F | T | F | T | F | - - - - - 5 | F | T | F | F | T | - - - - - So, for cell b1, the shortest possible path to a true value in row 5 is b1-a2-a3-b4-b5 (distance: sqrt(2) + 1 + sqrt(2) + 1). * Shortest paths are not necessarily unique, but I just need to find the length. * If it's computationally hard to guarantee the absolute shortest path, I can probably live with nearly shortest paths. * Paths can backtrack, so the shortest path from cell e2 to row 4 is e2-d1-c2-b3-b4-b5. I need to calculate the shortest path for all true cells to all rows further down the matrix. I'm afraid I'm going to have to write some sort of recursive path-tracing algorithm, but I'm hoping there's a package already in existence that accomplishes this already... -bryan On Tue, Mar 4, 2014 at 1:13 PM, McCloskey, Bryan bmcclos...@usgs.govwrote: I have a binary rectangular T/F matrix; I need to be able to calculate the shortest path (i.e., Pythagorean distance) between a populated cell in row j and any populated cell in some row j+n. For instance, if I have a chessboard with random black/white square colors, I need the shortest distance (linear distance, not number of steps) for a king to get from a specified black space on the first row, to _any_ black space in a specified further row, traveling only on black spaces. Any idea? Thanks, -bryan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Raster projection shift Biomod
Probably better to ask on r-sig-geo. Wouldn't it make more sense to export in a raster format, rather than csv? -Don -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925-423-1062 On 3/10/14 10:24 AM, Jenny Williams jenny.willi...@kew.org wrote: Hi all, I am running Biomod with Albers Equal Area Conic Projection for Africa. Within Biomod all seems to work: I can generate a plot with the raster data and the presence and absence points plotted on top. However, when I go to export this to a *.csv file and create a shapefile from the point data in ArcMap, the randomly generated absence point data no longer overlies the continent in the correct location. With a very obvious shift (north-west) over Madagascar The original presence points are in the correct location, but the values for the raster data extracted per point are also incorrect. It seems that at some point the projection is not recognised, but I can't work out which part of the process seems to fail. The projection details for the raster layer were specified through the ArcCatalog projection chooser. If this projection is not supported, what projection is everything getting pushed to? Thanks for any help or suggestions in the right direction. Jenny The Royal Botanic Gardens, Kew is a non-departmental public body with exempt charitable status, whose principal place of business is at Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom. The information contained in this email and any attachments is intended solely for the addressee(s) and may contain confidential or legally privileged information. If you have received this message in error, please return it immediately and permanently delete it. Do not use, copy or disclose the information contained in this email or in any attachment. Any views expressed in this email do not necessarily reflect the opinions of RBG Kew. Any files attached to this email have been inspected with virus detection software by RBG Kew before transmission, however you should carry out your own virus checks before opening any attachments. RBG Kew accepts no liability for any loss or damage which may be caused by software viruses. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Change of sign with division by zero, i.e. -1/0 = Inf ??
Hi R-users, I am facing a strange behaviour that changes the sign of Inf with a division by zero. In my script, I have defined the following 3 variables and the elementwise division: lambda_k[gamma_lambda] # numeric vector [1] -1 0 del_lambda[gamma_lambda] # numeric vector [1] 0 -1 gamma_lambda # integer vector with the indexes of the elements in lambda_k del_lambda [1] 74 11 lambda_k[gamma_lambda] / del_lambda[gamma_lambda] [1] Inf 0 The result is surprising instead of -Inf 0 which I would expect because the elementwise division of the elements with index 74 is -1/0. Surprisingly, if I try to do the division with just newly defined numeric vectors with the same values, I obtain the correct result, i.e. c(-1,0) / c(0,-1) [1] -Inf0 How can this be explained? Any input would be really welcomed. For your information, I'm using R version 3.0.2 (2013-09-25) and Rstudio Version 0.98.501 on Platform: x86_64-apple-darwin10.8.0 (64-bit). Thanks very much for your help, Cesar -- Cesar Caballero www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] using diff function with by function
I have been trying to process a data.frame (tr) on a grouping factor (Rmbr) using diff to find differences between srv_dt (a date) by Rmbr and keep getting the following error message tmp - by(tr,tr$Rmbr, diff, tr$srv_dt, lag=1, difference=1) Error in r[i1] - r[-length(r):-(length(r) - lag + 1L)] : non-numeric argument to binary operator # the only two arguments I supply are both numeric mode(tr$srv_dt) [1] numeric mode(tr$Rmbr) [1] numeric IMPORTANT NOTICE: This communication, including any attachment, contains information that may be confidential or privileged, and is intended solely for the entity or individual to whom it is addressed. If you are not the intended recipient, you should delete this message and are hereby notified that any disclosure, copying, or distribution of this message is strictly prohibited. Nothing in this email, including any attachment, is intended to be a legally binding signature. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] cum sums
Df $cumval - ave(Df$val, Df$val, cumsum) Df[-3] -- David On Mar 10, 2014, at 1:57 AM, Philip A. Viton vito...@osu.edu wrote: Suppose I have a dataframe beginning: id yr val a 1950 1 b 1950 10 a 1951 2 I'm trying to produce a table of cumulative sums of val, disaggregated by id and then yr, so the result should begin id yr cumval a 1950 1 a 1951 3 b 1950 10 I've been trying to do this using aggregate and passing the function cumsum, but I can't get it to work. Can someone tell me how to do this? Thanks! Philip A. Viton City Planning, Ohio State University 275 West Woodruff Avenue, Columbus OH 43210 vito...@osu.edu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Building R for better performance
CE, Sorry for the delay. I haven't installed any additional packages, so I don't know the answer to your question. Let me look into it and get back to you. Regards, Jonathan Anspach Sr. Software Engineer Intel Corp. jonathan.p.ansp...@intel.com 713-751-9460 -Original Message- From: ce [mailto:zadi...@excite.com] Sent: Wednesday, March 05, 2014 8:54 PM To: r-help@r-project.org; Anspach, Jonathan P Subject: Re: [R] Building R for better performance Hi Jonathan, I think most people would be interested in such a tool, because main complaint of R is its slowness for some operations and big data. Even thought the intel software is paying , I could install it free since I am not selling any software and work for non-profit. I compiled successfully on my opensuse.. My question is : after make install , do I need to give special options to install.packages or they will be complied with icc automatically ? Regards CE -Original Message- From: Anspach, Jonathan P [jonathan.p.ansp...@intel.com] Date: 03/05/2014 12:28 AM To: r-help@r-project.org r-help@r-project.org Subject: [R] Building R for better performance Greetings, I'm a software engineer with Intel. Recently I've been investigating R performance on Intel Xeon and Xeon Phi processors and RH Linux. I've also compared the performance of R built with the Intel compilers and Intel Math Kernel Library to a default build (no config options) that uses the GNU compilers. To my dismay, I've found that the GNU build always runs on a single CPU core, even during matrix operations. The Intel build runs matrix operations on multiple cores, so it is much faster on those operations. Running the benchmark-2.5 on a 24 core Xeon system, the Intel build is 13x faster than the GNU build (21 seconds vs 275 seconds). Unfortunately, this advantage is not documented anywhere that I can see. Building with the Intel tools is very easy. Assuming the tools are installed in /opt/intel/composerxe, the process is simply (in bash shell): $ . /opt/intel/composerxe/bin/compilervars.sh intel64 $ ./configure --with-blas=-L/opt/intel/composerxe/mkl/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm --with-lapack CC=icc CFLAGS=-O2 CXX=icpc CXXFLAGS=-O2 F77=ifort FFLAGS=-O2 FC=ifort FCFLAGS=-O2 $ make $ make check My questions are: 1) Do most system admins and/or R installers know about this performance difference, and use the Intel tools to build R? 2) Can we add information on the advantage of building with the Intel tools, and how to do it, to the installation instructions and FAQ? I can post my data if anyone is interested. Thanks, Jonathan Anspach Sr. Software Engineer Intel Corp. jonathan.p.ansp...@intel.com 713-751-9460 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] two maps with different color legends in spplot
Hi all, I am using spplot to plot two maps in the same device. In my case, I have a map of a certain variable and the same map of the standard deviation of the same variable. The range of the second is much smaller than the range of the first so my wish is to plot both but to have them on different scales for the color legend (hence, to have two separated legends). Is it possible? I have worked out a way to do that, which passes through stretching the second variable to the range of the first, and then work hardly on the key list from within the trellis object structure. I was wondering if there is a more straightforward way. Thanks, Gianluca -- Gianluca Filippa PhD ARPA-VdA Skype: gianluca.filippa [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Subsetting between two values (into a range)????
Hi, If 'dat' is the dataset: Try subset(dat, Start MapInfo End MapInfo) A.K. Dear All, I want to subset a column (MapInfo in the attached photo) in csv file if its values be ranged between values in two other columns (Start and End in the attached photo) using R 3.0.1. Thank you in advance for all nice guides. M.H. Banabazi __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Change of sign with division by zero, i.e. -1/0 = Inf ??
Hi, Without a reproducible example (providing data with dput(), please) it's hard to say for certain, but my suspicion is that this is a R FAQ 7.31 issue. Sarah On Mon, Mar 10, 2014 at 11:26 AM, Cesar Caballero c.caball...@bcbl.eu wrote: Hi R-users, I am facing a strange behaviour that changes the sign of Inf with a division by zero. In my script, I have defined the following 3 variables and the elementwise division: lambda_k[gamma_lambda] # numeric vector [1] -1 0 del_lambda[gamma_lambda] # numeric vector [1] 0 -1 gamma_lambda # integer vector with the indexes of the elements in lambda_k del_lambda [1] 74 11 lambda_k[gamma_lambda] / del_lambda[gamma_lambda] [1] Inf 0 The result is surprising instead of -Inf 0 which I would expect because the elementwise division of the elements with index 74 is -1/0. Surprisingly, if I try to do the division with just newly defined numeric vectors with the same values, I obtain the correct result, i.e. c(-1,0) / c(0,-1) [1] -Inf0 How can this be explained? Any input would be really welcomed. For your information, I'm using R version 3.0.2 (2013-09-25) and Rstudio Version 0.98.501 on Platform: x86_64-apple-darwin10.8.0 (64-bit). Thanks very much for your help, Cesar -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Change of sign with division by zero, i.e. -1/0 = Inf ??
On 10-03-2014, at 16:26, Cesar Caballero c.caball...@bcbl.eu wrote: Hi R-users, I am facing a strange behaviour that changes the sign of Inf with a division by zero. In my script, I have defined the following 3 variables and the elementwise division: lambda_k[gamma_lambda] # numeric vector [1] -1 0 del_lambda[gamma_lambda] # numeric vector [1] 0 -1 gamma_lambda # integer vector with the indexes of the elements in lambda_k del_lambda [1] 74 11 lambda_k[gamma_lambda] / del_lambda[gamma_lambda] [1] Inf 0 The result is surprising instead of -Inf 0 which I would expect because the elementwise division of the elements with index 74 is -1/0. Surprisingly, if I try to do the division with just newly defined numeric vectors with the same values, I obtain the correct result, i.e. c(-1,0) / c(0,-1) [1] -Inf0 How can this be explained? Any input would be really welcomed. Most likely the 0 you show for del_lambda is not exactly 0. Look at this c(-0.000,-1) [1] 0 -1 c(-1,0) / c(-0.000,-1) [1] Inf 0 Berend For your information, I'm using R version 3.0.2 (2013-09-25) and Rstudio Version 0.98.501 on Platform: x86_64-apple-darwin10.8.0 (64-bit). Thanks very much for your help, Cesar -- Cesar Caballero www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R Help
Hello, It's better to keep this on the list, the odds of getting more and better answers are greater. You need to type getwd() with the parenthesis and no arguments. It always returns something (the current wd). Rui Barradas Em 10-03-2014 18:00, Jon Nash escreveu: Hi Rui, Nothing of value is returned by getwd either. Jon On 11 March 2014 00:10, Rui Barradas ruipbarra...@sapo.pt mailto:ruipbarra...@sapo.pt wrote: Hello, The function setwd returns the previous working directory invisibly so nothing happens might mean that there is no apparent feedback. You can see if it changed the wd with getwd(). Hope this helps, Rui Barradas Em 10-03-2014 10:58, Pascal Oettli escreveu: Hello, And what are you expecting the command setwd to do? Regards, Pascal On Mon, Mar 10, 2014 at 5:59 PM, Jon Nash jon.n...@hvhs.school.nz mailto:jon.n...@hvhs.school.nz wrote: I have just installed R 3.0.3 on Windows 7. I open up the GUI and type setwd(c:/users/jon) and press return. Nothing happens, Ive tried manuals, forums etc ... An ex-student needs help using this program. I spent 7 years as an IT consultant before becoming a maths teacher so Im better than average with IT and I cant get it to do anything at all. What's up? Any help greatly appreciated. Jon [[alternative HTML version deleted]] R-help@r-project.org mailto:R-help@r-project.org mailing list https://stat.ethz.ch/mailman/__listinfo/r-help https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/__posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] using diff function with by function
Hello, Maybe you want by(tr$srv_dt, tr$Rmbr, diff, lag=1, difference=1) Can't you ?dput a data example? dput(head(tr, 30)) # paste the output of this in a post Hope this helps, Rui Barradas Em 10-03-2014 16:10, Mckinstry, Craig escreveu: I have been trying to process a data.frame (tr) on a grouping factor (Rmbr) using diff to find differences between srv_dt (a date) by Rmbr and keep getting the following error message tmp - by(tr,tr$Rmbr, diff, tr$srv_dt, lag=1, difference=1) Error in r[i1] - r[-length(r):-(length(r) - lag + 1L)] : non-numeric argument to binary operator # the only two arguments I supply are both numeric mode(tr$srv_dt) [1] numeric mode(tr$Rmbr) [1] numeric IMPORTANT NOTICE: This communication, including any attachment, contains information that may be confidential or privileged, and is intended solely for the entity or individual to whom it is addressed. If you are not the intended recipient, you should delete this message and are hereby notified that any disclosure, copying, or distribution of this message is strictly prohibited. Nothing in this email, including any attachment, is intended to be a legally binding signature. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Change of sign with division by zero, i.e. -1/0 = Inf ??
The double precision number system (in the IEEE 754 format) includes two zeroes, one of each sign. They are hard to tell apart, but their reciprocals are Inf's of the appropriate sign and, in R 3.0.2, sprintf(%g,...) distinguishes them. z - c(0.0, -0.0) z [1] 0 0 z[1] == z[2] [1] TRUE identical(z[1], z[2]) [1] TRUE 1/z [1] Inf -Inf sprintf(%g, z) [1] 0 -0 Bill Dunlap TIBCO Software wdunlap tibco.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Cesar Caballero Sent: Monday, March 10, 2014 8:27 AM To: r-help@r-project.org Subject: [R] Change of sign with division by zero, i.e. -1/0 = Inf ?? Hi R-users, I am facing a strange behaviour that changes the sign of Inf with a division by zero. In my script, I have defined the following 3 variables and the elementwise division: lambda_k[gamma_lambda] # numeric vector [1] -1 0 del_lambda[gamma_lambda] # numeric vector [1] 0 -1 gamma_lambda # integer vector with the indexes of the elements in lambda_k del_lambda [1] 74 11 lambda_k[gamma_lambda] / del_lambda[gamma_lambda] [1] Inf 0 The result is surprising instead of -Inf 0 which I would expect because the elementwise division of the elements with index 74 is -1/0. Surprisingly, if I try to do the division with just newly defined numeric vectors with the same values, I obtain the correct result, i.e. c(-1,0) / c(0,-1) [1] -Inf0 How can this be explained? Any input would be really welcomed. For your information, I'm using R version 3.0.2 (2013-09-25) and Rstudio Version 0.98.501 on Platform: x86_64-apple-darwin10.8.0 (64-bit). Thanks very much for your help, Cesar -- Cesar Caballero www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Subsetting between two values (into a range)????
On 14-03-10 10:47 AM, arun wrote: Hi, If 'dat' is the dataset: Try subset(dat, Start MapInfo End MapInfo) A bit of advice I think I read in The Elements of Programming Style: try to make complex conjunctions look like their mathematical equivalents, and they'll be easier to read. The mathematical way to write the test above would be Start MapInfo End, so the programmatic way to write it should be Start MapInfo MapInfo End This makes the character of the interval completely obvious. Duncan Murdoch A.K. Dear All, I want to subset a column (MapInfo in the attached photo) in csv file if its values be ranged between values in two other columns (Start and End in the attached photo) using R 3.0.1. Thank you in advance for all nice guides. M.H. Banabazi __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Course: Beginner's Guide to MCMC, mixed models and GLMM with R
We would like to announce the following stats course: Course: Introduction to MCMC, Linear mixed effects models and GLMM with R Where: CIMA Research Foundation, Savona, Italy URL flyer: http://www.highstat.com/Courses/Flyer2014_05CIMA.pdf Course website: http://www.highstat.com/statscourse.htm Kind regards, Alain -- Dr. Alain F. Zuur First author of: 1. Beginner's Guide to GAMM with R (2014). 2. Beginner's Guide to GLM and GLMM with R (2013). 3. Begginner's Guide to GAM with R (2012). 4. Zero Inflated Models and GLMM with R (2012). 5. A Beginner's Guide to R (2009). 6. Mixed effects models and extensions in ecology with R (2009). 7. Analysing Ecological Data (2007). Highland Statistics Ltd. 9 St Clair Wynd UK - AB41 6DZ Newburgh Tel: 0044 1358 788177 Email: highs...@highstat.com URL: www.highstat.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] catering for rescaling
On 03/10/2014 10:34 PM, Geoffrey wrote: My barplot has nicely left justified horizontal labels, the names of people. Written using text() . I use par(user)[1] - OFFSET to get the placed nicely. Now of course if i manually rescale/zoom the plot the labels get redrawn at the 'wrong' location, including off the left of the plot. I assume this is because the x-position is based off the size of a unit in the plot, which changes when i rescale. Can i get some pointers on how to adjust for this? Hi Geoffrey, This is a common problem when labels of arbitrary length are added to the axis of a plot. The gantt.chart function in the plotrix package works out the maximum length of the labels to be displayed and adjusts the margins of the plot to suit. gantt.chart uses the axis function to display the labels, and but you want left justification, so using mtext makes it a bit easier. I tried changing the size of the example in staircase.plot, which uses mtext, and it seemed to work okay. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Data Frame to list?
On 3/7/2014 7:41 PM, Keith S Weintraub wrote: Folks, I have a data frame as follows: foo-structure(list(name = c(A, B, C), num = c(3L, 2L, 1L)), .Names = c(name, num), row.names = c(NA, -3L), class = data.frame) str(foo) 'data.frame': 3 obs. of 2 variables: $ name: chr A B C $ num : int 3 2 1 foo name num 1A 3 2B 2 3C 1 I want to convert this to a list like so: oof-list(A = 3, B = 2, C = 1) You can do it as a one-liner as well: oof - setNames(as.list(foo$num), foo$name) str(oof) List of 3 $ A: num 3 $ B: num 2 $ C: num 1 oof $A [1] 3 $B [1] 2 $C [1] 1 Any Suggestions? Thanks, KW -- -- Brian S. Diggs, PhD Senior Research Associate, Department of Surgery Oregon Health Science University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] plotting tripgrid on PBSmapping
Hello, Sorry for the lack of a complete example but this is more of a class type question. I have a map of the coast that I generated through PBSmapping: xlims - c(292,303.5) ylims - c(41.5,49.5) plotMap(worldLLhigh, xlim=xlims, ylim=ylims, col=grey(0.1),bg=grey(0.9), xlab=, ylab=, las=1, tck=-0.015, axes=F) I want to add an intensity grid from an object that I created through the excellent 'trip' package (results in an sp class object (SpatialGridDataFrame)) and this is where I'm having difficulty. I know maptools allows you to change formats from sp to PBSmapping but I can't seem to identify how to do it for a SpatialGridDataFrame. I get the SpatialGridDataFrame object via: x2009.grid - makeGridTopology(data2009.sp, cells.dim = c(cell.x1, cell.y1), xlim=xlims, ylim=ylims,buffer = 0, cellsize = NULL,adjust2longlat = FALSE) x2009.final - tripGrid(data2009.sp, grid = x2009.grid, method = pixellate) For most of these maps I usually just add the grid layer using the image function but what I currently have worked out is quite messy and I think prone to error for other applications. Of course, I can plot the SpatialGridDataFrame object via: spplot(x2009.final) which would be great but I can't figure out how to add my coastline via the PBSmapping plotMap call. Could someone please suggest a more direct approach? Thank you. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Why does ar.ols manual caution against intercept=T, demean=F
The manual for ar.ols {stats} cautions against fitting a model with intercept
to a time series that is not demeaned. From the manual:
Some care is needed if intercept is true and demean is false. Only use this is
the series are roughly centred on zero. Otherwise the computations may be
inaccurate or fail entirely.
I was surprised by this warning. If a series is not centered on zero/not
demeaned by ar.ols, I would typically include an intercept in my AR/VAR model.
This takes care of fitting the unconditional mean.
Is this a typo? It would make sense to warn against fitting a model with
intercept=F, demean=F for a series that is not centered around zero.
I frequently fit AR/VAR models with intercept and without demeaning, couldn't
find any more information on this aspect of ar.ols, and therefore am asking my
first question on R-help (after several years as a very happy R user.)
Thank you,
Michael
---
Michael D. Bauer
Economist, Research Department
Federal Reserve Bank of San Francisco
101 Market Street MS 1130
San Francisco, CA 94105
415.974.3299 (w) 415.471.9136 (c)
michael.ba...@sf.frb.org
http://www.frbsf.org/economic-research/economists/michael-bauer/
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[R] How to know the what functions have used datasets in loaded packages.
Hi all, Once you start your R program, there are example data sets available within R along with loaded packages. Command data() will list all the datasets in loaded packages. Is there a method to know what R functions have used one of the datasets to present the function's utility, maybe at least for the basic R distribution. Thanks, Xing __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] plotting tripgrid on PBSmapping
Hi, this doesn't have much to do with tripGrid, since the object to plot is just a SpatialGridDataFrame. I don't use PBSmapping, so I haven't looked at that - perhaps there is an add = TRUE option to plotMap (?), so perhaps you could do this: image(x2009.final) plotMap(..., add = TRUE) Your main issue may be that you are using the Pacific view (0, 360) longitudes rather than (-180,180). I don't know how/if plotMap deals with that, Otherwise, I would use a different data set and just use the sp plot functions. image(x2009.final) library(maptools) data(wrld_simpl) plot(elide(wrld_simpl, shift = c(360, 0)), add = TRUE) You need to elide it to shift it 360 in longitude since your range is c(292,303.5) The same will work with other polygon data in longlat read with rgdal::readOGR or maptools::readShapePoly. To actually crop wrld_simpl you can use [ with matches on the data attributes, or use rgeos::gIntersection. You also could modify your input data to be in the range -180,180, or use a map projection before using the trip* functions. I know there's a lot of options listed above, but it really does depend on which aspects matter to you. HTH On Tue, Mar 11, 2014 at 10:09 AM, Trevor Davies davies.tre...@gmail.com wrote: Hello, Sorry for the lack of a complete example but this is more of a class type question. I have a map of the coast that I generated through PBSmapping: xlims - c(292,303.5) ylims - c(41.5,49.5) plotMap(worldLLhigh, xlim=xlims, ylim=ylims, col=grey(0.1),bg=grey(0.9), xlab=, ylab=, las=1, tck=-0.015, axes=F) I want to add an intensity grid from an object that I created through the excellent 'trip' package (results in an sp class object (SpatialGridDataFrame)) and this is where I'm having difficulty. I know maptools allows you to change formats from sp to PBSmapping but I can't seem to identify how to do it for a SpatialGridDataFrame. I get the SpatialGridDataFrame object via: x2009.grid - makeGridTopology(data2009.sp, cells.dim = c(cell.x1, cell.y1), xlim=xlims, ylim=ylims,buffer = 0, cellsize = NULL,adjust2longlat = FALSE) x2009.final - tripGrid(data2009.sp, grid = x2009.grid, method = pixellate) For most of these maps I usually just add the grid layer using the image function but what I currently have worked out is quite messy and I think prone to error for other applications. Of course, I can plot the SpatialGridDataFrame object via: spplot(x2009.final) which would be great but I can't figure out how to add my coastline via the PBSmapping plotMap call. Could someone please suggest a more direct approach? Thank you. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Michael Sumner Hobart, Australia e-mail: mdsum...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Rare Association Rule Mining
Hello: I´m searching for some Example R Code on Rare Association Rule Mining/Infrequent Itemset Mining. Thanks in advance for any help. Alex __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ts instead of xts object
Hello. I have a dataframe that has a date column. The intervals between dates vary. I want to convert this to a ts object. I was able to convert it to an xts object but the package I want to analyse this data with (called 'changepoint') does not seem to want to deal with xts. In the example they give they use the following: data(discoveries) dis.pelt=cpt.meanvar(discoveries,test.stat='Poisson',method='PELT') plot(dis.pelt,cpt.width=3) cpts.ts(dis.pelt) and if I check: str(discoveries) Time-Series [1:100] from 1860 to 1959: 5 3 0 2 0 3 2 3 6 1 ... If I try with my data str(testTSRad) An 'xts' object on 2011-07-16 07:08:02/2013-09-20 01:25:48 containing: Data: num [1:501, 1] 76 77 79 86 79 79 85 86 89 88 ... Indexed by objects of class: [POSIXct,POSIXt] TZ: xts Attributes: NULL where I used this: testTSRad=xts(radSampPerRegion[[2]][ ,2],order.by=as.POSIXct(radSampPerRegion[[2]][ ,1])) I get this: testt=cpt.mean(testTSRad) Error in single.mean.norm(data, penalty, pen.value, class, param.estimates) : Data must have atleast 2 observations to fit a changepoint model. My data is below. Is there a way to convert it to ts? head(testTSRad) [,1] 2011-07-16 07:08:02 76 2011-07-16 07:08:06 77 2011-07-16 07:08:12 79 2011-07-16 07:08:16 86 2011-07-16 07:08:22 79 2011-07-16 07:08:26 79 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
