[R] 3d barplot in rgl

1:3] A<-matrix(c( 0.21, 0.21,0.03, 0.55, 0.58, 0.09, 1.30, 1.35, 0.22), nrow=3, byrow=TRUE, dimnames=list(stages,stages) ) ## I can get a surface plot, but that's about it. persp3d(A, col="red", alpha=0.7, xlab="fate", ylab="stage", zlab="Sen

[R] reading tables from url

. Parent.ProjectID ProjectID 11973313694 Global Ocean Sampling Expedition Metagenome 220823 13696 5-Way (CG) Acid Mine Drainage Biofilm Metagenome 3-13699Waseca County

Re: [R] Stochastic (transition) matrices: how to determine distributions and variance?

atrix(numeric(1000*3), ncol=3) for(i in 1:1000) { z <- sample(nrow(y), replace = TRUE) y1<-y[z,] n2[i,] <-prop.table( table(y1[,2], y1[,1]), 2) %*% n } # the CIs are much wider here apply(n2, 2, quantile, c(0.025,0.975)) [,1] [,2] [,3] 2.5% 55.89959 132.6868 361.

Re: [R] Matrix multiplication and random numbers

0. 147.8957 0.0 0.0 136.36804 220.7370 [5,]0 0. 0. 0. 96.92715 0.00.0 108.6551 [6,]0 0. 0. 0. 0.0 69.875270.0 0. [7,]0 0. 0. 0. 0.0 0.0 65.86229 0. Chris St

Re: [R] popbio and stochastic lambda calculation

Shawn Morrison-2 wrote: > > # The paper reports a 95% CI of 0.79 - 1.10 > # "My" reproduced result for the CIs is much larger, especially on the > upper end. Why would this be? > # The authors report using the 'delta' method (Caswell, 2001) to > calculate the CI in which the > > Shawn, I p

[R] Using substitute in a print method

" ## This prints what I'd want, but I'm not sure why its different. print.diag(d) [1] "A diagonal matrix d" Thanks for any help, Chris Stubben -- View this message in context: http://n4.nabble.com/Using-substitute-in-a-print-method-tp1606635p1606635.html Sent fro

Re: [R] sampling quadrats of increasing size in a list of matrices

q[i]+1) with sample( 1:(n-q[i]+1), replace=TRUE) ? Also, if you have a list of matrices, then maybe combine the code above into a function and then apply it to your list using lapply. Chris Stubben -- View this message in context: http://www.nabble.com/sampling-quadrats-of-increasing-s

[R] Long character not truncated by str() after adding comment

longch)<-"100 ABCs" str(longch) # not truncated Thanks, Chris Stubben -- View this message in context: http://www.nabble.com/Long-character-not-truncated-by-str%28%29-after-adding-comment-tp24611767p24611767.html Sent from the R help mai

Re: [R] splitting scientific names into genus, species, and subspecies

Mark W. Miller wrote: > > I have a list of scientific names in a data set. I would like to split > the names into genus, species and subspecies. Not all names include a > subspecies. Could someone show me how to do this? > strsplit should work for your example... data.frame( genus=sappl

Re: [R] Looking for a quick way to combine rows in a matrix

- function(x) chartr("ACGT", "TGCA", x) n<-cbind(key, rev=reverse(comp(key))) n<-t(apply(n,1, sort)) do.call(rbind, by(a, n[,1], colSums)) V1 V2 V3 V4 AA 5 13 21 29 AT 2 6 10 14 TA 3 7 11 15 Chris Stubben jholtman wrote: > > Try this: > >&

Re: [R] how to calculate means of matrix elements

f (!all(n == dims[1, ]) || !all(p == dims[2, ])) stop("the matrices must have the same dimensions") mat <- matrix(unlist(x), n * p, length(x)) mm <- matrix(rowMeans(mat, ...), n, p) dimnames(mm) <- dimnames(x[[1]]) mm } Chris Stubben -- View this messa

Re: [R] [XML packages] how to get the sub-node according to the sub-node's attribute?

Europa']", xmlValue) [1] "30.4 4 95.1 113 3.77 1.513 16.90 1 152" #OR? xpathSApply(doc, "//record[@id='Lotus Europa']") getNodeSet(doc, "//record[@id='Lotus Europa']") # And to list all Ids... xpathSApply(doc, &qu

[R] convert delimited strings with ranges to numeric

Is there an easy way to convert character strings with comma-separated numbers and ranges to a numeric vector? x<- "2,5-7,10,12-15" [1] 2 5 6 7 10 12 13 14 15 Thanks, Chris -- Chris Stubben Los Alamos National Lab Bioscience Division MS M888 Los Ala

[R] rowspan and readHTMLTable

w.ncbi.nlm.nih.gov/pmc/articles/PMC3544749/table/T1";, which=1) Thanks, Chris t1<-readHTMLTable( "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3544749/table/T1";, which=1) -- Chris Stubben Los Alamos National Lab Bioscience Division MS M888 Los Alamos, NM 87545

Re: [R] create unique ID for each group

> I want to merge dat1 and dat2 based on "ID" in order Have you tried merge(dat1, dat2) ? If ID is the common column (and no others), then that should be all you need to join (see ?merge). And then order if needed. Chris -- Chris Stubben Los Alamos National Lab Bioscienc

Re: [R] recode categorial vars into binary data

mple(L3, 10, replace=TRUE)) Chris -- Chris Stubben Los Alamos National Lab Bioscience Division MS M888 Los Alamos, NM 87545 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide h

Re: [R] create unique ID for each group

raw datasets are pretty important, especially if observations are split into different files and you are trying to join them later. How do you know for ID 0001 and obs 1 that height is 3.2 and not 2.6, especially if order in the two files are "not exactly the same". Chris -- Chr

Re: [R] rowspan and readHTMLTable

Methoxy mycolic acid synthase 4 3 Mycolic acid synthesis pcaA Rv0470cMycolic acid synthase (cyclopropane synthase) 4 Mycolic acid synthesis pcaA Rv0470cMycolic acid synthase (cyclopropane synthase) -- Chris Stubben Los Alamos National Lab Bioscience Divis

Re: [R] rotate column names in large matrix

the 90 degree counter clockwise rotation image(t(x[nrow(x):1,]), axes=FALSE) ## add 100 column names y<-paste("column", 1:100) text( seq(0,1,length=100) , 1.01, y, pos = 2, srt = 270, offset=0, cex=.7) Chris Stubben Lara Poplarski wrote: > > I have a large (1600*1600) mat

Re: [R] rotate column names in large matrix

Just increase the margins on the left side and add the rownames x <- cor(matrix(rnorm(600), 60, 100)) rownames(x)<-paste("row", 1:100) op<-par(mar=c(1,5,1,1), xpd=TRUE) image(t(x[nrow(x):1,]), axes=FALSE) text(-0.01, seq(0,1,length=nrow(x) ), rownames(x), pos = 2, offset = 0, cex = .7) Another

Re: [R] R eat my data

Gene names often have single quotes like 5'-methylthioadenosine phosphorylase ATP synthase B' chain ppGpp 3'-pyrophosphohydrolase so maybe try adding quote="" to the read table options. Chris Stubben -- View this message in context: http://r.789695.n4

Re: [R] Markov transition matrices , missing transitions for certain years

To keep the table dimensions the same, try changing the columns to factors... boxes$y97<-factor(boxes$y97, 1:4) boxes$y98<-factor(boxes$y98, 1:4) boxes$y99<-factor(boxes$y99, 1:4) ... > table(boxes$y98, boxes$y97) 1 2 3 4 1 1 0 1 0 2 0 0 0 0 3 0 0 0 0 4 1 0 0 1 > table(boxes$y99,

[R] Remove superscripts from HTML objects

ct above, but I'd rather just work with the results from htmlParse if possible (and not use readLines to load raw HTML first). Thanks, Chris Stubben -- View this message in context: http://r.789695.n4.nabble.com/Remove-superscripts-from-HTML-objects-tp4550738p4550738

Re: [R] Remove superscripts from HTML objects

Sorry if I was not clear. I wanted to remove the superscripts using xpath queries if possible. For example this will get p nodes with superscripts, but how do I remove the superscripts if there are many matching nodes and different superscripts? xpathSApply(doc, "//p[sup]", xmlValue) [1] "Cata"

Re: [R] Getting codebook data into R

1 12700 8874.441 7 61 2 9 940 1 22883 8874.441 8 61 2 8 642 1 33016 8874.441 9 71 1 7 9 39 1

[R] how to save an updated dataset

y is located, if the user has permission to save to that directory, and probably some other complications I'm missing. Any suggestions? Thanks, Chris Stubben -- View this message in context: http://www.nabble.com/how-to-save-an-updated-dataset-tp17782584p17782584.html Sent from the R hel

Re: [R] SQL INSERT using RMySQL

Greg, If you have a MySQL table with an auto_increment field, you could just insert a NULL value into that column and the database will increment the key (it may not work in SQL STRICT mode, I'm not sure). I don't think there's any way to specify which columns you want to load data into using db

Re: [R] Generating these matrices going backwards

Sorry, I wasn't sure what you meant. This way will return more than one answer, right? N<-c(1,2,1,3) R<-c(1.75,3.5,1.75,1.3125) ## get all 126 combinations of five 0's and four 1's for matrix cbn<-as.matrix(expand.grid( rep( list(0:1), 9))) cbn<- cbn[rowSums(cbn)==4,] ans<-list() ctr<-0 ## lo

Re: [R] Inserting a subsequence between values of a vector

You could use a combination of rle, cumsum and append. > x <- c(1,1,1,2,2,3,3,3,3,3,4) > y<-rle(x)$lengths > y [1] 3 2 5 1 > z<-cumsum(y)[y>1] > z [1] 3 5 10 > > for(i in rev(z)) x <- append(x, c(0,0,0), after = i) > x [1] 1 1 1 0 0 0 2 2 0 0 0 3 3 3 3 3 0 0 0 4 Chris Serguei Kaniovski-3

Re: [R] Diagonal matrix with off diagonal elements

Also try the odiag function in the demogR package odiag( 1:5, -1) [,1] [,2] [,3] [,4] [,5] [,6] [1,]000000 [2,]100000 [3,]020000 [4,]003000 [5,]000400 [6,]000

Re: [R] stochastic growth rate (package popbio)

privalan wrote: > > However, I cannot figure out the way to compute the asymptotic stochastic > population growth rate using “popbio”. I would like to perform a > stochastic model in which my demographic rates are sampled from beta > distribution with known mean and SD. For example, rather than

Re: [R] Population model question

-Halcyon- wrote: > > My question is : How do I arbitrarily assign the animals being "FALSE" > ***according to the uniformal chance generation*** to the array > Dead.Animals, there being "TRUE"? > Maybe I'm missing something, but aren't dead animals just the ones that aren't alive? Why do you

Re: [R] Download daily weather data

99 40 77 -- Chc -- -- -- 3 50 43 44 17 SW99 40 77 -- Chc -- -- -- 4 48 43 42 16 SW99 40 83 -- Chc -- -- -- 5 45 43 38 15WSW 100 40 93 -- Chc -- -- -- 6 42 42 35 14 W

Re: [R] projection.matrix() {popbio} for more than one matrix

Michelle, I would probably run a loop as well and save all matrices to a single list (see hudsonia and calathea on working with lists of matrices). First, run the example(test.census) to get the stage-fate data frame "trans" and then run this code to save the matrices into a list "all". years<-

Re: [R] graphs with gradients of colors

2[j], y2[j+1]), border=0, col = rev(heat.colors(100))[j]) } } Chris Stubben Van Dongen Stefan wrote: > > Hi All, > > I would like to fill the area under a curve with a gradient of colors. Are > there any packages or trick I could use > > Thanks > > Stefan &g

Re: [R] 3d barplot in rgl

hadley wickham gmail.com> writes: > > Why do you want a 3d barchart? They are generally a bad way to > present information as tall bars can obscure short bars, and it is > hard to accurately read off the height of a bar. While adding > rotation can reduce some of these problems, why not create

Re: [R] 3d barplot in rgl

Duncan Murdoch stats.uwo.ca> writes: > That demo gives you the basics of the code, so it shouldn't be too hard > to put your own together: just strip out the counting part. > Thanks, I did download the source to check the hist3d demo, but honestly it didn't look very easy to simplify. I sw

Re: [R] 3d barplot in rgl

>Transition matrices are Markov transition matrices among different > life stages of organisms -- in the simplest case (Leslie matrices, Ben, Thanks for your clear explanation and plot examples. I like the dotplots alot and added a few modifications below. Since I often compare rows and col

Re: [R] RMySQL NA/NULL value storage error

Adam Wilson-4 wrote: > > I am running R 2.5.1, RMySQL 0.6 , and DBI 0.2-3 on Windows XP > > Like others, I am having trouble with NA/Null value conversions between R > and a MySQL database via DBI, but I could not find my exact problem in the > archives. Most of the time NA values in R get tra

Re: [R] collapsing a data frame

> On 10/12/07, Ben Bolker ufl.edu> wrote: > > > > Trying to find a quick/slick/easily interpretable way to > > collapse a data set. > > Another alternative for SQL fans is the sqldf package. I used the MySQL driver here since SQLite does not support standard deviation. sqldf("select BROOD,

Re: [R] Elasticity in Leslie Matrix

> I would like to calculate elasticities and sensitivities of each parameters > involved in the following transition matrix: > > A <- matrix(c( > sigma*s0*f1, sigma*s0*f2, >s, v > ), nrow=2, byrow=TRUE,dimnames=list(stage,stage)) > > The command "eigen.analysis" a

Re: [R] Elasticity in Leslie Matrix

Sorry, I didn't think carefully about your question on my first reply, so please ignore it. Chapter 9 in Morris and Doak (2002) cover vital rate elasticities and sensitivities (see Box 9.1 for Matlab code http://www.sinauer.com/PVA/vitalsens.m). Simon, thanks for posting your code, I will add

Re: [R] Generating these matrices going backwards

Maybe something like this? N<-c(1,2,1,3) ## create empty matrix x<-diag(0,3) ## fill off diagonal x[row(x)==col(x)+1]<-N[1:2] # fill 3rd column x[1:2,3]<-N[3:4] Or create a function and return both x and y mat3<-function(N) { x<-diag(0,3) # fill each element separately x[2,1]<-N[1] x[3,2]<-N