similar to: Re-post data format question (apologies)

I've been comparing variables among objects (taxa) related by known trees, using phylogentically independent contrasts in the ape package, and want to move on to more complex models e.g. by using gls with appropriate correlation terms. My trees contain lots of (hard) polytomies and information about ancestors, which I've been including- creating fully dichotomous trees by using zero branch

Hello I apologise for the length of this entry but please bear with me. In short: I need a way of subsampling communities from all possible communities of n taxa taken 1:n at a time without having to calculate all possible combinations (because this gives me a memory error - using combn() or expand.grid() at least). Does anyone know of a function? Or can you help me edit the combn or

Dear all, I was wondering if you could help me with the following. I want to do calculate this equation: Ps(t)= (?_(r=1)^N Xtr* 1/?drs)/(?_(r=1)^N 1/?drs) Ps(t) ? Probability that taxon t will occur at site s (300 sites s) N ? Number of sites = from 1 to 49 Xtr ? Value for taxon t at site r (I have this information in a table, 40 taxa (columns) t, 49 sites r) drs ? Distance from site r to

I'm not sure if this is a bug, or if I'm doing something wrong. =20 =46rom the worms dataframe, which is at in a file called worms.txt at =20 http://www.imperial.ac.uk/bio/research/crawley/therbook <http://www.imperial.ac.uk/bio/research/mjcraw/therbook/index.htm>=20 =20 the idea is to extract a subset of the rows, sorted in declining order of worm density, with only the maximum

Dear All, I would like to make partial sums (or means or any other function) of the values in intervals along a sequence (spatial transect) where groups are defined. For instance: habitats<-rep(c("meadow","forest","meadow","pasture"),c(10,5,12,6)) observations<-rpois(length(habitats),2)

Full_Name: Joerg Rauh Version: 2.5.0 OS: Windows 2000 Submission from: (NULL) (84.168.226.163) Following Michael J. Crawley "Statistical Computing" on page 9 the worms.txt is required. After downloading it from the book's supporting website, which is http://www.bio.ic.ac.uk/research/mjcraw/statcomp/data/ I visually check the data against the book and they look identical. Then I do

I have a vector of land cover class data from a GIS: > landcov[1:10,2] #the first ten examples of a large (100k+) object 1 2 3 4 5 6 7 8 9 10 12 12 01 12 01 15 15 15 15 15 etc. I also have a lookup table for the class data that gives the cover type as a string: > cnd.names #the look up table, i.e., landcov[3,2] == 1 == "Montane Meadow" CndVal

Dear R users, i am fairly new to R and am having trouble creating code to solve a problem. I've searched the list, combed Crawley's 'R book' and several others, but can't quite find what i want. I want to generate permutations of various 'blocks' of 14 numbers. Each number within a block is a character state for a particular biological taxon. In the example below, for

Dear R community, I am running R 2.0.1 on a Windoze XP OS. I recently upgraded from R 1.9x to 2.0.1 and I am currently upgrading a my personal function packages. My other packages compiled without a hitch but I am having a difficult time with my largest package. Can someone please help me with the following error message "Error in parse(file, n, text, prompt) : syntax error on line

Hi Helpers: I have a factor object that has 314k entries of 39 land cover types. (This object can be coerced to characters neatly should that be easier to work with.) > length(foo) [1] 314482 > foo[1:10] [1] Montane Chaparral Barren Red Fir Red Fir [5] Red Fir Red Fir Red Fir Red Fir [9] Red Fir Red Fir 39 Levels:

R users, I recently upgraded (?) to Windows XP from 2000. I am trying to build an R package. I have done this many times on my old system and I am not sure why it is not working in XP. To build the package I call a bat file that specifies all the necessary paths -- but the "build" file (which appears to be a perl script) is looking for a "src" subdirectory in the src

I would like to revisit a problem that was discussed previously (see quoted discussion below). I am trying to do the same thing, using a string to indicate a column with the same name. I am making "foo" a string taken from a list of names. It matches the row where "item" = 5, and picks the corresponding "taxon" > foo <- list$taxon[match(5,list$item)] Let's

Dear R experts I am running a negative-binomial GLM (glm.nb) to test the null hypotheses that species 1 and 2 are equally abundant between site 1 and site2, and between each other. So, I have a 2x2 factorial design with factors Site (1,2) and Taxon (1,2). Since the Site:Taxon interaction is significant, I need to do the equivalent to a "post-hoc test" for ANOVA, however, the same tests

I don't see what's missing in my statements to add rows to a data frame and someone else will probably see what needs to be added to the statements. The data frame has this structure (without any data): $ PHYLUM : chr $ SUBPHYLUM : chr $ SUPERCLASS : chr $ CLASS : chr $ SUBCLASS : chr $ INFRACLASS : chr $ SUPERORDER : chr $ ORDER : chr $ SUBORDER :

I am new to R. I have a data set like this (given below is a fictional dataset): AgeCat FINWT 1 98 2 62 1 75 3 39 4 28 2 47 2 66 4 83 1 19 3 50 I need to calculate the weighted distribution of the variable AgeCat. In SAS i can do: proc freq data=ageval; tables agecat; weight finwt; run; What or is there an equivalent in R? TIA, Krishnan -- Krishnan Viswanathan 1101 High Meadow Dr

I am trying to put my app on heroku, following the instructions, when I get here I get this error: $ git push heroku master Enter passphrase for key ''/c/Users/Laurence/.ssh/id_rsa'': Counting objects: 277, done. Delta compression using up to 2 threads. Compressing objects: 100% (246/246), done. Read from remote host heroku.com: The connection was aborted fatal: sha1 file

Hi all Bear with me on this one... We have a problem connecting to a specific port via Oracle TNSPING There are two PC's in our office that are on the same network as the server (i.e. my desktop PC can not get to the server) The server has multiple network interfaces, the primary is a gigabit fibre card on IP xx.16. The secondary is a megabit card on IP xx.80 The tnsping command fails

I have the following sample dataset (CSV input here:http://goo.gl/YR8LP. CSV output here: http://goo.gl/EFCC8) which I want to transform as follows. For each person in a household I want to create two new variables OrigTAZ and DestTAZ. It should take the value in TripendTAZ and put that in DestTAZ. For OrigTAZ it should put value of TripendTAZ from the previous row. For the first trip of every

Ok guys, as requested, I will add more info so that you understand why a simple vector operation is not possible. It's not easy to explain in few words but let's see. I have a huge amount of points over a 2D space. I divide my space in a grid with a given resolution,say, 100m. The main loop that I am not sure if it's mandatory or not (any alternative is welcomed) is to go through EACH

From Peter Dalgaard announcement earlier today. CHANGES IN R 3.4.3: INSTALLATION on a UNIX-ALIKE: * A workaround has been added for the changes in location of time-zone files in macOS 10.13 'High Sierra' and again in 10.13.1, so the default time zone is deduced correctly from the system setting when R is configured with --with-internal-tzcode (the default on