similar to: using xyplot to plot frequencies

Hey all, I feel like the solution to this problem should be relatively simple, but for some reason I can't find answers or come up with my own solution. Given the dataframe: (SpA and SpB not important, want to look at distribution of cooccurance for each year) Year SpA SpB Coocc 2000 0 2000 2 2000 1 2001 8 2001 2 2001 0 2001 0 2002 1 2002 2 How can I apply different functions to

Hi Everyone, Does anyone know of any projects for running an interactive R session within a web browser? I'm looking for something similar to the one on the Ruby website (http://tryruby.org), except for R. Thanks for your responses in advance! Lanna ----- Lanna Jin lannajin at gmail.com 510-898-8525 -- View this message in context:

Hi All, If given a dataframe (long form) with Year, Species, and Location, How would I write a function that would create a unique matrix of Species & Location for each Year? What I've tried doing is the following: data #dataframe dataT<-table(data$Species,data$Location,data$Year) #creates tables of Species vs Location for each Year But I'm encountering issues individually

I need to replace <NA> occurrences in multiple columns in a data.frame with "000/000" how do I achieve this? Thanks Nevil Amos

as a r noob i am having another problem: i have a big dataframe where each row corresponds to one entry and each column is a field... for instance, i have the column ID and time and many more... Id like to get a dataframe where all IDs are just included once (some users with that ID might have several entries but Id like to kepp only one).. when i use unique I only get a list of the levels (or

Hey All, So, I am confused how exactly to use nesting loop functions in R to spit out data frames. I've managed to create a working function for my data set that generates a data frame for a given set of Year i and Location j; but how would I do it for all Years and Locations? Here is my working function: test<-function(i,j){ a<-x[which(x$Year==i & x$Location==j),]

Hi guys, I have a matrix with values varying from approximately -0.7 to 0.33 that I want to create a heatmap/levelplot with. When I execute the levelplot function for my matrix, I end up getting colors that are adjusted to the max and min rather than around 0. In other words, ideally I would like to have a color ramp that goes from red (negative number), to white (0), to blue (positive);

Hi all, So let's say I have a matrix, mdat and I only know the index number. How do I retrieve the column and row names? For example, > mdat <- matrix(c(1,2,3, 11,12,13), nrow = 2, ncol=3, byrow=TRUE, dimnames = list(c("row1", "row2"), c("C.1", "C.2", "C.3"))) > mdat[4] [1] 12 >

Hello All! I am trying to plot the frequency of species coocurrance. If given a data set similar like this...(V1="species A", V2="species B", V3="frequency of cooccurance") > data V1 V2 V3 1 A B 0 2 A C 2 3 A D 5 4 B C 0 5 B D 1 6 C D 0 > data1<-as.data.frame(lapply(data,function(x)(rep(x,data$V3)))) > as.data.frame(data1[-1]) >

Hi all, Consider the following. a<-list(c("MHsub","MHsub","SFD","Duplex")) b<-list(c("MHsub","MHsub","SFD")) c<-list(c("MHpark","SFD","SFD")) d<-list(c("MultiFam","MultiFam","MultiFam","Duplex")) all<-list(a,b,c,d)

Dear all, i need some help with plotting. the specific problem is the following: #FYI a=100 b=95 d=94.5 e=70 all=c(a,b) all2=c(d,e) plot(all,type="b",col="blue",xlim=c(1,4),ylim=c(20,150)) lines(all2,type="o",col="yellow") this does work so far, but ... i´d like to have 4 intersects, just named by characters.. no scale please. the second problem is,

Dear R-help subscribers, I have a quite stupid question about using lapply. I have the following function: create.gradient <- function(i){ colorgrad01<-color.scale(seq(0,1,by=0.01), extremes=c("red","blue")) tree1$edge[i,1] -> x tree1$edge[i,2] -> y print(x) print(y) all2[x] -> z all2[y] -> z2 round(z, digits = 2) -> z round(z2, digits = 2) -> z2

Dear group, I am losing my mind with a simple question. Sorry if obvious, but I maybe start to be confused after days and days of reading documentations. Df : df <- structure(list(a = 1:3, b = 4:6, c = structure(c(1L, 1L, 1L), class = "factor", .Label = "w")), .Names = c("a", "b", "c"), row.names = c(NA, -3L), class =

Hi, I am a Ph.D. student from Québec, Canada. I’m a beginner with R and Bioconductor. Until now the only experience I have is in analyzing microarray data using affy and limma packages. Now I am trying to analyze Rat Gene 10 st arrays and I would like to run RMA analysis and Smyth moderated t test on those arrays. Since no cdf official package is available for those arrays, after reading many

hello, I am using R1.2.2 on win98 with 64 meg of RAM I try to read a big csv file and get the error : a <- read.csv("c:/all2.csv",header=T) Error: vector memory exhausted (limit reached?) In addition: Warning message: Reached total allocation of 16Mb: see help(memory.size) Lost warning messages from there on, nothing works File-Exit, ^F4, q() , top right cross, the same message

Hi, I need to find the z-score of the data present in a speardsheet. The values needs to be calculated for each gene across the samples (refer the example). And, it should be a simple thing, but I am unable to do it right now ! The example re the structure of the spreadsheet is - # Example: MyFile <- read.csv( text= "Names,'Sample_1','Sample_2','Sample_3'

Dear, I am using the solnp command (package Rsolnp) for a problem with equality and inequality constraints. I am not getting convergence for my problem but apart that I get 1 warning per iteration saying: ?In cbind(temp, funv) : number of rows of result is not a multiple of vector length (arg 1)?. I checked for equality and inequality functions and they seem fine to me. Where this

Hi, I'm trying to build a thesaurus that will sensible values for rare words. I suspect the best algorithm to use is k-means although I'm not sure about that -- I would have preferred a k dimensional space with a binary cluster in each dimension so a word can belong to 0..k clusters, but I digress... I can measure the strength of correlation between words fairly easily by counting

I've been struggling with this for a while and cannot get it to work. Is there a simple way to add grid lines ---- I'd like to only add the horizontal ones --- when using the groups argument in xyplot? I can get the grid lines to plot, or the points/lines, but not both. Here is a simple example of the sort of thing that I'm working with. Thanks, in advance. >all est STE

Sorry, some things got garbled in that request for help that might make my request unintelligible, probably it being too late at night when I posted, here is the corrected function call for which I would like to learn how to add horizontal grid lines. Any suggestions would be appreciated. Apologies for the posting error xyplot(est ~ STE, data = all, groups = AREA, type = "b",