Silene acaulis

The following code will download the 25 projection matrices in Supplement 1 from

Morris, W.F. and D.F. Doak. 2005. How general are the determinants of the stochastic population growth rate across nearby sites? Ecological Monographs 75:119–137.

The matrices are stored in 25 separate comma-delimited files and one file (PA98.txt) has two field delimiters (spaces and commas), so some additional code is added to the loop to fix this error. The paper includes details on the study sites and stage classes which are defined below

site   <- c("CC", "GU", "PA", "RG", "RI")
years  <- 95:99
stages <- c("seed", "sdling", "1R", "5R", "10R", "20R", "12cm", "25cm", "50cm", "100cm", "200cm", "200+cm")

Paste together the site and year to create the file name, loop through the 25 files and save the results to a list.

pop <- paste(rep(site,each=5),years, sep="")
n <- length(pop)
silene <- vector('list', n) 
names(silene) <- pop
for ( i in 1:n)
{  
   url <- paste("http://www.esapubs.org/archive/mono/M075/004/", pop[i],".txt", sep="")
   if(pop[i] == "PA98"){
      # missing commas in row 2, last 3 values
      y <- read.table(url , sep=",", fill=TRUE, stringsAsFactors=FALSE)
      y[2,10:12] <- unlist(strsplit(y[2,10], "   "))
   }else{
      y <- read.table(url,  sep=",")
   }
   y <- data.matrix(y)
   dimnames(y) <- list(stages,stages)
   silene[[i]] <- y
}
# check results
sapply(silene, lambda)
 CC95  CC96  CC97  CC98  CC99  GU95  GU96  GU97  GU98  GU99  PA95  PA96  PA97 
0.991 1.006 1.000 1.006 0.999 1.000 0.996 0.998 1.000 1.004 0.995 0.995 1.015 
 PA98  PA99  RG95  RG96  RG97  RG98  RG99  RI95  RI96  RI97  RI98  RI99 
1.034 0.973 0.991 0.985 1.000 1.003 1.000 0.997 1.005 0.983 0.998 1.007 
# view mean matrix
image2( mean(silene) , cex=.5, log=FALSE)