[R-sig-Epi] Help! Help! Help!

[John Mlyahilu]

​I have simulated the SIR model  with the following reactions
I[i] + S[j]  -> I[i] +I[j]
I[i] + S[i]  -> 2*I[i]

I have the row data having the matrix with "i"  being the home RTO and "j"
being the RTO. what I need is to improve this function so that it can give
the good results as I expect. Here are  the codes in R then anyone can help
to improve this
etwd()
setwd("C:/Users/Dr M/Desktop")
list.files()
RTODATA = read.csv(file = 'RTODATA.csv')
RTODATA
N <- length(RTODATA$Home_RTO)
fc <- file("reactionsRTO.xml")
for(k in 1:N) {
  Home_RTO <- RTODATA$Home_RTO[k]
  RTO <- RTODATA$RTO[k]
  Rate <- RTODATA$Share20160811_1429[k]
  i = j= rtoIndex
 if(i!=j){
  str <- paste("<reaction rate='",Rate,
   "'>\nS[",rtoIndex,"] + I[",rtoIndex,"] -> I[",rtoIndex,"]+
I[",rtoIndex,"]\n",
   "</reaction>\n",sep="")
 } else {
  str <- paste("<reaction rate='",Rate,
   "'>\nS[",rtoIndex,"] + I[",rtoIndex,"] -> 2*I[",rtoIndex,"]\n",
   "</reaction>\n",sep="")
 }
 cat(str, file=fc)
}
close(fc)


The results from the codes above is as follows
source("model4today.R")
There were 50 or more warnings (use warnings() to see the first 50)
After viewing the xml The following is the content
 <reaction rate='2.72e-07'>
S[1020] + I[1020] -> 2*I[1020]
</reaction>
It has skipped the first, second ......... up to  1019 rows
Since the excel data file appears as follows
Home_RTO RTO Share20160811_1429
Area Outside RTO Kawerau-Whakatane 0.0842
West Coast RTO Christchurch 0.009159
West Coast RTO Waitaki RTO 0.006376
Area Outside RTO Hawkes Bay RTO 0.029911
West Coast RTO Nelson Tasman RTO 0.005027
West Coast RTO South Canterbury 0.004778
West Coast RTO North Canterbury 0.002869
Area Outside RTO Bay of Plenty RTO 0.019968
West Coast RTO Auckland RTO 0.001996
West Coast RTO Queenstown RTO 0.001849
West Coast RTO Marlborough RTO 0.001654
West Coast RTO Wellington RTO 0.001268
West Coast RTO Lake Wanaka RTO 0.001153
West Coast RTO Southland RTO 0.001033
West Coast RTO Dunedin RTO 0.000955
West Coast RTO Waikato RTO 0.000952
West Coast RTO Fiordland RTO 0.000791

Hence therefore,  How can I read all the data in the excel file in

Sincerely,
John

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