R Error - subscript out of bounds, with error=recover message -

i trying create bivariate ellipse see if true values fall within 95% confidence ellipse. getting subscript out of bounds error in r following code. not sure causing it. used options(error=recover) suggested in other posts not sure make out of it..

library(mass) set.seed(1234)  #set working directory setwd("c://tina/usb_backup_042213/paper ii/mln automation/csvs_equal_20s") p1<- .136 p2<- .069 nn<-60  y<-null >     y <- read.csv(file=paste0("mvn",i,".csv"), header=t) >  > y<-as.matrix(y) > xx <- ifelse(y==0,y+.5,y) > nnn <- ifelse(y==0,nn+.5,nn) >  > xx<-as.matrix(xx) > y1<-xx/nnn # estimates of p >  >  > #print(y1) >  > sigma2<- matrix(c(var(y1[,1]),cov(y1[,1],y1[,2]),cov(y1[,1],y1[,2]),var(y1[,2])),2,2) > print(sigma2)            [,1]        [,2] [1,] 0.02142909 0.010810225 [2,] 0.01081023 0.008138709 >  > rho<-sigma2[1,2]/sqrt(sigma2[1,1]*sigma2[2,2]) >  > rate<-y1[2,] # change each site > print(rate)         y1         y2  0.13333333 0.06666667  >  > rate1<-rate/(1-rate) >  > #print(rate1) >  > rate2<-log(rate1) >  > sigma11<-(1/(rate[1]*(1-rate[1]))^2)*sigma2[1,1] > sigma22<-(1/(rate[2]*(1-rate[2]))^2)*sigma2[2,2] > sigma12<-(1/((rate[1]*(1-rate[1]))*(rate[2]*(1-rate[2]))))*sigma2[1,2] >  > sigma2<-matrix(c(sigma11,sigma12,sigma12,sigma22),2,2) >  > #print(sigma2) >  > rate3<-mvrnorm(1000, mu=c(rate2[1],rate2[2]), sigma2) >  > #print(rate3) >  > x<-exp(rate3[,1])/(1+exp(rate3[,1])) > y<-exp(rate3[,2])/(1+exp(rate3[,2])) >  > ## points within polygons > library(mass) > dens <- kde2d(x, y, n=25)  > image(dens) >  >  > #filled.contour(dens,color.palette=colorramppalette(c('white','blue','yellow','red','darkred'))) >  >  > prob <- c(0.975, 0.025) > dx <- diff(dens$x[1:2]) > dy <- diff(dens$y[1:2]) > sz <- sort(dens$z) >  > c1 <- cumsum(sz) * dx * dy  > levels <- sapply(prob, function(x) {  +     approx(c1, sz, xout = 1 - x)$y + }) > #plot(p1,p2) > #contour(dens, levels=levels, labels=prob, add=t) > ls <- contourlines(dens, level=levels) > print(ls) [[1]] [[1]]$level [1] 0.2149866  [[1]]$x  [1] 0.004397130 0.004568786 0.020836478 0.032862816 0.040885850 0.049303040  [7] 0.077374571 0.095771788 0.113863291 0.139211514 0.127080458 0.139599553 [13] 0.150352011 0.186840732 0.201445193 0.223329452 0.239170012 0.245315258 [19] 0.259818172 0.296306893 0.332795613 0.369284333 0.405773053 0.415153288 [25] 0.442261774 0.472911758 0.478750494 0.515239214 0.536208449 0.551727935 [31] 0.588216655 0.624705375 0.646392119 0.624705375 0.618407028 0.607497171 [37] 0.624705375 0.661194096 0.697682816 0.734171536 0.750443060 0.770660257 [43] 0.780548310 0.807148977 0.823897778 0.815766169 0.807148977 0.770660257 [49] 0.745293482 0.750888227 0.734171536 0.733822194 0.734171536 0.770660257 [55] 0.780165097 0.807148977 0.821208006 0.807148977 0.770975720 0.770660257 [61] 0.734171536 0.712245087 0.697682816 0.693122349 0.693977032 0.697682816 [67] 0.704425811 0.719174523 0.700076998 0.706464923 0.711329752 0.697682816 [73] 0.661194096 0.624705375 0.588216655 0.577866122 0.588216655 0.589258511 [79] 0.588216655 0.551727935 0.515239214 0.478750494 0.469648285 0.442261774 [85] 0.405773053 0.395062033  [[1]]$y  [1] 0.1783278616 0.1786369552 0.2142104572 0.2497839592 0.2640206283  [6] 0.2853574612 0.3109011130 0.3209309632 0.3351406407 0.3565044651 [11] 0.3920779671 0.4276514691 0.4342808892 0.4573891723 0.4632249711 [16] 0.4823023723 0.4987984731 0.5343719750 0.5402153675 0.5529088973 [21] 0.5541833087 0.5511966122 0.5658454057 0.5699454770 0.5780502406 [26] 0.5699454770 0.5677285953 0.5582423238 0.5699454770 0.5766348870 [31] 0.5899083535 0.6007347908 0.6055189790 0.6249103884 0.6410924810 [36] 0.6766659830 0.6936330128 0.7051209093 0.7052210613 0.7104009871 [41] 0.7122394849 0.7175712767 0.7122394849 0.7002511608 0.6766659830 [46] 0.6410924810 0.6338424511 0.6130127829 0.6055189790 0.5699454770 [51] 0.5348306032 0.5343719750 0.5340918150 0.5053232008 0.4987984731 [56] 0.4728407406 0.4632249711 0.4535094747 0.4276514691 0.4274565392 [61] 0.4021096213 0.3920779671 0.3724826039 0.3565044651 0.3209309632 [66] 0.3068930025 0.2853574612 0.2497839592 0.2142104572 0.1786369552 [71] 0.1430634533 0.1356917738 0.1315167472 0.1273426210 0.1140927079 [76] 0.1074899513 0.0744396356 0.0719164493 0.0703319222 0.0509793010 [81] 0.0542138537 0.0417716905 0.0363429473 0.0207462171 0.0047801760 [86] 0.0007694453   [[2]] [[2]]$level [1] 0.2149866  [[2]]$x [1] 0.2963069 0.2847163 0.2802502 0.2963069 0.3327956 0.3517197 0.3563875 [8] 0.3327956 0.2963069  [[2]]$y [1] 0.5929265 0.6055190 0.6410925 0.6510478 0.6520754 0.6410925 0.6055190 [8] 0.5877331 0.5929265   [[3]] [[3]]$level [1] 0.2149866  [[3]]$x [1] 0.8059980 0.8071490 0.8436377 0.8449198 0.8436377 0.8071490 0.7848487 [8] 0.7706603 0.7584362  [[3]]$y [1] 0.8545335 0.8530500 0.8207634 0.8189600 0.8169512 0.8104161 0.8189600 [8] 0.8304354 0.8545335   > library(sp) > inner <- point.in.polygon(p1, p2, ls[[2]]$x, ls[[2]]$y) # whether points in inner ellipse > out <- point.in.polygon(p1, p2, ls[[1]]$x, ls[[1]]$y) # whether points in outter ellipse >  > within<-(inner+out) >  > print(within) [1] 0