RDX2 X  .Traceback @matrix(c(admb3, sas3), ncol = 2, dimnames = list(c(rep("b", 3), @ "log(sigma_1)", "log(sigma_2)", "log(sigma_3)", "w1", "w2", . "w3", "log(alpha)"), c("ADMB-RE", "SAS"))) "eval.with.vis(expr, envir, enclos) eval.with.vis(ei, envir) source("gen_tables.s") a@4 admb2 py,?~ ؟6МUm?Q~J֗̅E?4ϾO?Psiz' wR MѦ;Ȯvr,X"b?\6T"Ͽa帣7?HL?$bL ?>=?.\4ʿAh75?Te?k1XCUӷ|d?1é?`G]1 ?^!?=[? >O ?)?608̸Ns?PѰ.? S\?'jRο?҆Y ,4!q"S=ܿ/"?qX?yM#0C?pQΆSpwb?JVPUXbM(" b log_sigma1 log_sigma2 rho log_alpha z1 z2 loglik gradient f2d !function(f,x,delta) { I if(length(x)!=length(delta)) stop("x and delta must have same lengths")  d <- x  for(i in 1:length(x))  {  tmp <- numeric(length(x))  tmp[i] <- 1 - d[i] <- (f(x+delta[i]*tmp)-f(x))/delta[i]  }  d } f9  :9  "x and delta must have same lengths d<=? $ numeric$=?]=5>?\@A9=$\9=] f3 Л*?Q֌i?ۨ2d#7T7#%SS 9Ywl&3w?c ;;?9 8?2'?teխ?b ?~U%t?W?1&*5aT?ӹ(Q$@Ɨ ?Nk X?l '?1俓J@ީ>ymQԧ 0 ?<[G:b@M?cya? WĿd%UN@˂|"=;=PtT곿-+21S#PFGw>zjL>^k"b&|? 9J>ѴzfN4B|>'=L>܇i.]D ڥU2(!?Stsl?E$R>nSG$)&U]ӿ * D![>4ܨ>ź${?&8 &?@AYw? w F܋Cy@>[D¿YpMp"9S>uCY>dF85.-''] s)/ǹ,up^ ?Dܑ>>Ü?M~Ҿ= ;>[j.[Vz>I"|?!L\-?< }?MgYvR>ag{C?^Œ? Β7b(׿ _DF]ce6?260?:,x;?-V?.E?>zܻ?7>Tf @ +F;u?:;MB?@#53@fIu@M?P!S?**b? U?ms! kV7.,/j]Gu/fsA8?TP[C&(>d?(7=v?:Q}p"?%Rq?MT*5 0,@#?%umEi?//L-b*K4+ہ8]\Y?0&=?(_6,8O_?JDb4t?33j0?*uA8l&mS\ɿ',RBU5Sՙ?5pjc >/>=?vBАs>>oZH?G_O15v u-+ J0`?5|; QB@@I>ґ[?ICAPi|@έE`A7[ނiµ" b log_sigma w log_alpha z1 z2 z3 loglik gradient fit2 py,??z[?H Qޟsub;\/HſeVd;)̍sBڣWd?S"U@:f2g?T+,?} DpZM$?;?ӝnhH4?f B?1$M _6 Djf/?I`?ܴMɬ?,g9?:}? TDcϯ~-/=D[9nq8v~?Ǘ?\hJ8̳!?Pz?e6?'e@?h last.warning" @cannot open file 'epil3.par', reason 'No such file or directory' logit "function(x,inverse=F,derivative=F) {  if(!inverse)  { 1 if(any(x<=0|x>=1)) stop("x must be in (0,1)")  if(!derivative)  tmp <- log(x/(1-x))  else  tmp <- x^-1 + (1-x)^-1  }  else  if(!derivative)  tmp <- exp(x)/(1+exp(x))  else tmp <- exp(x)/(1+exp(x))^2  tmp } inverse- derivative-   k   any | <= >=?  x must be in (0,1)  l$ log5>??$@ ^??r>????  l$5h>@?h$5hr>@?h@$ map.nea >function(file="/home/u5/skaug/s/maps/nea.txt",xlab="",ylab="") {  tmp <- read.table(file) 3 plot(tmp[,2],tmp[,1],pch=".",xlab=xlab,ylab=ylab) }L /home/u5/skaug/s/maps/nea.txt xlab  ylab  $ read.tableL plot$@$? pch .ttuu member function(x,y) !is.na(match(x,y)) y  is.na matchz Motif +function() motif("-geometry 300x300+100+0") motif -geometry 300x300+100+0 msort function(X,m=1,reverse=F) { # if( !is.matrix(X) || m>ncol(X) )  stop("Feil i msort") if(reverse)  ind <- rev(order(X[,m]))  else  ind <- order(X[,m]) X[ind,] }3? reverse-   ||   >3 ncol  Feil i msort  indX order33 par_read) Ifunction(name,ncols=list()) # matrices must be specified by name and ncol {  n = nchar(name) ( endelse = substring(name,max(1,n-3),n) / har_endlese = (substring(endelse,1,1) == ".")  if(har_endlese)  file_name = name  else ) file_name = paste(name,".par",sep="") ' tmp = scan(file_name,what="",quiet=T) $ tmp2 = split(tmp,cumsum(tmp=="#")) x = tmp2  if(endelse ==".par") x = x[-1]  for(i in 1:length(x))  {  y = x[[i]]  n = nchar(y[2]) " x[[i]] = as.numeric(y[-(1:2)]) ' names(x)[i] = substring(y[2],1,n-1)  } 2 # Convert to matrix for those arguments relevant  if(length(ncols)>0)  for(i in 1:length(ncols))  {  NN = names(ncols)[i] 8 x[[NN]] <- matrix(x[[NN]],ncol=ncols[[i]],byrow=T)  }  if(endelse == ".par")  { ) x$loglik = -as.numeric(tmp2[[1]][11]) + x$gradient = -as.numeric(tmp2[[1]][16])  }  x }C ncols! 0+EC0 endelseGC max??+@+0 har_endlese>FG?? . 0HC0HC .parI 0$ scanH what  quiet/0 split$ cumsumF$ #0 F .par0??<=? 0z'=0+Ez@0'= as.numericz?>?@0"=Gz@??+? <=? 0 NN"='''= byrow/ F .par 0 $ loglik?'?@&0 gradient?'?@0 pin_write function(name,L) {  n = nchar(name) # if(substring(name,n-3,n)==".pin")  file_name = name  else ) file_name = paste(name,".pin",sep="") g cat("# \"",name,".pin\" produced by pin_write() from ADMButils; ",date(),"\n", file=file_name,sep="")  for(i in 1:length(L))  {  x = L[[i]] if(data.class(x)=="numeric") E cat("#",names(L)[i],"\n",L[[i]],"\n\n",file=file_name,append=T)  if(data.class(x)=="matrix")  { 7 cat("#",names(L)[i],"\n",file=file_name,append=T) F write.table(L[[i]],,col=F,row=F,quote=F,file=file_name,append=T) ' cat("\n",file=file_name,append=T)  }  } }CD 0+EC FGC?+@+ .pin0HC0HC .pinI J # "C ..pin" produced by pin_write() from ADMButils; K  LHI <=?D 0'D= FM numericJ #"D=  'D=  LHN/ FM matrix J #"D=  LHN/O'D=P-Q-R-LHN/J  LHN/ rcf (function(n,file) # read column from file {  if(isfile(file)) ; tmp <- unix(paste("awk '{print $",n,"}' ",file,sep=""))  else  tmp <- NULL  tmp }+L  eL$f awk '{print $+ }' LI $$ rcpois function(n,mu,V) # n: sample size # mu: expectated value # V: variance { F # A gamma mixture of Poission variables (which is Neg. bin variable) > if(any(!member(c(length(mu),length(V)),c(1,n)))| any(mu<=0)) stop("Error in mu or V") # if(length(mu)==1) mu <- rep(mu,n) ! if(length(V)==1) V <- rep(V,n) ind <- V>mu  if(any(V?r@$?@>A rgamma sum shape rpois+ readH! function(file,n,cor=F) {  N = n*(n+1)/2+4*n ) tmp = scan(file,what="",skip=2,quiet=T) * if(length(tmp)@+?@A@+0$L  skip@/ &$  n is too large0$$?0 stdtab^+0;1+<=?+ 0=$@0$$?>?@0;=?=$?=0$$?>?= :$  print$  Det er noe galt0;@;%;01;?  0;441;1; rmnorm 7function(n, mu=0, vmat=diag(1,length(mu)), tol = 1e-06) { < p <- ncol(vmat) #dimension of the multinormal vector * if(max(abs(vmat - t(vmat))) > tol) - stop("vmat is not symmetric")  vs <- svd(vmat) 3 vsqrt <- t(vs$v %*% (t(vs$u) * sqrt(vs$d))) 7 ans <- matrix(rnorm(n * p), nrow = n) %*% vsqrt % ans <- sweep(ans, 2, mu, "+")  drop(ans) }+ vmat1? tol>  p  abs?%  vmat is not symmetric vs svd vsqrt%4 v>A% u6] ans4 rnormA++ sweep@ + drop rmultinom function(n, p) { 7 table(c(1:length(p),sample(seq(along=p), n, T, p)))-1 }+ ? tableV? sample seq along+/? rtrinom function(p) { . if(!is.numeric(p)) stop("p must be numeric")  if(!is.matrix(p)) p <- t(p) 7 if(ncol(p)!=3|!all(p>0)) stop("Error in format of p")   # Scaling of p  tmp <- apply(p,1,sum)  tmp <- p/tmp  P <- t(apply(tmp,1,cumsum))  u <- runif(nrow(p),0,1)  out <- apply(u?z? tab1py,? 0] I string.vec[pos.to.replace] <- LETTERS[lc.letters[pos.to.replace]] @ new.string <- paste(string.vec, sep = "", collapse = "")  new.string } string  string.len.vec?E string.vecG lc.letters| letters nomatch pos.to.replace LETTERS new.stringI   tt> Ϣ6> d]I> i>F=>xm[>J> fu[>~q$>p<>po[F>|>PYP E>"d>0v>@BKN>+xio!>ҭ >x> > ے2>!f P>"KH>#$>$8Q>%,>&)>'<<\>)( 0>*s7>+ν>-<N>.57>0(l>0KD1hB>1v`FS>268>3g:>4\`>5з*>6Xo0>8d>9Y}>:ޣ><Ż>=tC>>Gv>@G`\>ACe>A ?>Bꇊ>C趿*>D[W3`>EH >GlR>HK| >I*>JH˳6>L; mJ>Mk>O3nY>PfW>Q>{'c >R! k>S>i >T |>U_>V%<%>WH>Xz>YEwGͱ>[g>\qz>]T>_p=p>`Ϩ'>a_>bD=0 >c4=u>>d0y!>e9ԕZ>fPp>gu>h(7M>i9f#>kB*\P>lR>n!v>oA>p+>qs,p>rgP>sY*ȇ>tWŊ$>uc7>v|i}>ws Tx>xU>z ?>{wNs>|༱>~\(k}.>J z>6\=>e>k<>N,y><j>' >o>Th> E>>SD$v>'O'>>X>&>O>kIm>i 2>}->iY>^8>ӤO6>d]>:(I>]g>2>QCOR>vhz>3՜>SQ>dN>Ӯ>> ]@>qd>=>x>.#u>kN[>ש.>J>*ػ>H>S)Rԡ>)> &Gg&>8&&>uZ>}dq> ^e>,>]i>-2>7LY>Od>HU>J >rr]>JY?>.*:HY> , \\>)> .O>5;>Y=>ȌYf>b>!̆wvW>AG!>χGZ4Xn>В4䀔>lD>Qq>BX>?' >I,sN>`רt>׆ݿā>ػ|>{XQ]>Vu>ܽͰ>7o>q@]> T>Q>t֒>g{'>fm2>ru>>?\A>N%> )#>3cR>닢5é)>k(>r>b1+>J`6>Z> >>Ģ>2>>pE{>?&>f(^>!M&>-?G$>זG? 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