new tests, start from scratch with leman example

R/empirical.prior.R

@@ -11,7 +11,7 @@
   ret$formula<-formula
   ft<-terms(formula)
   ret$variables<-attr(ft,"variables")
-  ret$ntr<-dim(model.matrix.default(formula=formula,data=x))[2]
+  ret$ntr<-dim(model.matrix(object=formula,data=x))[2]
            
   if(length(ret$variables)!=4 & length(ret$variables)!=2) stop("need 1 or 3 variables (\"z ~ f(x, y)\" or \"z ~ 1\")  in formula!")
   if(length(ret$variables)==4){

R/print.bk.prior.R

@@ -10,7 +10,7 @@ print.bk.prior<-function(x){
     cat("prior ",i,"\n")
     cat("  type is ", x$type[i],"\n")
     if(x$type[i]=="empirical"){
-      cat("  based on a additional dataset of size", x$info,"\n\n")
+      cat("  based on an additional dataset of size", x$info[i],"\n\n")
     }
     cat("prior guess for regression parameter:\n")
     print(x$mu[[i]])    

R/zzz.R

 .First.lib <- function(lib, pkg) {
+  require(rgeostat)
+  if(version$major==0 && version$minor < 62)
+    stop("This version for R 0.62 or later")
   library.dynam("baykrig", pkg, lib)
-  require(sgeostat)
-  require(tripack)
 }
-  
 
-if(version$minor < "62") {
-  library.dynam("baykrig")
-  require(sgeostat)
-  require(tripack)
-}

devel/.Rhistory

-str(leman.bk.ord)
 q()
 library(rgeostat);library(baykrig);
 library(rgeostat);library(baykrig);
@@ -8,11 +7,9 @@ leman.bk.ord <- bk.grid(point = leman.pt, at = "cadpbm", prior=leman.prior.ord,v
 library(rgeostat);library(baykrig);
 leman.bk.ord <- bk.grid(point = leman.pt, at = "cadpbm", prior=leman.prior.ord,var.mod.obj = leman.sph, xsw=min(leman.bank$x),ysw=min(leman.bank$y), xne=max(leman.bank$x), yne=max(leman.bank$y), nx=20, ny=20, trend=0, rsearch = 10, extrap = F,border=leman.bank, duplicate="mean");
 ls(ans)
-ls()
 library(rgeostat);library(baykrig);
 library(rgeostat);library(baykrig);
 library(rgeostat);library(baykrig);
-ls()
 library(rgeostat);library(baykrig);
 library(rgeostat);library(baykrig);
 dyn.load("getpid.so")
@@ -30,3 +27,5 @@ dyn.load("getpid.so")
 .C("R_getpid",integer(1))
 library(rgeostat);library(baykrig);
 leman.bk.ord <- bk.grid(point = leman.pt, at = "cadpbm", prior=leman.prior.ord,var.mod.obj = leman.sph, xsw=min(leman.bank$x),ysw=min(leman.bank$y), xne=max(leman.bank$x), yne=max(leman.bank$y), nx=5, ny=5, trend=0, rsearch = 10, extrap = T,border=leman.bank, duplicate="mean");
+ls()
+q()

devel/fresh/leman-example.R

+library(sgeostat)
+library(rgeostat)
+library(baykrig)
+
+data(leman)
+# loads "leman.78" "leman.83" "leman.88"
+data(leman.bank)
+
+leman.78.pt<-point(leman.78)
+leman.83.pt<-point(leman.83)
+leman.88.pt<-point(leman.88)
+
+plot(leman.78.pt,v="cadpbm")
+lines(leman.bank)
+
+plot(leman.83.pt,v="cadpbm")
+lines(leman.bank)
+
+plot(leman.88.pt,v="cadpbm")
+lines(leman.bank)
+
+leman.88.pr.30<-pair(leman.88.pt,maxdist=30)
+
+spacebox(leman.88.pt,leman.88.pr.30,"cadpbm")
+
+leman.88.ev30<-est.variogram(leman.88.pt,leman.88.pr.30,"cadpbm")
+
+plot(leman.88.ev30)
+
+leman.88.vmsph<-fit.variogram("spherical",leman.88.ev30,0.1,0.2,25,plot.it=T)
+
+plot(leman.88.ev30,var.mod.obj=leman.88.vmsph)
+
+# crash:
+# leman.krg<-krige.grid(min(leman.bank$x),min(leman.bank$y), max(leman.bank$x), max(leman.bank$y), nx=100, ny=100, point = leman.88.pt, at = "cadpbm", var.mod.obj = leman.88.vmsph, rsearch = 7.5, extrap = F,border=leman.bank)
+
+leman.krg<-krige.grid.c(min(leman.bank$x),min(leman.bank$y), max(leman.bank$x), max(leman.bank$y), nx=100, ny=100, point = leman.88.pt, at = "cadpbm", var.mod.obj = leman.88.vmsph, rsearch = 7.5, extrap = F,border=leman.bank)
+
+leman.prior<-empirical.prior(leman.83,cadpbm~x+y,leman.88.vmsph,duplicate="mean")
+
+leman.prior<-empirical.prior(leman.78,cadpbm~x+y,leman.88.vmsph,prior=leman.prior,duplicate="mean")
+
+leman.bk <- bk.grid(point = leman.88.pt , at = "cadpbm", prior=leman.prior,var.mod.obj = leman.88.vmsph, xsw=min(leman.bank$x),ysw=min(leman.bank$y), xne=max(leman.bank$x), yne=max(leman.bank$y), nx=50, ny=50, trend=0, rsearch = 10, extrap = T,border=leman.bank, duplicate="mean")

devel/fresh/leman-example.R~

+library(sgeostat)
+library(rgeostat)
+library(baykrig)
+
+data(leman)
+# loads "leman.78" "leman.83" "leman.88"
+data(leman.bank)
+
+leman.78.pt<-point(leman.78)
+leman.83.pt<-point(leman.83)
+leman.88.pt<-point(leman.88)
+
+plot(leman.78.pt,v="cadpbm")
+lines(leman.bank)
+
+plot(leman.83.pt,v="cadpbm")
+lines(leman.bank)
+
+plot(leman.88.pt,v="cadpbm")
+lines(leman.bank)
+
+leman.88.pr.30<-pair(leman.88.pt,maxdist=30)
+
+spacebox(leman.88.pt,leman.88.pr.30,"cadpbm")
+
+leman.88.ev30<-est.variogram(leman.88.pt,leman.88.pr.30,"cadpbm")
+
+plot(leman.88.ev30)
+
+leman.88.vmsph<-fit.variogram("spherical",leman.88.ev30,0.1,0.2,25,plot.it=T)
+
+plot(leman.88.ev30,var.mod.obj=leman.88.vmsph)
+
+# crash:
+# leman.krg<-krige.grid(min(leman.bank$x),min(leman.bank$y), max(leman.bank$x), max(leman.bank$y), nx=100, ny=100, point = leman.88.pt, at = "cadpbm", var.mod.obj = leman.88.vmsph, rsearch = 7.5, extrap = F,border=leman.bank)
+
+leman.krg<-krige.grid.c(min(leman.bank$x),min(leman.bank$y), max(leman.bank$x), max(leman.bank$y), nx=100, ny=100, point = leman.88.pt, at = "cadpbm", var.mod.obj = leman.88.vmsph, rsearch = 7.5, extrap = F,border=leman.bank)

devel/fresh/s1.txt

+
+R : Copyright 2001, The R Development Core Team
+Version 1.4.0  (2001-12-19)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type `license()' or `licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type `contributors()' for more information.
+
+Type `demo()' for some demos, `help()' for on-line help, or
+`help.start()' for a HTML browser interface to help.
+Type `q()' to quit R.
+
+[Previously saved workspace restored]
+
+> library(sgeostat)
+Loading required package: mva 
+> library(rgeostat)
+> leman.krg<-krige.grid(min(leman.bank$x),min(leman.bank$y), max(leman.bank$x), max(leman.bank$y), nx=100, ny=100, point = leman.88.pt, at = "cadpbm", var.mod.obj = leman.88.vmsph, rsearch = 7.5, extrap = F,border=leman.bank)
+
+Process R segmentation fault at Fri Jan  4 09:44:36 2002
+
+
+R : Copyright 2001, The R Development Core Team
+Version 1.4.0  (2001-12-19)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type `license()' or `licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type `contributors()' for more information.
+
+Type `demo()' for some demos, `help()' for on-line help, or
+`help.start()' for a HTML browser interface to help.
+Type `q()' to quit R.
+
+[Previously saved workspace restored]
+
+> library(sgeostat)
+Loading required package: mva 
+> library(rgeostat)
+> leman.krg<-krige.grid(min(leman.bank$x),min(leman.bank$y), max(leman.bank$x), max(leman.bank$y), nx=100, ny=100, point = leman.88.pt, at = "cadpbm", var.mod.obj = leman.88.vmsph, rsearch = 7.5, extrap = F,border=leman.bank)
+
+Process R segmentation fault at Fri Jan  4 09:45:14 2002
+
+
+R : Copyright 2001, The R Development Core Team
+Version 1.4.0  (2001-12-19)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type `license()' or `licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type `contributors()' for more information.
+
+Type `demo()' for some demos, `help()' for on-line help, or
+`help.start()' for a HTML browser interface to help.
+Type `q()' to quit R.
+
+[Previously saved workspace restored]
+
+> library(sgeostat)
+Loading required package: mva 
+> library(rgeostat)
+> leman.krg<-krige.grid(min(leman.bank$x),min(leman.bank$y), max(leman.bank$x), max(leman.bank$y), nx=100, ny=100, point = leman.88.pt, at = "cadpbm", var.mod.obj = leman.88.vmsph, rsearch = 7.5, extrap = F,border=leman.bank)
+
+Process R segmentation fault at Fri Jan  4 09:47:32 2002
+
+
+R : Copyright 2001, The R Development Core Team
+Version 1.4.0  (2001-12-19)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type `license()' or `licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type `contributors()' for more information.
+
+Type `demo()' for some demos, `help()' for on-line help, or
+`help.start()' for a HTML browser interface to help.
+Type `q()' to quit R.
+
+[Previously saved workspace restored]
+
+> library(sgeostat)
+Loading required package: mva 
+> library(rgeostat)
+> leman.krg<-krige.grid(min(leman.bank$x),min(leman.bank$y), max(leman.bank$x), max(leman.bank$y), nx=100, ny=100, point = leman.88.pt, at = "cadpbm", var.mod.obj = leman.88.vmsph, rsearch = 7.5, extrap = F,border=leman.bank)
+
+Process R segmentation fault at Fri Jan  4 09:52:43 2002
+
+
+R : Copyright 2001, The R Development Core Team
+Version 1.4.0  (2001-12-19)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type `license()' or `licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type `contributors()' for more information.
+
+Type `demo()' for some demos, `help()' for on-line help, or
+`help.start()' for a HTML browser interface to help.
+Type `q()' to quit R.
+
+[Previously saved workspace restored]
+
+> library(sgeostat)
+Loading required package: mva 
+> library(rgeostat)
+> leman.krg<-krige.grid(min(leman.bank$x),min(leman.bank$y), max(leman.bank$x), max(leman.bank$y), nx=100, ny=100, point = leman.88.pt, at = "cadpbm", var.mod.obj = leman.88.vmsph, rsearch = 7.5, extrap = F,border=leman.bank)
+
+Process R segmentation fault at Fri Jan  4 10:05:48 2002
+
+
+R : Copyright 2001, The R Development Core Team
+Version 1.4.0  (2001-12-19)
+
+R is free software and comes with ABSOLUTELY NO WARRANTY.
+You are welcome to redistribute it under certain conditions.
+Type `license()' or `licence()' for distribution details.
+
+R is a collaborative project with many contributors.
+Type `contributors()' for more information.
+
+Type `demo()' for some demos, `help()' for on-line help, or
+`help.start()' for a HTML browser interface to help.
+Type `q()' to quit R.
+
+[Previously saved workspace restored]
+
+> library(sgeostat)
+Loading required package: mva 
+> library(rgeostat)
+> leman.krg<-krige.grid.c(min(leman.bank$x),min(leman.bank$y), max(leman.bank$x), max(leman.bank$y), nx=100, ny=100, point = leman.88.pt, at = "cadpbm", var.mod.obj = leman.88.vmsph, rsearch = 7.5, extrap = F,border=leman.bank)
+> 
+> str(leman.krg)
+List of 8
+ $ x   : num [1:100] 500 501 502 502 503 ...
+ $ y   : num [1:100] 118 119 119 119 120 ...
+ $ z   : num [1:100, 1:100] NA NA NA NA NA NA NA NA NA NA ...
+ $ var : num [1:100, 1:100] NA NA NA NA NA NA NA NA NA NA ...
+ $ done: int [1:100, 1:100] 0 0 0 0 0 0 0 0 0 0 ...
+ $ snb : int [1:200, 1:10000] 0 0 0 0 0 0 0 0 0 0 ...
+ $ data:Classes point  and `data.frame':	200 obs. of  3 variables:
+  ..$ x     : num [1:200] 501 502 501 503 502 501 504 503 502 504 ...
+  ..$ y     : num [1:200] 119 120 121 121 122 123 122 123 124 124 ...
+  ..$ cadpbm: num [1:200] 0.73 0.74 0.45 1.09 1.32 0.29 0.17 0.51 0.93 0.59 ...
+ $ at  : chr "cadpbm"
+ - attr(*, "class")= chr "krige.map"
+> plot(leman.krg)
+> plot(leman.krg,show.snb=T)
+select points to place search neighbourhoods ...
+
+> leman.krg30<-krige.grid.c(min(leman.bank$x),min(leman.bank$y), max(leman.bank$x), max(leman.bank$y), nx=100, ny=100, point = leman.88.pt, at = "cadpbm", var.mod.obj = leman.88.vmsph, rsearch = 30, extrap = F,border=leman.bank)
+> plot(leman.krg30,show.snb=T)
+select points to place search neighbourhoods ...
+
+> plot(leman.krg,show.snb=T)
+select points to place search neighbourhoods ...
+
+> leman.krg10<-krige.grid.c(min(leman.bank$x),min(leman.bank$y), max(leman.bank$x), max(leman.bank$y), nx=100, ny=100, point = leman.88.pt, at = "cadpbm", var.mod.obj = leman.88.vmsph, rsearch = 10, extrap = F,border=leman.bank)
+> plot(leman.krg10,show.snb=T)
+select points to place search neighbourhoods ...
+
+> plot(leman.krg10,show.snb=T)
+select points to place search neighbourhoods ...
+
+> plot(leman.krg10,show.snb=T)
+select points to place search neighbourhoods ...
+
+> plot(leman.krg10,show.snb=T)
+select points to place search neighbourhoods ...
+
+> plot(leman.krg10,show.snb=T)
+select points to place search neighbourhoods ...
+
+> plot(leman.krg10,show.snb=T)
+select points to place search neighbourhoods ...
+
+> plot(leman.krg10,show.snb=T)
+select points to place search neighbourhoods ...
+
+> plot(leman.krg10,show.snb=T)
+select points to place search neighbourhoods ...
+
+> plot(leman.krg10,show.snb=T)
+select points to place search neighbourhoods ...
+
+> plot(leman.krg10,show.point=F,show.snb=T)
+Error in plot.krige.map(leman.krg10, show.point = F, show.snb = T) : 
+	unused argument(s) (show.point ...)
+> plot(leman.krg10,show.data=F,show.snb=T)
+select points to place search neighbourhoods ...
+
+> plot(leman.krg,show.point=F,show.snb=T)
+Error in plot.krige.map(leman.krg, show.point = F, show.snb = T) : 
+	unused argument(s) (show.point ...)
+> plot(leman.krg,show.data=F,show.snb=T)
+select points to place search neighbourhoods ...
+
+> plot(leman.krg,show.data=F,show.snb=T)
+select points to place search neighbourhoods ...
+
+> leman.krg10.2<-krige.grid.c(min(leman.bank$x),min(leman.bank$y), max(leman.bank$x), max(leman.bank$y), nx=200, ny=200, point = leman.88.pt, at = "cadpbm", var.mod.obj = leman.88.vmsph, rsearch = 10, extrap = F,border=leman.bank)
+> plot(leman.krg10,show.data=F,show.snb=T)
+select points to place search neighbourhoods ...
+
+> x11()
+> plot(leman.krg10.2,show.data=F,show.snb=T)
+select points to place search neighbourhoods ...
+
+> save.image()
+> q()
+Save workspace image? [y/n/c]: y
+
+Process R finished at Sat Jan  5 00:30:32 2002