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##
## scaleboot: R package for multiscale bootstrap
## Copyright (C) 2006-2007 Hidetoshi Shimodaira
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 2 of the License, or
## (at your option) any later version.
##
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with this program; if not, write to the Free Software
## Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
##
######################################################################
###
### OPTIONS
###
## model names
sbmodelnames <- function(m=1:3,one.sided=TRUE,two.sided=FALSE,rev.sided=FALSE,
poly,sing,poa,pob,poc,pod,sia,sib,sic,sid,sphe,pom,sim){
if(missing(poly)) poly <- if(one.sided) m else 0
if(missing(sing)) sing <- if(one.sided) m else 0
if(missing(poa)) poa <- if(two.sided) m else 0
if(missing(sia)) sia <- if(two.sided) m else 0
if(missing(pob)) pob <- if(rev.sided) m else 0
if(missing(sib)) sib <- if(rev.sided) m else 0
if(missing(poc)) poc <- if(two.sided) m else 0
if(missing(sic)) sic <- if(two.sided) m else 0
if(missing(pod)) pod <- if(rev.sided) m else 0
if(missing(sid)) sid <- if(rev.sided) m else 0
# if(missing(sphe)) sphe <- if(one.sided) m else 0
if(missing(sphe)) sphe <- 0
if(missing(pom)) pom <- 0
if(missing(sim)) sim <- 0
make1 <- function(na,mm,min=1,max=Inf) {
k <- mm[mm>=min & mm<=max]
if(length(k)>0) paste(na,k,sep=".") else NULL
}
## one sided models
polyk <- make1("poly",poly,1)
singk <- make1("sing",sing,3)
## two sided models (polynomial-difference)
poa1k <- make1("poa1",poa,2)
poa2k <- make1("poa2",poa,4)
pob1k <- make1("pob1",pob,2)
pob2k <- make1("pob2",pob,4)
poc1k <- make1("poc1",poc,2)
poc2k <- make1("poc2",poc,4)
pod1k <- make1("pod1",pod,2)
pod2k <- make1("pod2",pod,4)
## two sided models (singular-difference)
sia1k <- make1("sia1",sia,4)
sia2k <- make1("sia2",sia,5)
sib1k <- make1("sib1",sib,4)
sib2k <- make1("sib2",sib,5)
sic1k <- make1("sic1",sic,4)
sic2k <- make1("sic2",sic,5)
sid1k <- make1("sid1",sid,4)
sid2k <- make1("sid2",sid,5)
## modified models
# sim0k <- make1("sim0",sim,3,3)
pomk <- make1("pom",pom,3)
simk <- make1("sim",sim,4)
## specialized models
sphek <- make1("sphe",sphe,3,3)
## output model names
c(polyk,singk,pomk,simk,sphek,
poa1k,poa2k,pob1k,pob2k,sia1k,sia2k,sib1k,sib2k,
poc1k,poc2k,pod1k,pod2k,sic1k,sic2k,sid1k,sid2k)
}
## default options (local variable)
.onLoad <- function(libname, pkgname) {
op <- list(
## sbfit
models = sbmodelnames(), # default models for fitting
control = list(reltol=1e-14), # for optim
method = NULL, # for optim
## poly model
mag.poly = c(1,0.1,0.01,0.001), # mag factor for par in poly model
omg.poly = c(0.1,1,1,1), # weights
low1.poly = c(-10,-10,-10), # lower limits
upp1.poly = c(10,10,10), # upper limits
## sing model
mag1.sing = 0.1, # mag factor for singularity parameter
omg1.sing = 1.0, # weight
## sphe model
mag.sphe = c(1.0,1.0,0.01), # mag factor for spherical model
omg.sphe = c(0.1,1.0,1.0), # weights
chisq.sphe = FALSE, # use chisq for pvalues instead of extrapolation for k >= 2
## dif parms of poa and pob models
mag1.poa = c(1,0.1), # mag factor for dif parm
low1.poa = c(0.01,-3), # lower limits of dif parm
upp1.poa = c(10,3), # upper limits of dif parm
trg1.poa = c(12,0), # targets of dif parm
omg1.poa = c(0.1,1.0), # weights of dif parm
## sim model
mag1.sim = 0.1, # mag factor for sim parm
omg1.sim = 1.0, # weight
## pom model
mag1.pom = 0.1, # mag factor for pom parm
omg1.pom = 1.0, # weight
## switch
cor.pom = TRUE, # change the method
## print parameters
percent = TRUE, # print p-values in percent
digits.pval = 2, # significant digits for pvalue
digits.coef = 4, # significant digits for coefficients
## averaging models
th.aicw = 1e-4, # threshold for akaike weights
## sbconf; only experimental...
probs0=c(0.001,0.01,0.1,0.9,0.99,0.999), # initial grid
prob0=0.5, # for starting value
tol.mono=0.1, # for monotonicity checking
tol.conv=0.01, # for convergence
tol.relconv=0.5, # tolerance with respect to s.e.
max.loop=100, # max iterations
## for debug
debug=FALSE
)
options(scaleboot=op)
}
## to show and change options
sboptions <- function(x,value) {
op <- getOption("scaleboot")
if(missing(x)) return(op)
if(length(x)==1) y <- op[[x]]
else y <- op[x]
if(!missing(value)) {
op[[x]] <- value
options(scaleboot=op)
}
y
}
######################################################################
### EOF
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