[Distr-commits] r611 - in branches/distr-2.2/pkg/distrTEst: . tests tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Oct 16 05:56:53 CEST 2009
Author: stamats
Date: 2009-10-16 05:56:53 +0200 (Fri, 16 Oct 2009)
New Revision: 611
Added:
branches/distr-2.2/pkg/distrTEst/tests/
branches/distr-2.2/pkg/distrTEst/tests/Examples/
branches/distr-2.2/pkg/distrTEst/tests/Examples/distrTEst-Ex.Rout.save
Log:
added *-Ex.Rout.save to new tests/Examples folder. We will have to check and probably to slightly modify these files with every new R version.
Added: branches/distr-2.2/pkg/distrTEst/tests/Examples/distrTEst-Ex.Rout.save
===================================================================
--- branches/distr-2.2/pkg/distrTEst/tests/Examples/distrTEst-Ex.Rout.save (rev 0)
+++ branches/distr-2.2/pkg/distrTEst/tests/Examples/distrTEst-Ex.Rout.save 2009-10-16 03:56:53 UTC (rev 611)
@@ -0,0 +1,586 @@
+
+R version 2.10.0 beta (2009-10-15 r50107)
+Copyright (C) 2009 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+
+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.
+
+ Natural language support but running in an English locale
+
+R is a collaborative project with many contributors.
+Type 'contributors()' for more information and
+'citation()' on how to cite R or R packages in publications.
+
+Type 'demo()' for some demos, 'help()' for on-line help, or
+'help.start()' for an HTML browser interface to help.
+Type 'q()' to quit R.
+
+> ### * <HEADER>
+> ###
+> attach(NULL, name = "CheckExEnv")
+> assign("nameEx",
++ local({
++ s <- "__{must remake R-ex/*.R}__"
++ function(new) {
++ if(!missing(new)) s <<- new else s
++ }
++ }),
++ pos = "CheckExEnv")
+> ## Add some hooks to label plot pages for base and grid graphics
+> assign("base_plot_hook",
++ function() {
++ pp <- par(c("mfg","mfcol","oma","mar"))
++ if(all(pp$mfg[1:2] == c(1, pp$mfcol[2]))) {
++ outer <- (oma4 <- pp$oma[4]) > 0; mar4 <- pp$mar[4]
++ mtext(sprintf("help(\"%s\")", nameEx()), side = 4,
++ line = if(outer)max(1, oma4 - 1) else min(1, mar4 - 1),
++ outer = outer, adj = 1, cex = .8, col = "orchid", las=3)
++ }
++ },
++ pos = "CheckExEnv")
+> assign("grid_plot_hook",
++ function() {
++ grid::pushViewport(grid::viewport(width=grid::unit(1, "npc") -
++ grid::unit(1, "lines"), x=0, just="left"))
++ grid::grid.text(sprintf("help(\"%s\")", nameEx()),
++ x=grid::unit(1, "npc") + grid::unit(0.5, "lines"),
++ y=grid::unit(0.8, "npc"), rot=90,
++ gp=grid::gpar(col="orchid"))
++ },
++ pos = "CheckExEnv")
+> setHook("plot.new", get("base_plot_hook", pos = "CheckExEnv"))
+> setHook("persp", get("base_plot_hook", pos = "CheckExEnv"))
+> setHook("grid.newpage", get("grid_plot_hook", pos = "CheckExEnv"))
+> assign("cleanEx",
++ function(env = .GlobalEnv) {
++ rm(list = ls(envir = env, all.names = TRUE), envir = env)
++ RNGkind("default", "default")
++ set.seed(1)
++ options(warn = 1)
++ .CheckExEnv <- as.environment("CheckExEnv")
++ delayedAssign("T", stop("T used instead of TRUE"),
++ assign.env = .CheckExEnv)
++ delayedAssign("F", stop("F used instead of FALSE"),
++ assign.env = .CheckExEnv)
++ sch <- search()
++ newitems <- sch[! sch %in% .oldSearch]
++ for(item in rev(newitems))
++ eval(substitute(detach(item), list(item=item)))
++ missitems <- .oldSearch[! .oldSearch %in% sch]
++ if(length(missitems))
++ warning("items ", paste(missitems, collapse=", "),
++ " have been removed from the search path")
++ },
++ pos = "CheckExEnv")
+> assign("ptime", proc.time(), pos = "CheckExEnv")
+> ## at least one package changes these via ps.options(), so do this
+> ## before loading the package.
+> ## Use postscript as incomplete files may be viewable, unlike PDF.
+> ## Choose a size that is close to on-screen devices, fix paper
+> grDevices::ps.options(width = 7, height = 7, paper = "a4", reset = TRUE)
+> grDevices::postscript("distrTEst-Ex.ps")
+>
+> assign("par.postscript", graphics::par(no.readonly = TRUE), pos = "CheckExEnv")
+> options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly"))
+> options(warn = 1)
+> library('distrTEst')
+Loading required package: setRNG
+Loading required package: distr
+Loading required package: startupmsg
+:startupmsg> Utilities for start-up messages (version 0.7)
+:startupmsg>
+:startupmsg> For more information see ?"startupmsg",
+:startupmsg> NEWS("startupmsg")
+
+Loading required package: sfsmisc
+Loading required package: SweaveListingUtils
+:SweaveListingUtils> Utilities for Sweave together with
+:SweaveListingUtils> TeX listings package (version 0.4)
+:SweaveListingUtils>
+:SweaveListingUtils> Some functions from package 'base'
+:SweaveListingUtils> are intentionally masked ---see
+:SweaveListingUtils> SweaveListingMASK().
+:SweaveListingUtils>
+:SweaveListingUtils> Note that global options are
+:SweaveListingUtils> controlled by
+:SweaveListingUtils> SweaveListingoptions() ---c.f.
+:SweaveListingUtils> ?"SweaveListingoptions".
+:SweaveListingUtils>
+:SweaveListingUtils> For more information see
+:SweaveListingUtils> ?"SweaveListingUtils",
+:SweaveListingUtils> NEWS("SweaveListingUtils")
+:SweaveListingUtils> There is a vignette to this
+:SweaveListingUtils> package; try
+:SweaveListingUtils> vignette("ExampleSweaveListingUtils").
+
+
+Attaching package: 'SweaveListingUtils'
+
+
+ The following object(s) are masked from package:base :
+
+ library,
+ require
+
+:distr> Object orientated implementation of distributions (version
+:distr> 2.2)
+:distr>
+:distr> Attention: Arithmetics on distribution objects are
+:distr> understood as operations on corresponding random variables
+:distr> (r.v.s); see distrARITH().
+:distr>
+:distr> Some functions from package 'stats' are intentionally masked
+:distr> ---see distrMASK().
+:distr>
+:distr> Note that global options are controlled by distroptions()
+:distr> ---c.f. ?"distroptions".
+:distr>
+:distr> For more information see ?"distr", NEWS("distr"), as well as
+:distr> http://distr.r-forge.r-project.org/
+:distr> Package "distrDoc" provides a vignette to this package as
+:distr> well as to several extension packages; try
+:distr> vignette("distr").
+
+
+Attaching package: 'distr'
+
+
+ The following object(s) are masked from package:stats :
+
+ df,
+ qqplot,
+ sd
+
+Loading required package: distrSim
+:distrSim> Simulation classes based on package distr (version
+:distrSim> 2.2)
+:distrSim>
+:distrSim> Some functions from package 'stats' are intentionally
+:distrSim> masked ---see distrSimMASK().
+:distrSim>
+:distrSim>
+:distrSim> For more information see ?"distrSim",
+:distrSim> NEWS("distrSim"), as well as
+:distrSim> http://distr.r-forge.r-project.org/
+:distrSim> Package "distrDoc" provides a vignette to this package
+:distrSim> as well as to several related packages; try
+:distrSim> vignette("distr").
+
+
+Attaching package: 'distrSim'
+
+
+ The following object(s) are masked from package:stats :
+
+ simulate
+
+
+ The following object(s) are masked from package:base :
+
+ rbind
+
+:distrTEst> Estimation and Testing classes based on package
+:distrTEst> distr (version 2.2)
+:distrTEst>
+:distrTEst> For more information see ?"distrTEst",
+:distrTEst> NEWS("distrTEst"), as well as
+:distrTEst> http://distr.r-forge.r-project.org/
+:distrTEst> Package "distrDoc" provides a vignette to this
+:distrTEst> package as well as to several related packages; try
+:distrTEst> vignette("distr").
+
+>
+> assign(".oldSearch", search(), pos = 'CheckExEnv')
+> assign(".oldNS", loadedNamespaces(), pos = 'CheckExEnv')
+> cleanEx(); nameEx("Evaluation-class")
+> ### * Evaluation-class
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: Evaluation-class
+> ### Title: Class "Evaluation"
+> ### Aliases: Evaluation-class initialize,Evaluation-method
+> ### Keywords: manip
+>
+> ### ** Examples
+>
+> N <- Norm() # N is a standard normal distribution.
+> C <- Cauchy() # C is a Cauchy distribution
+> cs <- Contsimulation(filename = "csim",
++ runs = 5,
++ samplesize=5000,
++ seed=setRNG(),
++ distribution.id = N,
++ distribution.c = C,
++ rate = 0.1)
+> simulate(cs)
+> # Each of the 25000 random numbers is ideal (N-distributed) with
+> # probability 0.9 and contaminated (C-distributed) with probability = 0.1
+> summary(cs)
+name of simulation: csim
+rate of contamination: 0.100000
+real Data:
+dimension of the observations: 1
+number of runs: 5
+size of sample: 5000
+, , 1
+
+ [,1]
+Min. -4.633e+02
+1st Qu. -6.888e-01
+Median -9.882e-03
+Mean -5.081e-02
+3rd Qu. 7.174e-01
+Max. 1.133e+02
+
+, , 2
+
+ [,1]
+Min. -70.36000
+1st Qu. -0.69270
+Median -0.01484
+Mean -0.03787
+3rd Qu. 0.65770
+Max. 35.49000
+
+, , 3
+
+ [,1]
+Min. -198.00000
+1st Qu. -0.72410
+Median -0.05111
+Mean 0.41380
+3rd Qu. 0.67300
+Max. 1753.00000
+
+, , 4
+
+ [,1]
+Min. -3.247e+02
+1st Qu. -6.898e-01
+Median 5.874e-04
+Mean -1.625e-01
+3rd Qu. 6.886e-01
+Max. 4.682e+01
+
+, , 5
+
+ [,1]
+Min. -339.10000
+1st Qu. -0.65140
+Median 0.05992
+Mean -0.01367
+3rd Qu. 0.69830
+Max. 131.50000
+
+> ev1 <- evaluate(cs, mean, resname="mean") # estimates the data with mean
+> ev1 # bad results
+An Evaluation Object
+name of Dataobject: object
+name of Datafile: csim
+estimator: mean
+Result: 'data.frame': 5 obs. of 2 variables:
+ $ mean.id: num -0.00319 -0.00989 -0.02207 0.01369 0.02614
+ $ mean.re: num -0.0508 -0.0379 0.4138 -0.1625 -0.0137
+> ev2 <- evaluate(cs,median, resname="median") # estimates the data with median
+> ev2 # better results because median is robust
+An Evaluation Object
+name of Dataobject: object
+name of Datafile: csim
+estimator: median
+Result: 'data.frame': 5 obs. of 2 variables:
+ $ medn.id: num -0.01549 -0.01739 -0.04523 0.00723 0.05344
+ $ medn.re: num -0.009882 -0.014837 -0.051108 0.000587 0.059924
+> savedata(ev1)
+[1] "csim.mean"
+[1] "ev1"
+[1] "csim.mean.comment"
+[1] "ev1.comment"
+> # saves the evaluation with result as "csim.mean" and without result as
+> # "csim.mean.comment" in the working directory # of R - "csim" is the
+> # filename of the Contsimulation object, mean the name of the estimator
+> rm(ev1)
+> cload("csim.mean")
+> # loads the evaluation without result - the object is called ev1.comment
+> ev1.comment
+An Evaluation Object
+name of Dataobject: object
+name of Datafile: csim
+estimator: mean
+> load("csim.mean") # loads the evaluation with result
+> ev1
+An Evaluation Object
+name of Dataobject: object
+name of Datafile: csim
+estimator: mean
+Result: 'data.frame': 5 obs. of 2 variables:
+ $ mean.id: num -0.00319 -0.00989 -0.02207 0.01369 0.02614
+ $ mean.re: num -0.0508 -0.0379 0.4138 -0.1625 -0.0137
+> plot(ev1)
+> #
+> #another function to be evaluated:
+> severalThings<- function(x) {list("mean"=mean(x),"sd"=sd(x), "mad"=mad(x))}
+> ev3 <- evaluate(cs, severalThings, resname="several")
+> plot(ev3)
+> plot(ev3, ylim=c(0,10), col=c("blue","green", "red"))
+>
+>
+>
+> cleanEx(); nameEx("EvaluationList-class")
+> ### * EvaluationList-class
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: EvaluationList-class
+> ### Title: Class "EvaluationList"
+> ### Aliases: Elist EvaluationList EvaluationList-class
+> ### initialize,EvaluationList-method savedata,EvaluationList-method
+> ### name,EvaluationList-method name<-,EvaluationList-method
+> ### Elist,EvaluationList-method
+> ### Keywords: list manip
+>
+> ### ** Examples
+>
+> N <- Norm() # N is a standard normal distribution.
+> C <- Cauchy() # C is a Cauchy distribution
+> cs <- Contsimulation(filename = "csim",
++ runs = 15,
++ samplesize=500,
++ seed=setRNG(),
++ distribution.id = N,
++ distribution.c = C,
++ rate = 0.1)
+> simulate(cs)
+> # Each of the 25000 random numbers is ideal (N-distributed) with
+> # probability 0.9 and contaminated (C-distributed) with probability = 0.1
+> summary(cs)
+name of simulation: csim
+rate of contamination: 0.100000
+real Data:
+dimension of the observations: 1
+number of runs: 15
+size of sample: 500
+, , 1
+
+ [,1]
+Min. -7.832000
+1st Qu. -0.592900
+Median -0.006142
+Mean 0.262100
+3rd Qu. 0.681900
+Max. 76.610000
+
+, , 2
+
+ [,1]
+Min. -20.18000
+1st Qu. -0.79010
+Median -0.03902
+Mean 0.09946
+3rd Qu. 0.71340
+Max. 69.34000
+
+, , 3
+
+ [,1]
+Min. -107.60000
+1st Qu. -0.71170
+Median -0.07457
+Mean -0.23260
+3rd Qu. 0.72740
+Max. 4.94800
+
+, , 4
+
+ [,1]
+Min. -16.20000
+1st Qu. -0.67080
+Median 0.02934
+Mean 0.17750
+3rd Qu. 0.76710
+Max. 52.53000
+
+, , 5
+
+ [,1]
+Min. -4.05100
+1st Qu. -0.69020
+Median -0.05908
+Mean 0.01636
+3rd Qu. 0.73180
+Max. 14.23000
+
+, , 6
+
+ [,1]
+Min. -6.67900
+1st Qu. -0.60520
+Median -0.01256
+Mean -0.01041
+3rd Qu. 0.67910
+Max. 6.83300
+
+> ev1 <- evaluate(cs, mean) # estimates the data with mean
+> ev1 # bad results
+An Evaluation Object
+name of Dataobject: object
+name of Datafile: csim
+estimator: mean
+Result: 'data.frame': 15 obs. of 2 variables:
+ $ mean.id: num 0.02264 -0.04594 -0.00299 -0.02954 0.0091 ...
+ $ mean.re: num 0.2621 0.0995 -0.2326 0.1775 0.0164 ...
+> ev2 <- evaluate(cs,median) # estimates the data with median
+> ev2 # better results because median is robust
+An Evaluation Object
+name of Dataobject: object
+name of Datafile: csim
+estimator: median
+Result: 'data.frame': 15 obs. of 2 variables:
+ $ medn.id: num -0.0368 -0.0213 -0.0536 -0.0189 -0.0482 ...
+ $ medn.re: num -0.00614 -0.03902 -0.07457 0.02934 -0.05908 ...
+> savedata(ev1)
+[1] "csim.mean"
+[1] "ev1"
+[1] "csim.mean.comment"
+[1] "ev1.comment"
+> # saves the EvaluationList with result as "csim.mean" and without result as
+> # "csim.mean.comment" in the working directory # of R - "csim" is the
+> # filename of the Contsimulation object, mean the name of the estimator
+> rm(ev1)
+> cload("csim.mean")
+> # loads the EvaluationList without result - the object is called ev1.comment
+> ev1.comment
+An Evaluation Object
+name of Dataobject: object
+name of Datafile: csim
+estimator: mean
+> load("csim.mean") # loads the EvaluationList with result
+> ev1
+An Evaluation Object
+name of Dataobject: object
+name of Datafile: csim
+estimator: mean
+Result: 'data.frame': 15 obs. of 2 variables:
+ $ mean.id: num 0.02264 -0.04594 -0.00299 -0.02954 0.0091 ...
+ $ mean.re: num 0.2621 0.0995 -0.2326 0.1775 0.0164 ...
+> ElistObj <- EvaluationList(ev1,ev2,name0="myEvalList")
+Warning in all(lapply(object at Elist, function(x) identical(x at call.ev$object, :
+ coercing argument of type 'list' to logical
+Warning in all(lapply(object at Elist, function(x) identical(x at Data@seed, object at Elist[[1]]@Data at seed))) :
+ coercing argument of type 'list' to logical
+Warning in all(lapply(object at Elist, function(x) identical(body(x at Data@distribution.id at p), :
+ coercing argument of type 'list' to logical
+Warning in all(lapply(object at Elist, function(x) identical(body(x at Data@distribution.c at p), :
+ coercing argument of type 'list' to logical
+> plot(ElistObj,ylim=matrix(c(-0.5,0.5,0.5,4),nrow=2),main=c("location","scale"))
+Warning in par(op) : graphical parameter "cin" cannot be set
+Warning in par(op) : graphical parameter "cra" cannot be set
+Warning in par(op) : graphical parameter "csi" cannot be set
+Warning in par(op) : graphical parameter "cxy" cannot be set
+Warning in par(op) : graphical parameter "din" cannot be set
+> plot(ElistObj,ylim=c(-0.5,0.5),main=c("location"),runs0=3:12,dims0=1,evals0=2)
+Warning in par(op) : graphical parameter "cin" cannot be set
+Warning in par(op) : graphical parameter "cra" cannot be set
+Warning in par(op) : graphical parameter "csi" cannot be set
+Warning in par(op) : graphical parameter "cxy" cannot be set
+Warning in par(op) : graphical parameter "din" cannot be set
+> ElistObj
+An EvaluationList Object
+name of Evaluation List: myEvalList
+name of Dataobject: object
+name of Datafile: csim
+----------------------------------
+An Evaluation Object
+estimator: mean
+Result: 'data.frame': 15 obs. of 2 variables:
+ $ mean.id: num 0.02264 -0.04594 -0.00299 -0.02954 0.0091 ...
+ $ mean.re: num 0.2621 0.0995 -0.2326 0.1775 0.0164 ...
+----------------------------------
+An Evaluation Object
+estimator: median
+Result: 'data.frame': 15 obs. of 2 variables:
+ $ medn.id: num -0.0368 -0.0213 -0.0536 -0.0189 -0.0482 ...
+ $ medn.re: num -0.00614 -0.03902 -0.07457 0.02934 -0.05908 ...
+> summary(ElistObj)
+name of Evaluation List: myEvalList
+name of Dataobject: object
+name of Datafile: csim
+----------------------------------
+name of Evaluation: object
+estimator: mean
+Result:
+ mean.id mean.re
+ Min. :-0.056414 Min. :-0.33898
+ 1st Qu.:-0.031666 1st Qu.:-0.03277
+ Median :-0.006922 Median : 0.02029
+ Mean :-0.006906 Mean : 0.02481
+ 3rd Qu.: 0.005326 3rd Qu.: 0.13042
+ Max. : 0.089858 Max. : 0.26208
+----------------------------------
+name of Evaluation: object
+estimator: median
+Result:
+ medn.id medn.re
+ Min. :-0.09221 Min. :-0.13948
+ 1st Qu.:-0.05020 1st Qu.:-0.03568
+ Median :-0.02996 Median :-0.02969
+ Mean :-0.01646 Mean :-0.01515
+ 3rd Qu.: 0.01899 3rd Qu.: 0.02496
+ Max. : 0.08584 Max. : 0.07802
+>
+>
+>
+> cleanEx(); nameEx("distrTEstoptions")
+> ### * distrTEstoptions
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: distrTEstoptions
+> ### Title: functions to change the global variables of the package
+> ### `distrTEst'
+> ### Aliases: distrTEstoptions getdistrTEstOption
+> ### MaxNumberofPlottedEvaluationDims MaxNumberofPlottedEvaluations
+> ### MaxNumberofSummarizedEvaluationDims MaxNumberofSummarizedEvaluations
+> ### Keywords: misc
+>
+> ### ** Examples
+>
+> distrTEstoptions()
+$MaxNumberofPlottedEvaluationDims
+[1] 6
+
+$MaxNumberofPlottedEvaluations
+[1] 6
+
+$MaxNumberofSummarizedEvaluations
+[1] 15
+
+$MaxNumberofPrintedEvaluations
+[1] 15
+
+> distrTEstoptions("MaxNumberofPlottedEvaluationDims")
+$MaxNumberofPlottedEvaluationDims
+[1] 6
+
+> distrTEstoptions("MaxNumberofPlottedEvaluationDims" = 5)
+> # or
+> getdistrTEstOption("MaxNumberofPlottedEvaluationDims")
+[1] 5
+>
+>
+>
+> ### * <FOOTER>
+> ###
+> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
+Time elapsed: 3.116 0.036 3.233 0 0
+> grDevices::dev.off()
+null device
+ 1
+> ###
+> ### Local variables: ***
+> ### mode: outline-minor ***
+> ### outline-regexp: "\\(> \\)?### [*]+" ***
+> ### End: ***
+> quit('no')
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