[Distr-commits] r711 - in pkg/distrMod: man tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 5 17:43:34 CET 2011
Author: stamats
Date: 2011-01-05 17:43:34 +0100 (Wed, 05 Jan 2011)
New Revision: 711
Modified:
pkg/distrMod/man/NBinomFamily.Rd
pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save
Log:
updated distrMod-Ex.Rout.save files to R 2.12.1 patched, we need to check the new Nbinom-families!
Modified: pkg/distrMod/man/NBinomFamily.Rd
===================================================================
--- pkg/distrMod/man/NBinomFamily.Rd 2011-01-05 13:53:42 UTC (rev 710)
+++ pkg/distrMod/man/NBinomFamily.Rd 2011-01-05 16:43:34 UTC (rev 711)
@@ -34,9 +34,9 @@
Kohl, M. (2005) \emph{Numerical Contributions to the
Asymptotic Theory of Robustness}. Bayreuth: Dissertation.
- Kohl, M. and Ruckdeschel, P. (2010).
+ Kohl, M. and Ruckdeschel, P (both authors contributed equally).
R Package distrMod: S4 Classes and Methods for
- Probability Models. To appear in Journal of Statistical Software.
+ Probability Models. \emph{Journal of Statistical Software} 2010, 35(10), 1-27.
}
\author{Peter Ruckdeschel \email{peter.ruckdeschel at itwm.fraunhofer.de}}
%\note{}
@@ -50,6 +50,10 @@
plot(N1.w)
FisherInfo(N1.w)
checkL2deriv(N1.w)
+(N2.w <- NbinomMeanSizeFamily(size = 25, mean = 10))
+plot(N2.w)
+FisherInfo(N2.w)
+checkL2deriv(N2.w)
}
\concept{Negative Binomial model}
\keyword{models}
Modified: pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save
===================================================================
--- pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save 2011-01-05 13:53:42 UTC (rev 710)
+++ pkg/distrMod/tests/Examples/distrMod-Ex.Rout.save 2011-01-05 16:43:34 UTC (rev 711)
@@ -1,7 +1,8 @@
-R version 2.10.1 Patched (2010-01-12 r50990)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R version 2.12.1 Patched (2011-01-04 r53913)
+Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -31,8 +32,7 @@
Loading required package: sfsmisc
Loading required package: SweaveListingUtils
:SweaveListingUtils> Utilities for Sweave together with
-:SweaveListingUtils> TeX listings package (version
-:SweaveListingUtils> 0.4.1)
+:SweaveListingUtils> TeX listings package (version 0.5)
:SweaveListingUtils>
:SweaveListingUtils> Some functions from package 'base'
:SweaveListingUtils> are intentionally masked ---see
@@ -53,14 +53,12 @@
Attaching package: 'SweaveListingUtils'
+The following object(s) are masked from 'package:base':
- The following object(s) are masked from package:base :
+ library, require
- library,
- require
-
-:distr> Object orientated implementation of distributions (version
-:distr> 2.2.1)
+:distr> Object oriented implementation of distributions (version
+:distr> 2.3)
:distr>
:distr> Attention: Arithmetics on distribution objects are
:distr> understood as operations on corresponding random variables
@@ -81,25 +79,21 @@
Attaching package: 'distr'
+The following object(s) are masked from 'package:stats':
- The following object(s) are masked from package:stats :
+ df, qqplot, sd
- df,
- qqplot,
- sd
-
Loading required package: distrEx
Loading required package: evd
Loading required package: actuar
Attaching package: 'actuar'
+The following object(s) are masked from 'package:grDevices':
- The following object(s) are masked from package:grDevices :
+ cm
- cm
-
-:distrEx> Extensions of package distr (version 2.2.1)
+:distrEx> Extensions of package distr (version 2.3)
:distrEx>
:distrEx> Note: Packages "e1071", "moments", "fBasics" should be
:distrEx> attached /before/ package "distrEx". See distrExMASK().
@@ -114,16 +108,12 @@
Attaching package: 'distrEx'
+The following object(s) are masked from 'package:stats':
- The following object(s) are masked from package:stats :
+ IQR, mad, median, var
- IQR,
- mad,
- median,
- var
-
Loading required package: RandVar
-:RandVar> Implementation of random variables (version 0.7)
+:RandVar> Implementation of random variables (version 0.8)
:RandVar>
:RandVar> For more information see ?"RandVar", NEWS("RandVar"), as
:RandVar> well as
@@ -134,7 +124,7 @@
Loading required package: MASS
Loading required package: stats4
:distrMod> Object oriented implementation of probability models
-:distrMod> (version 2.2.1)
+:distrMod> (version 2.3)
:distrMod>
:distrMod> Some functions from pkg's 'base' and 'stats' are
:distrMod> intentionally masked ---see distrModMASK().
@@ -145,22 +135,27 @@
:distrMod> For more information see ?"distrMod",
:distrMod> NEWS("distrMod"), as well as
:distrMod> http://distr.r-forge.r-project.org/
-:distrMod> Package "distrDoc" provides a vignette to this package
+:distrMod> There is a vignette to this package; try
+:distrMod> vignette("distrMod").
+:distrMod> Package "distrDoc" provides a vignette to the other
+:distrMod> distrXXX packages,
:distrMod> as well as to several related packages; try
:distrMod> vignette("distr").
Attaching package: 'distrMod'
+The following object(s) are masked from 'package:stats4':
- The following object(s) are masked from package:stats4 :
+ confint
- confint
+The following object(s) are masked from 'package:stats':
+ confint
- The following object(s) are masked from package:stats :
+The following object(s) are masked from 'package:base':
- confint
+ norm
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
@@ -587,7 +582,7 @@
{
((x - 0)/1 * LogDeriv((x - 0)/1) - 1)/1
}
-<environment: 0x5757930>
+<environment: 0x4bf9798>
> checkL2deriv(E1)
precision of centering: -1.511810e-06
@@ -764,7 +759,7 @@
{
LogDeriv(x - 0)
}
-<environment: 0x70c22d0>
+<environment: 0x32bc0e8>
> checkL2deriv(G1)
precision of centering: 1.511810e-06
@@ -803,7 +798,7 @@
Slot "fct":
function (x)
QuadFormNorm(x, A = A)
-<environment: 0x6629a80>
+<environment: 0x52e1898>
>
> ## The function is currently defined as
@@ -1081,7 +1076,7 @@
{
((x - 0)/1 * LogDeriv((x - 0)/1) - 1)/1
}
-<environment: 0x7996620>
+<environment: 0x5c0dd08>
> checkL2deriv(L1)
precision of centering: -0.003003394
@@ -1328,10 +1323,10 @@
samplesize: 50
estimate:
scale shape
-0.3296938 4.2907460
+0.3419487 4.1663559
Criterion:
CvM distance
- 0.02872404
+ 0.02879881
>
> ## von Mises minimum distance estimator with default mu
> MDEstimator(x = x, ParamFamily = G, distance = CvMDist,
@@ -1344,15 +1339,15 @@
samplesize: 50
estimate:
scale shape
- 0.32969378 4.29074603
- (0.08369777) (1.03063291)
+ 0.34194869 4.16635591
+ (0.08687677) (0.99985006)
asymptotic (co)variance (multiplied with samplesize):
scale shape
-scale 0.3502659 -4.007671
-shape -4.0076714 53.110210
+scale 0.3773787 -4.026502
+shape -4.0265023 49.985008
Criterion:
CvM distance
- 0.02872404
+ 0.02879881
> #*** variance routine is still in testing phase so not yet
> #*** exported to namespace
> ## von Mises minimum distance estimator with mu = N(0,1)
@@ -1365,10 +1360,10 @@
samplesize: 50
estimate:
scale shape
-0.3543892 4.0587606
+0.3407495 4.2127808
Criterion:
CvM distance
- 0.01586171
+ 0.01574483
>
> ## Total variation minimum distance estimator
> ## gamma distributions are discretized
@@ -1661,6 +1656,111 @@
>
> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
> cleanEx()
+> nameEx("NBinomFamily")
+> ### * NBinomFamily
+>
+> flush(stderr()); flush(stdout())
+>
+> ### Name: NbinomFamily
+> ### Title: Generating function for Nbinomial families
+> ### Aliases: NbinomFamily NbinomwithSizeFamily NbinomMeanSizeFamily
+> ### Keywords: models
+>
+> ### ** Examples
+>
+> (N1 <- NbinomFamily(size = 25, prob = 0.25))
+An object of class "NbinomFamily"
+### name: Negative Binomial family
+
+### distribution: Distribution Object of Class: Nbinom
+ size: 25
+ prob: 0.25
+
+### param: An object of class "ParamFamParameter"
+name: probability of success
+prob: 0.25
+fixed part of param.:
+ size: 25
+
+### props:
+[1] ""
+> plot(N1)
+> FisherInfo(N1)
+An object of class "PosSemDefSymmMatrix"
+ prob
+prob 533.3333
+> checkL2deriv(N1)
+precision of centering: 0.001177892
+precision of Fisher information:
+ prob
+prob -0.1601189
+$maximum.deviation
+[1] 0.1601189
+
+> (N1.w <- NbinomwithSizeFamily(size = 25, prob = 0.25))
+An object of class "NbinomwithSizeFamily"
+### name: Negative Binomial family
+
+### distribution: Distribution Object of Class: Nbinom
+ size: 25
+ prob: 0.25
+
+### param: An object of class "ParamFamParameter"
+name: NegBinomParameter
+size: 25
+prob: 0.25
+
+### props:
+[1] ""
+> plot(N1.w)
+> FisherInfo(N1.w)
+An object of class "PosSemDefSymmMatrix"
+ size prob
+size 0.03044946 -4.0000
+prob -4.00000000 533.3333
+> checkL2deriv(N1.w)
+precision of centering: 2.772558 0.001177892
+precision of Fisher information:
+ size prob
+size 7.687142566 0.004113952
+prob 0.004113952 -0.160118938
+$maximum.deviation
+[1] 7.687143
+
+> (N2.w <- NbinomMeanSizeFamily(size = 25, mean = 10))
+An object of class "NbinomMeanSizeFamily"
+### name: Negative Binomial family
+
+### distribution: Distribution Object of Class: Nbinom
+ size: 25
+ prob: 0.714285714285714
+
+### param: An object of class "ParamFamParameter"
+name: probability of success
+size: 25
+mean: 10
+
+### props:
+[1] ""
+> plot(N2.w)
+> FisherInfo(N2.w)
+An object of class "PosSemDefSymmMatrix"
+ size mean
+size 0.0114921 68.6046
+mean 68.6045968 411826.3818
+> checkL2deriv(N2.w)
+precision of centering: 0.3249777 0.1010739
+precision of Fisher information:
+ size mean
+size 0.0941289 -70.55341
+mean -70.5534100 -170.57314
+$maximum.deviation
+[1] 170.5731
+
+>
+>
+>
+> cleanEx()
> nameEx("NonSymmetric-class")
> ### * NonSymmetric-class
>
@@ -2468,7 +2568,7 @@
Slot "fct":
function (x)
QuadFormNorm(x, A = A0)
-<environment: 0x78c9f88>
+<environment: 0x52cfe50>
>
> ## The function is currently defined as
@@ -2506,7 +2606,7 @@
Slot "fct":
function (x)
QuadFormNorm(x, A = A)
-<environment: 0x77fb088>
+<environment: 0x4cea9a0>
>
> ## The function is currently defined as
@@ -2896,7 +2996,7 @@
> flush(stderr()); flush(stdout())
>
> ### Name: confint-methods
-> ### Title: Methods for function confint in Package `distrMod'
+> ### Title: Methods for function confint in Package 'distrMod'
> ### Aliases: confint-methods confint confint,ANY,missing-method
> ### confint,Estimate,missing-method confint,mle,missing-method
> ### confint,profile.mle,missing-method
@@ -3035,7 +3135,7 @@
>
> ### Name: distrModOptions
> ### Title: Function to change the global variables of the package
-> ### `distrMod'
+> ### 'distrMod'
> ### Aliases: distrModOptions getdistrModOption distrModoptions show.details
> ### Keywords: misc distribution
>
@@ -3454,7 +3554,7 @@
> flush(stderr()); flush(stdout())
>
> ### Name: print-methods
-> ### Title: Common `print' Methods for S4 classes in Package `distrMod'
+> ### Title: Common 'print' Methods for S4 classes in Package 'distrMod'
> ### Aliases: print-methods print,ShowDetails-method
> ### Keywords: models
>
@@ -3629,7 +3729,7 @@
> flush(stderr()); flush(stdout())
>
> ### Name: qqplot
-> ### Title: Methods for Function qqplot in Package `distrMod'
+> ### Title: Methods for Function qqplot in Package 'distrMod'
> ### Aliases: qqplot qqplot-methods qqplot,ANY,ProbFamily-method
> ### qqplot,ANY,UnivariateDistribution-method
> ### Keywords: hplot distribution
@@ -3826,7 +3926,7 @@
> flush(stderr()); flush(stdout())
>
> ### Name: trafo-methods
-> ### Title: Methods for function trafo in Package `distrMod'
+> ### Title: Methods for function trafo in Package 'distrMod'
> ### Aliases: trafo-methods trafo trafo,Estimate,missing-method
> ### trafo,Estimate,ParamFamParameter-method
> ### trafo,ParamFamParameter,missing-method
@@ -3880,7 +3980,7 @@
> flush(stderr()); flush(stdout())
>
> ### Name: trafoEst
-> ### Title: Function trafoEst in Package `distrMod'
+> ### Title: Function trafoEst in Package 'distrMod'
> ### Aliases: trafoEst
> ### Keywords: models
>
@@ -3924,7 +4024,7 @@
> flush(stderr()); flush(stdout())
>
> ### Name: validParameter-methods
-> ### Title: Methods for function validParameter in Package `distrMod'
+> ### Title: Methods for function validParameter in Package 'distrMod'
> ### Aliases: validParameter-methods validParameter
> ### validParameter,ParamFamily-method validParameter,L2ScaleFamily-method
> ### validParameter,L2LocationFamily-method
@@ -3954,7 +4054,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 66.45 0.18 66.683 0.01 0.01
+Time elapsed: 49.12 0.09 49.434 0 0
> grDevices::dev.off()
null device
1
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