[Georob-commits] r15 - in pkg: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Sep 6 18:05:46 CEST 2013
Author: papritz
Date: 2013-09-06 18:05:46 +0200 (Fri, 06 Sep 2013)
New Revision: 15
Modified:
pkg/DESCRIPTION
pkg/NAMESPACE
pkg/R/georob.exported.functions.R
pkg/man/S3methods.georob.Rd
pkg/man/georob.Rd
pkg/man/georob.control.Rd
pkg/man/internal.functions.Rd
Log:
changes in imports and depends and namespace declaration, released to cran
as version 0.1-1 (and not as 0.1-2 as specified in previous commit)
M pkg/R/georob.exported.functions.R
M pkg/DESCRIPTION
M pkg/man/georob.Rd
M pkg/man/internal.functions.Rd
M pkg/man/S3methods.georob.Rd
M pkg/man/georob.control.Rd
M pkg/NAMESPACE
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2013-09-06 12:05:27 UTC (rev 14)
+++ pkg/DESCRIPTION 2013-09-06 16:05:46 UTC (rev 15)
@@ -1,15 +1,15 @@
Package: georob
Type: Package
Title: Robust Geostatistical Analysis of Spatial Data
-Version: 0.1-2
-Date: 2013-06-20
+Version: 0.1-1
+Date: 2013-09-06
Authors at R: c(
person( "Andreas", "Papritz", role = c( "cre", "aut" ),
email = "andreas.papritz at env.ethz.ch" ),
person( "Cornelia", "Schwierz", role = "ctb" ))
-Depends: R(>= 2.14.0), lmtest, nlme, robustbase, sp(>= 0.9-60)
-Imports: constrainedKriging(>= 0.2-1), nleqslv, quantreg,
- RandomFields(>= 2.0.55), spatialCovariance(>= 0.6-4)
+Depends: R(>= 2.14.0), sp(>= 0.9-60)
+Imports: constrainedKriging(>= 0.2-1), lmtest, nlme, nleqslv, quantreg,
+ RandomFields(>= 2.0.55), robustbase(>= 0.9-5)
Suggests: geoR
Description: The georob package provides functions for fitting linear models
with spatially correlated errors by robust and Gaussian Restricted
Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE 2013-09-06 12:05:27 UTC (rev 14)
+++ pkg/NAMESPACE 2013-09-06 16:05:46 UTC (rev 15)
@@ -1,4 +1,4 @@
-import( stats, parallel )
+import( stats, parallel, sp )
# importFrom( BB, BBsolve )
importFrom( constrainedKriging, covmodel, f.point.block.cov, K, preCKrige )
@@ -7,6 +7,7 @@
importFrom( nleqslv, nleqslv )
importFrom( quantreg, rq.fit )
importFrom( RandomFields, Variogram )
+importFrom( robustbase, lmrob.control, lmrob.fit, Qn, summarizeRobWeights )
# exported functions
@@ -17,23 +18,28 @@
cv, # ok
dfwd.transf, # ok
expand, # ok
+ fixed.effects, # ok export of generic fixed.effects{nlme}
+ fixef, # ok export of generic fixef{nlme}
fwd.transf, # ok
param.bounds, # ok
param.names, # ok
fit.variogram.model, # ok
georob.control, # ok
georob, # ok
- K, # ok re-export of K{constrainedKriging}
+ K, # ok export of K{constrainedKriging}, which is (indirectly) needed by f.point.block.cov{constrainedKriging}
lgnpp, # ok
nleqslv.control, # ok
optim.control, # ok
param.transf, # ok
+ random.effects, # ok export of generic random.effects{nlme}
+ ranef, # ok export of generic ranef{nlme}
rq.control, # ok
sample.variogram, # ok
- validate.predictions # ok
+ validate.predictions, # ok
+ waldtest # ok export of generic waldtest{lmtest}
)
-# documented but not exported functions
+# documented but unexported functions
#
# deviance.georob, # ok
# fixed.effects.georob, # ok
Modified: pkg/R/georob.exported.functions.R
===================================================================
--- pkg/R/georob.exported.functions.R 2013-09-06 12:05:27 UTC (rev 14)
+++ pkg/R/georob.exported.functions.R 2013-09-06 16:05:46 UTC (rev 15)
@@ -18,7 +18,7 @@
)[ names(param) ],
aniso = c( f1 = 1., f2 = 1., omega = 90., phi = 90., zeta = 0. ),
fit.aniso = c( f1 = FALSE, f2 = FALSE, omega = FALSE, phi = FALSE, zeta = FALSE ),
- tuning.psi = 2, initial.param = c( "minimize", "exclude", "no" ),
+ tuning.psi = 2, initial.param = c( "exclude", "minimize", "no" ),
## root.finding = c( "nleqslv", "bbsolve" ),
control = georob.control( ... ), verbose = 0,
...
Modified: pkg/man/S3methods.georob.Rd
===================================================================
--- pkg/man/S3methods.georob.Rd 2013-09-06 12:05:27 UTC (rev 14)
+++ pkg/man/S3methods.georob.Rd 2013-09-06 16:05:46 UTC (rev 15)
@@ -1,10 +1,12 @@
-% 2013-05-23 A. Papritz
+% 2013-09-06 A. Papritz
% R CMD Rdconv -t html -o bla.html S3methods.georob.Rd ; open bla.html; R CMD Rd2pdf --force S3methods.georob.Rd;
\encoding{macintosh}
\name{georob-S3methods}
\alias{deviance.georob}
+\alias{fixed.effects}
\alias{fixed.effects.georob}
+\alias{fixef}
\alias{fixef.georob}
\alias{georobMethods}
\alias{logLik.georob}
@@ -13,7 +15,9 @@
\alias{nobs.georob}
\alias{print.georob}
\alias{print.summary.georob}
+\alias{random.effects}
\alias{random.effects.georob}
+\alias{ranef}
\alias{ranef.georob}
\alias{resid.georob}
\alias{residuals.georob}
@@ -21,6 +25,7 @@
\alias{rstudent.georob}
\alias{summary.georob}
\alias{vcov.georob}
+\alias{waldtest}
\alias{waldtest.georob}
\title{Common S3 Methods for Class \code{georob}}
Modified: pkg/man/georob.Rd
===================================================================
--- pkg/man/georob.Rd 2013-09-06 12:05:27 UTC (rev 14)
+++ pkg/man/georob.Rd 2013-09-06 16:05:46 UTC (rev 15)
@@ -1,4 +1,4 @@
-% 2013-07-12 A. Papritz
+% 2013-09-06 A. Papritz
% R CMD Rdconv -t html -o bla.html georob.Rd ; open bla.html; R CMD Rd2pdf --force georob.Rd;
\encoding{macintosh}
@@ -28,7 +28,7 @@
aniso = c(f1 = 1, f2 = 1, omega = 90, phi = 90, zeta = 0),
fit.aniso = c(f1 = FALSE, f2 = FALSE, omega = FALSE,
phi = FALSE, zeta = FALSE),
- tuning.psi = 2, initial.param = c("minimize", "exclude", "no"),
+ tuning.psi = 2, initial.param = c("exclude", "minimize", "no"),
% root.finding = c("nleqslv", "bbsolve"),
control = georob.control(...),
verbose = 0, ...)
Modified: pkg/man/georob.control.Rd
===================================================================
--- pkg/man/georob.control.Rd 2013-09-06 12:05:27 UTC (rev 14)
+++ pkg/man/georob.control.Rd 2013-09-06 16:05:46 UTC (rev 15)
@@ -1,4 +1,4 @@
-% 2013-07-12 A. Papritz
+% 2013-09-06 A. Papritz
% R CMD Rdconv -t html -o bla.html georob.control.Rd ; open bla.html; R CMD Rd2pdf --force georob.control.Rd;
\encoding{macintosh}
\name{georob.control}
Modified: pkg/man/internal.functions.Rd
===================================================================
--- pkg/man/internal.functions.Rd 2013-09-06 12:05:27 UTC (rev 14)
+++ pkg/man/internal.functions.Rd 2013-09-06 16:05:46 UTC (rev 15)
@@ -1,4 +1,4 @@
-% 2013-06-03 A. Papritz
+% 2013-09-06 A. Papritz
% R CMD Rdconv -t html -o bla.html internal.functions.Rd ; open bla.html; R CMD Rd2pdf --force internal.functions.Rd
\name{internal.functions}
\alias{compute.covariances}
@@ -18,23 +18,29 @@
\title{Internal Functions of Package \pkg{georob}}
%
\description{
-The internal, unexported functions
-\code{compute.covariances},
-\code{compute.estimating.equations},
-\code{compute.semivariance},
-\code{dcorr.dparam},
-\code{estimate.xihat},
-\code{gcr},
-\code{georob.fit},
-\code{getCall.georob},
-\code{gradient.negative.restricted.loglikelihood},
-\code{K},
-\code{negative.restr.loglikelihood},
-\code{prepare.likelihood.calculations},
-\code{update.xihat}
+The internal unexported functions
+\itemize{
+ \item\code{compute.covariances},
+ \item\code{compute.estimating.equations},
+ \item\code{compute.semivariance},
+ \item\code{dcorr.dparam},
+ \item\code{estimate.xihat},
+ \item\code{gcr},
+ \item\code{georob.fit},
+ \item\code{getCall.georob},
+ \item\code{gradient.negative.restricted.loglikelihood},
+ \item\code{negative.restr.loglikelihood},
+ \item\code{prepare.likelihood.calculations},
+ \item\code{update.xihat}
+}
are not intended for direct use. However, as any unexported function they
can be accessed by typing
-\code{georob:::\var{function-name}}.
+\code{georob:::\var{function-name}}.
+
+In addition, the (exported) function \code{K} is required for computing
+block kriging predictions by the (unexported) function
+\code{f.point.block.cov} of the package
+\pkg{constrainedKriging}.
}
\author{
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