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CHANGES
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CHANGES
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=====================================
CHANGES IN geoR VERSION 1.7-5
=====================================
BUGS/Fixes
o call to sp::overlay changed to sp::over()
o changes to fix issues on CRAN reported errors/warnings
regarding namespaces and foreign calls
=====================================
CHANGES IN geoR VERSION 1.7-4
=====================================
NEW FEATURES
o
BUGS
o fix points.geodata when argument "pt.divide" gets an scalar
o fix in krige.conv() when a single prediction location is provided
o package tcktl moved to "Suggests". eyefit() has require(tcltk)
o clarifictions in the documentation of "plot.variogram" for plotting the variogram cloud
=====================================
CHANGES IN geoR VERSION 1.7-3
=====================================
NEW FEATURES
o
BUGS
o fix in cov.spatial() to prevent defining array of 0 dimension
o $altitude is now consistently a vector in sic.100, sic.all and sic.367
o fix in dup.coords() to adjust for jitterDupCoords() with equal number of replicates at replicated locations
o package tcktl back as Depends dependence
=====================================
CHANGES IN geoR VERSION 1.7-2
=====================================
NEW FEATURES
o trend.spatial() search for variables in formula in Spatial*DataFrame objects (package(sp))
BUGS
o fix in dup.coords() to adjust for jitterDupCoords() with equal number of replicates at replicated locations
o package tcktl back as Depends dependence
o .nlmP() is now exported and visible again
=====================================
CHANGES IN geoR VERSION 1.7-1
=====================================
NEW FEATURES
o geoR has now a NAMESPACE exporting/importing functions
o changes in the DESCRIPTION file with dependends and suggests
o boxcox.fit() replaced by boxcoxfit() (also the S3 class name and methods)
o cite.geoR() now removed. Standard citation(package="geoR") should be used instead
o CITATION information changed including Diggle & Ribeiro (2007)
BUGS
o krige.control() now reads trend specification from obj.model properly
=====================================
CHANGES IN geoR VERSION 1.6-34/1.6-35
=====================================
NEW FEATURES
o little changes in grf() to check for regular grid on coordinates
provides by the user
BUGS
o fix in documentation of functions completing names of arguments
o change in geoR2RF: "whittlematern" to "whittle" com conform with changes in RandomFields
===============================
CHANGES IN geoR VERSION 1.6-33
===============================
NEW FEATURES
o replacement of pythag by hypot in the C code
o new geoR2RF() to adjust for changes in RandomFields
(thanks to Martin Schlather)
BUGS
o
===============================
CHANGES IN geoR VERSION 1.6-31
===============================
NEW FEATURES
o
BUGS
o fix in proflik() which was passing wrong argument name for likfit() (lik.method/method.lik)
when computing the profile for the lambda parameter
o practicalRange() now returns Inf for power and linear correlation functions
o fixes in variofit() for linear correlation model
===============================
CHANGES IN geoR VERSION 1.6-30
===============================
NEW FEATURES
o variofit() and likfit() now extracts "cov.model" if a "variomodel" (or eyefit)
object is passed to "ini.cov.pars"
BUGS
o as.geodata() was handling units.m wrongly in case of duplicated locations. (Thanks Barry Rowligson)
===============================
CHANGES IN geoR VERSION 1.6-29
===============================
NEW FEATURES
o new functions jitterDupCoords(), jitterDupCoords.default(),
jitterDupCoords.geodata(), jitter2d(), allowing for jittering
(*Dup* for duplicated only) 2D coordinates
BUGS
o variog.model.env() now deals with "eyefit" objects. Runs for a object with a single model and issues an error if there is more than one model in the object, asking for rerun indicationg which one is the list to be used
===============================
CHANGES IN geoR VERSION 1.6-27/28
===============================
NEW FEATURES
o lines.variomodel.grf() with simpler argument list
o more general passing arguments mechanism in image.*(), countour.*(), persp.*()
BUGS
o variofit() was mistakenly printing "matern" while running
o points.geodata() now pass all plotting parameters correctly
o lines.variomodel.krige.bayes() was printing always the exponential model
now fixed
o more general passing arguments mechanism in image.*(), countour.*(), persp.*()
===============================
CHANGES IN geoR VERSION 1.6-26
===============================
NEW FEATURES
o
BUGS
o bug fix/change in prepare.graph.kriging() ordering values
as well as coordinates allowing for unusual/not standard kriging grids
as, for instance, imported from other systems (thanks to Olivier Briet)
o internal change in check for duplicated locations in as.geodata.default()
for better handling of memory
=================================
CHANGES IN geoR VERSION 1.6-24/25
=================================
NEW FEATURES
o practical() range replaces internally optimise() by uniroot() as the search algorithm
o logLik.likGRF() now returns object of the class "logLik"
which also allows usage of AIC
o new tutorial section on converting geoR <--> sp
exemple on converting kriging results
BUGS
o fix in the format of the $data component subset.geodata()
=================================
CHANGES IN geoR VERSION 1.6-23
=================================
NEW FEATURES
o check.parameter.values() rename for .check.geoRparameter.values()
BUGS
o fix in messages issued by likfit()
o data(ca20) fix of two points with wrong values for covariate "areas"
=================================
CHANGES IN geoR VERSION 1.6-22
=================================
NEW FEATURES
o improved handling of realisations in geodata objects by summary.geodata() and likfit()
o new data set "soja98"
o new data set "wrc"
o new data set "soil250"
o new argument "borders" in {image,persp,countour}.grf, and better handling of borders
provided in grf()
BUG FIXES
o fixes for subset.geodata() handle units.m and realisations
o several fixes preventing warnings on `R CMD check` regarding `no visible binding for global variable`
o fix in a bug in likfit() introduced in the previous version
o fix in the calculation of loglikBGCCM()
o fixes on krige.bayes() and hist.krige.bayes() to prevent warnings
o fixes in lines.variomodel() for computing nested variogramas
=================================
CHANGES IN geoR VERSION 1.6-21
=================================
NEW FEATURES
o likfit(), variofit(), eyefit() and likfitBGCCM() and the corresponding
print() and summary() functions now reports on the practical range
o likfit() now allow other than L-BFGS-B methods to be passed to optim()
o the latter requires argument name to be change from "method.lik"
"lik.method"
BUG FIXES
o fixes in likfitBGCCM() for allowing more flexible passing arguments tom optim()
o fix in all() to be OK with R-2.7-0
o print.BGCCM was ot printing kappa parameter values
o likfitBGCCM was not passing values of the kappa parameter
for the correlation functions
o fix in likfit() when checking valid values for kappa for the
powered exponential, stable e gencauchy correlation functions
o fix in documentation, correlation function equations, for cov.spatial()
=================================
CHANGES IN geoR VERSION 1.6-20
=================================
NEW FEATURES
o new function practicalRange() provinding values of practical ranges
for the covariance models inplemented in geoR
o internal variable ".geoR.cov.models" allowing for cleaner internal code
(in particular user in match.call(cov.model, choices = .geoR.cov.models)
o transparent internal changes in points.geodata() and
greater compatibility with legend() arguments to locate the legend
o small changes in documentation concerning legends
BUG FIXES
o fix in legends for points.geodata()
=================================
CHANGES IN geoR VERSION 1.6-19
=================================
NEW FEATURES
o internal changes in varcov.spatial() (and other) to speed up
matrix computations based on results from eigen() or svd()
o grf() now takes argument borders
o improvements in plot 1 dimentional results from krige.bayes()
(image/persp/contour.krige.bayes() )
BUG FIXES
o some minor/partial fixes to eliminate creation of objects not used
(rf. "visible bindings" -- still many left behind ...)
=================================
CHANGES IN geoR VERSION 1.6-18
=================================
NEW FEATURES
o plot.geodata() now adds by default a density estimation (from density())
and a rug plot (from rug()) to the histogram. The histogram now uses
prob=TRUE as default.
o grf() now return boders when argments "xlims" and "ylims" are used
BUG FIXES
o serious fix in points.geodata() which was ploting with worng sizes
in some cases
o small fixed in doc for liffitBGCCM() and geoR tutorial
on "Simulating bivariate proccess"
o fixes in image/countour/persp.kriging/krige.bayes()
in the reference to the environmento of atributes to allow
call from within other functions
o fix in subset.geodata() and related functions to deal with
"units.m" properly
=================================
CHANGES IN geoR VERSION 1.6-17
=================================
NEW FEATURES
o
BUG FIXES
o fix in subset() docs to allow pass in windows checks
=================================
CHANGES IN geoR VERSION 1.6-16
=================================
NEW FEATURES
o
BUG FIXES
o fix in grf() changing error() by stop()
o fixes in docs for subarea() and pars.limits()
=================================
CHANGES IN geoR VERSION 1.6-15
=================================
NEW FEATURES
o Changes in the DESCRIPTION file, now with:
LazyLoad: yes
LazyData: yes
o components argument in likfit() now defaults to TRUE
BUG FIXES
o fixes in fitted.likGRF() and resid.likGRF()
o "Suggests" in DESCRIPTION file now includes \pkg{tcltk}
o fix in points.geodata(), option pt.div="rank.proportional" was not working
o critical bug fix in sample.beta.posterior() which was reading wrong arguments
o internal fix in condition check for beta$iv in krige.bayes()
=================================
CHANGES IN geoR VERSION 1.6-14
=================================
NEW FEATURES
o new data set "kattegat"
o
o
BUG FIXES
o fix in docs for data(elevation)
o fix in print names of "other" elements in summary.geodata()
o further checks for valid fixed parameter values in likfit()
o fix in chack.parameter.values() called by likfit()
o
=================================
CHANGES IN geoR VERSION 1.6-13
=================================
NEW FEATURES
o
BUG FIXES
o adjusts in boxcox.fit()
o replaces of names.default() by getS3method("names", "default")
to adjust for Rdevel
=================================
CHANGES IN geoR VERSION 1.6-12
=================================
NEW FEATURES
o logLik.likGRF() to extract maximised log-likelihood
from an likfit() output
o fitted.likGRF() and residuals.likGRF() to extract fitted values
and residuals from an likfit() output
BUG FIXES
o parameters were returned in wrong place by likfitBCCGM()
affeting prediction variances
o change in tests for equality of lambda to 0, 1 and 0.5
in several functions
o fix in simulating anisotropic models in grf()
when calling GaussRF() from package RandomFields
=================================
CHANGES IN geoR VERSION 1.6-10/11
=================================
NEW FEATURES
BUG FIXES
o fixes in documentation and code to conform with
R devel
==============================
CHANGES IN geoR VERSION 1.6-9
==============================
NEW FEATURES
o new covariance function generalised cauchy
(gencauchy) now implemented
BUG FIXES
o plot.variogram() now passes arguments to the plot
function when argument 'ylim' is provided.
Better handling of '...'
o error message about object xpts removed from grf()
=======================================
CHANGES IN geoR VERSION 1.6-7 and 1.6-8
=======================================
NEW FEATURES
o grf() now call GaussRF() from RandomFileds
with nicer defaults
=======================================
CHANGES IN geoR VERSION 1.6-7 and 1.6-8
=======================================
NEW FEATURES
o new covariance function generalised cauchy
(gencauchy) now implemented
o grf() now call GaussRF() from RandomFileds
with nicer defaults
BUG FIXES
o fixes in docs for krige.bayes()
o fix in variofit() when using variogram cloud as input object
=============================
CHANGES IN geoR VERSION 1.6-6
=============================
NEW FEATURES
o as.geodata.default(), points.geodata() and
plot.geodata() now checks if all units.m > 0
BUG FIXES
o variog.model.env() when lambda != 1
o image.kriging(), image.krige.bayes()
contour.kriging(), contour.krige.bayes() now recognises
geodata$borders
o fix in .geoR_pip() when calling .check.borders()
o positions of optional elements in as.geodata.default()
o dependencies from splancs removed from image.krige.bayes()
o default upper limit limit for numerical optimisation in
likfit() changed to 50*max.dist (was 1000*max.dist before)
=============================
CHANGES IN geoR VERSION 1.6-5
=============================
BUG FIXES
o internal change in krige.bayes() to prevent
overflow weh exponentiating values in the computation
of the discrete probabilities (previous ha a wrong
plus/minus signal)
=============================
CHANGES IN geoR VERSION 1.6-4
=============================
NEW FEATURES
o substantial internal changes in several functions
(likfit/krige.bayes/krige.conv families)
to avoid inversion of the covariance matrix
and also avoiding several call to C code
(other changes in this direction still to be made)
==============================================
CHANGES IN geoR VERSION 1.6-1, 1.6-2 and 1.6-3
==============================================
NEW FEATURES
o krige.conv() and krige.bayes() now by default
recognises the element "borders" (if present) in the
geodata object
o new method predict.BGCCMfit to predict using the
bivariate Gaussian common component model.
o new function to fit the bivariate Gaussian
common component model. See likfitBGCCM()
and others related functions.
o new method names.geodata()
o new method subset.geodata()
o new function sample.geodata()
o new argument "units.m" for the functions
read.geodata() and as.geodata()
(relevant to geoRglm)
o plot.geodata() and points.geodata() now, by default
searches for an element "borders" in the geodata object
and pass it to the argument borders
o plot.geodata() and points.geodata() now, by default, divides
data object element "data" by "units.m".
This is meant to be used with objects to be analysed
using the package geoRglm.
o new function globalvar()
o geoR now depends on the package sp and is starting
moving towards sp standards and compatibility
o as.geodata() is now a generic S3 with previous set as default
method and methods for sp's class "SpatialPointsDataFrame"
and "geodata.frame"
o method as.data.frame.geodata() returning an object
of the class "geodata.frame"
o dup.geodata() copied as a method duplicated.geodata()
o dependency from splancs removed
(thanks Roger Bivand for the code)
o new internal functions: .geoR_inout()
.geoR_pip(), .check.borders(), .check.coords()
(thanks Roger Bivand for the code)
o new function boot.variog()
o image.kriging(), contour.kriging()
image.krige.bayes(), contour.krige.bayes()
now accepts `coords.data=TRUE`
BUGS
o fix in points.geodata() when using argument "cex.var"
combinet with pt.divide="data" our "rank"
o fixes is several internal calls to attach()
which were causing warnings messages
o exponential prior for phi in prior.control()
and plots nos add to 1
o geoR now depends on R-2.2.0
o fix in grf() when calling GaussRF() from RandomFields
- the mean was been added twice
o kriging variances < -1e12 are now rounded to zero
o fixes in contour.krige.bayes() regarding passing the
argument "add"
o fixes in print method for eyefit() and summary.eyefit()
==============================
CHANGES IN geoR VERSION 1.5-7
==============================
NEW FEATURES
o several functions meant for internal usage had their
names changed adding a "." in their names in order
to make them invisible for the ls() command
BUGS
o statistics.predictive() now tests for missing arguments
o mode calculation removed from backtransform.moments()
==============================
CHANGES IN geoR VERSION 1.5-6
==============================
NEW FEATURES
o classes assignments changed from class<-
to oldClass<-
o internal changes in the methods for image(), persp()
and contour() for better handling of the ... mechanism
including a new geoR-internal function ldots.set()
o new method contour.grf()
o new data sets "head" and "tce" from Kitanidis' book
BUGS
o fixes in locations.inside()
o changes in eyefit() and xvalid() such that xvalid()
can take an model provided by eyefit()
o fix in summary.geodata() when lambda != 1
==============================
CHANGES IN geoR VERSION 1.5-5
==============================
NEW FEATURES
o new argument "mean" in grf()
o changes in .First.lib() such it no longer depends
on 'utils' function packageDescription()
(following post by Brian Ripley and Adrian Baddeley on R-help)
o changes in krige.conv() and krige.bayes() to
recognise objects of the class "trend.spatial"
passed to the arguments trend.l and trend.d
BUGS
o DESCRIPTION file in 1.5-4 have date 2004 when it
should have been 2005
o fixes in some docs to allow latin1 encondings
==============================
CHANGES IN geoR VERSION 1.5-4
==============================
NEW FEATURES
o the function grf() has now new argument "RF"
and new option "RF" for the argument "method",
and accepts again "circular.embbeding".
The changes basically allows grf() to internally call
the function GaussRF() from the packages RandomFields.
o the name "stable" can also be used to specify a
correlation model and it is internally
changed to "powered.exponential"
o new argument "permute" in points.geodata()
o new argument "add.to.trend" in trend.spatial
o backtransform.moments() now returns also the modes of the
backtransformed distribution
o variog.model.env() now check com compatible trend sizes in
the objects passed to the arguments "obj.vario" and "model.pars"
o bits in the code of the type apply(x,1,mean) and similar replaced
by the faster functions: colSums(), rowSums(), colMeans(), rowMeans()
BUGS
o fixes and changes in the computation of the "power"
correlation model
o fix in the computation of the "wave" correlation model
in the C code
o fix in computation of the Gneiting correlation model which
now return the same values as in the package RandomFields
o fix in variofit() for cov.model="powered" and fix.kappa=F
o fix in reported loss function value for the best initial fit values
o summary.geodata() no lenger list "units.m"
as "other" element in the geodata object
o documentation for as.geodata() now call the data(topo)
from MASS
o yet another bug fix to prevent error in krige.conv()
when kriging with a model object with sigmasq=0 and phi=0
==============================
CHANGES IN geoR VERSION 1.5-3
==============================
NEW FEATURES
o points.geodata() has a new optional argument "cex.var" which can
receive a vector of values defining the size os the points
o output.control() now allows krige.conv() and krige.bayes()
to return the mean and variance of each conditional simulation
using the arguments "sim.means" and "sim.vars"
o new function nearloc()
o summary.geodata() now accepts the argument "lambda"
o print.eyefit() now prints the same as print.summary.eyfit()
o improvements im summary.geodata() when $realisations is available
including new argument "by.realisations"
o likfit() now has a default serch for initial values if
they are not provided and checks for unreasonable initial values
(not yet fully implemented)
o argument "ini" in variofit can now take an object of the class
"eyefit" or "variomodel", extracting the initial values from it
o points.geodata() can now take an scalar in the argument "pt.divide"
defining the number of quantiles
BUGS
o bug fix in cov.spatial() to prevent error in krige.conv()
when kriging with a model object with sigmasq=0 and phi=0
o fix in calls in backtranform.moments() to BCtransform()
o fix in grf(), krige.bayes() and krige.conv() to force initilisation
of the random seed when it is not available
o fix in variofit() for fix.kappa=F wich cov.model="powered"
o summary.geodata now returns an object of the class
"summary.geodata" in print.summary.geodata
o internal calls to "splancs"'s function inout() now always uses
the argument "bound=TRUE"
o fix in summary.eyefit()
o fix em geoR.messages (was not returning logical inside the functions)
o fix in points.geodata() for col="gray" with pt.divide="data.proportional"
or pt.divide="rank.proportional"
==============================
CHANGES IN geoR VERSION 1.5-2
==============================
NEW FEATURES
o summary method for "xvalid" object
BUGS
o in eyefit() when pressing the SAVE button
o likfit() was reporting wrong number of parameters for the non-spatial model
==============================
CHANGES IN geoR VERSION 1.5-1
==============================
NEW FEATURES
o grf() no longer implements the "circular embedding".
Users shoud use the package RandomFields for simulations with
larger number of locations.Future realeases
may contain a wrapper for RandomFields functions
o variofit() now has a default search for initial values
if they are not provided and checks for unreasonable initial values
o new internal function check.locations() used to test
the argument 'locations' in krige.conv(), ksline() and
krige.bayes()
o summary.geodata() now handles "realisations", providing (by default)
separate summaries for each of them
o new internal function check.cov.model() to check input parameters
So far used by lines.variomodel() and cov.spatial()
but may be used by other in future.
The ideia is to unify the checks to facilitate futere upgrades in
the package
o lines.variomodel() can now handle nested variograms
o modifications in "Suggests" and "Depends" in the DESCRIPTION file
o sliding bar for the kappa parameters in the tcl/tk interface
implemented in eyefit()
BUGS
o bug fix in maximum value of range (phi) in eyefit()
o plot.grf() now produces by default ylim compatible with both
empirical and theoretical parameters
o more changes in krige.bayes() to avoid problems computing