2012-12-18 Andreas Papritz * georob.cv.R (print.cv.georob, print.summary.cv.georob): return invisible(x) * georob.S3methods.R (print.georob, print.summary.georob): return invisible(x) * variogram.R (print.summary.sample.variogram, print.fitted.variogram) (print.summary.fitted.variogram): return invisible(x) 2012-12-18 Andreas Papritz * georob.S3methods.R (model.frame.georob, model.matrix.georob) (nobs.georob): new respective methods for class "georob" 2012-12-18 Andreas Papritz * variogram.R (plot.sample.variogram, plot.georob): correction of error in processing col and pch arguments 2012-12-22 Andreas Papritz * georob.S3methods.R (logLik.georob): computation of unrestricted loglikelihood (deviance.georob): new function 2013-01-19 Andreas Papritz * georob.predict.R (predict.georob): computation of lag vectors 2013-01-20 Andreas Papritz * NAMESPACE (--): changed imports for constrainedKriging and spatialCovariance * DESCRIPTION (--): changed imports for constrainedKriging and spatialCovariance * internal.functions.Rd (--): new help file for unexported functions 2013-04-23 Andreas Papritz * georob.exported.functions.R (georob, georob.control): new names for robustness weights * georob.predict.R (predict.georob): new names for robustness weights * georob.private.functions.R (compute.covariances, update.betahat.bhat, estimate.betahat.bhat, compute.estimating equations, georob.fit): new names for robustness weights * georob.S3methods.R (ranef.georob, rstandard.georob, summary.georob, print.summary.georob): new names for robustness weights * georob.cv.R (cv.georob): changes for parallelization on windows os 2013-04-29 Andreas Papritz * georob_example.R: correction of argument names in examples 2013-05-12 Andreas Papritz * variogram.R (plot.sample.variogram): correction of handling optional arguments 2013-05-14 Andreas Papritz * DESCRIPTION: attaching instead of importing functionS of package parallel * NAMESPACE: attaching instead of importing functionS of package parallel 2013-05-23 Andreas Papritz * georob.cv.R (cv.georob): correct handling of missing observations * georob.exported.functions.R (georob): improved way to handle missing observations and to construct model.frame * georob.predict.R (predict.georob): correct handling of missing observations * georob.S3methods.R (georob.residuals): new argument "terms" * georob.S3methods.R (ranef.georob, residuals.georob, rstandard.georob, deviance.georob): correct handling of missing observations * variogram.R (plot.georob): correct handling of missing observations 2013-05-24 Andreas Papritz * georob.cv.R (cv.georob): separate initial variogram parameters for each cross-validation set 2013-05-31 Andreas Papritz * georob.S3methods.R (ranef.georob, residuals.georob,rstandard.georob,deviance.georob): correct handling of missing observations * georob.S3methods.R (deviance.georob, ranef.georob, rstandard.georob, summary.georob): revised expansion of covariance matrices 2013-06-06 Andreas Papritz * georob.exported.function.R (georob, georob.control): handling fixed effects model matrices with rank < ncol(x) for robust estimation * georob.private.function.R (prepare.likelihood.calculations, compute.estimating.equations, negative.restr.loglikelihood, gradient.negative.restricted.loglikelihood, georob.fit) : solving estimating equations for xi * georob.S3methods.R ranef.georob, rstandard.georob) : solving estimating equations for xi * georob.private.function.R (estimate.xihat, prepare.likelihood.calculations, compute.estimating.equations, negative.restr.loglikelihood, gradient.negative.restricted.loglikelihood, georob.fit): handling fixed effects model matrices with rank < ncol(x) for robust estimation 2013-06-11 Andreas Papritz * georob.exported.function.R (georob): handling fixed effects model matrices with rank < ncol(x) for non-robust estimation * georob.private.function.R (estimate.xihat, prepare.likelihood.calculations, compute.estimating.equations, negative.restr.loglikelihood, gradient.negative.restricted.loglikelihood, georob.fit): handling fixed effects model matrices with rank < ncol(x) for non-robust estimation 2013-06-12 Andreas Papritz * georob.cv.R (all functions): substituting [["x"]] for $x in all lists * georob.exported.functions.R (all functions): substituting [["x"]] for $x in all lists * georob.lgnpp.R (all functions): substituting [["x"]] for $x in all lists * georob.predict.R (all functions): substituting [["x"]] for $x in all lists * georob.private.functions.R (all functions): substituting [["x"]] for $x in all lists * georob.S3methods.R (all functions): substituting [["x"]] for $x in all lists * variogram.R (all functions): substituting [["x"]] for $x in all lists 2013-07-02 Andreas Papritz * georob.exported.functions.R (georob, param.transf, fwd.transf, dfwd.transf, bwd.transf): new transformation of rotation angles * georob.private.functions.R (georob.fit, prepare.likelihood.calculations): new transformation of rotation angles * georob.S3methods.R (print.georob, summary.georob): new transformation of rotation angles * georob.cv.R (cv.georob): passing initial values of aniso and fit.aniso to georob via update 2013-07-05 Andreas Papritz * georob.cv.R (cv.georob): return "variogram.model" as part of 'fit' component 2013-07-09 Andreas Papritz * georob.private.functions.R (georob.fit): catching errors occuring when fitting anisotropic variogram models with default anisotropy parameters 2013-07-10 Andreas Papritz * georob.exported.functions.R (georob): computing robust initial variogram parameter estimates by minimizing sum of squared estimating equations * georob.private.functions.R (georob.fit, compute.estimating.equations): computing robust initial variogram parameter estimates by minimizing sum of squared estimating equations 2013-07-12 Andreas Papritz * georob.exported.functions.R (georob, georob.control, bbsolve.control): solving estimating equations by BBsolve{BB} (in addition to nleqlsv) * georob.private.functions.R (compute.estimating.equations, compute.expanded.estimating.equations, estimating.eqations.xihat, estimate.xihat, georob.fit, gradient.negative.restricted.loglikelihood, negative.restr.loglikelihood, prepare.likelihood.calculations): solving estimating equations by BBsolve{BB} (in addition to nleqlsv) 2013-09-06 Andreas Papritz * georob.exported.functions.R (georob, georob.control, bbsolve.control): code for solving estimating equations by BBsolve{BB} commented out (released to CRAN as version 0.1-1) * georob.private.functions.R (compute.estimating.equations, compute.expanded.estimating.equations, estimating.eqations.xihat, estimate.xihat, georob.fit, gradient.negative.restricted.loglikelihood, negative.restr.loglikelihood, prepare.likelihood.calculations): code for solving estimating equations by BBsolve{BB} commented out (released to CRAN as version 0.1-1) 2014-01-23 Andreas Papritz * georob.private.functions.R (prepare.likelihood.calculations): correct comparison of trial parameter values with safe.param 2014-02-06 Andreas Papritz * georob.exported.functions (georob): correcting error that occurred for rank-deficient design matrices * georob.private.functions.R (gerorob.fit): correcting error that occurred for rank-deficient design matrices 2014-02-11 Andreas Papritz * georob.predict.R (predict.georob): suppressing warnings caused by use of version 2 function of package RandomFields * georob.private.functions.R (gcr, compute.semivariance): suppressing warnings caused by use of version 2 function of package RandomFields 2014-02-19 Andreas Papritz * georob.exported.functions (georob): changes for now exported function robMD{robustbase}, correcting error when model contains offset * georob.private.functions.R (gerorob.fit): correcting error when model contains offset * georob.predict.R (predict.georob): correcting error when model contains offset * georob.S3methods.R (waldtest.georob): handling verbose output when re-fitting model 2014-02-21 Andreas Papritz * georob.cv.R (cv.georob): changes for dealing with problem when factor are very unbalanced 2014-02-27 Andreas Papritz * georob.S3methods.R (deviance.georob): computing 'pseudo' deviance for robustly fitted models 2014-03-01 Andreas Papritz * georob.S3methods.R (add1.georob, drop1.georob, extractAIC.georob, step, step.default, step.georob): functions for stepwise selection of fixed-effects terms 2014-03-05 Andreas Papritz * georob.private.functions.R (compute.semivariance, gar): changes for RandomFields version 3 * georob.predict.R (predict.georobcd R. ): changes for RandomFields version 3 * georob.S3methods.R (add1.georob, drop1.georob, step.georob): changes in functions for stepwise selection of fixed-effects terms * georob.cv.R (cv.georob): catching attempt to re-estimate variogram parameters when all parameters in object are fixed 2014-03-12 Andreas Papritz * georob.S3methods.R (add1.georob, deviance.georob, drop1.georob, extractAIC.georob, logLik.georob, step.georob): changes in functions for parallelized stepwise selection of fixed-effects terms 2014-04-23 Andreas Papritz * georob.predict.R (predict.georob): correcting error when newdata contains data locations 2014-04-23 Andreas Papritz * georob.S3methods.R (add1.georob, drop1.georob, step.georob): changes in functions for reducing memory demand 2014-05-08 Andreas Papritz * variogram.R (plot.georob,lines.georob): changes for plotting covariances and correlations 2014-05-15 Andreas Papritz * georob.cv.R (cv.georob): changes for version 3 of RandomFields * georob.exported.functions.R (georob, georob.control, param.transf, param.names, param.bounds): changes for version 3 of RandomFields * georob.private.functions.R (gcr, prepare.likelihood.calculations, dcorr.dparam, compute.semivariance): changes for version 3 of RandomFields * georob.S3methods.R (waldtest.georob, add1.georob, drop1.georob): changes for version 3 of RandomFields * variogram.R (fit.variogram.model): changes for version 3 of RandomFields 2014-05-15 Andreas Papritz * georob.exported.functions.R (georob) changes for selecting intitial.param and initial.method 2014-05-28 Andreas Papritz * georob.cv.R (georob.cv) catching error when all variogram parameters are fixed * georob.exported.functions.R (georob, param.bounds, param.names) minor changes in arguments * georob.predict.R (predict.georob) further changes for version 3 of RandomFields * georob.private.functions.R (georob.fit) change in check for initial variogram parameter values * variogram.R (fit.variogram.model) minor changes in arguments 2014-06-02 Andreas Papritz * georob.exported.functions.R (georob) partial matching of names of variogram parameters * georob.exported.functions.R (georob.control) new default value for argument irwls.reltol 2014-08-18 Andreas Papritz * georob.cv.R (georob) parallelized matrix multiplication * georob.exported.functions.R (georob, georob.control, nleqslv.control, optim.control, parallel.control, pmm, rq.control) parallelized matrix multiplication, ML estimation * georob.private.functions.R (compute.covariances, compute.estimating.equations, estimating.eqations.xihat, estimate.xihat, f.aux.eeq, f.aux.gradient.nll, f.aux.Q, f.aux.Valpha, f.stop.cluster, gcr, gradient.negative.restricted.loglikelihood, negative.restr.loglikelihood, prepare.likelihood.calculations, georob.fit) parallelized matrix multiplication, ML estimation * georob.predict.R (predict.georob, predict.georob.control, cv.georob) parallelized matrix multiplication, renamed and restructured arguments * georob.S3methods.R (waldtest.georob, add1.georob, drop1.georob. step.georob) improved computational performance 2014-08-19 Andreas Papritz * georob.private.functions.R (compute.covariances) correcting error in computation of covariance of regression residuals * georob.S3methods.R (rstandard.georob) correcting error when computing covariance of residuals 2014-08-26 Andreas Papritz * georob.exported.functions.R (georob) changes for returning and printing ml.method * georob.S3methods.R (summary.georob, print.summary.georob) changes for returning and printing ml.method * georob.S3methods.R (step.georob) correcting error for stepwise covariate selection with non-fixed variogram parameters 2015-04-03 Andreas Papritz * georob.private.functions.R (compute.covariances) correcting error in computing result.new[["cov.bhat"]] for full.cov.bhat == FALSE * georob.private.functions.R (f.aux.eeq) changes to optimize computing effort * georob.predict.R (predict.georob) changes to optimize computing effort 2015-04-13 Andreas Papritz * georob.cv.R (cv.georob) minor changes if models are not re-estimated; scatterplot smoothing in plots * georob.cv.R (plot.cv.georob) smoothing of scatter plots * georob.exported.functions.R (georob.control, param.transf, fwd.transf, dfwd.transf, bwd.transf) extended variogram parameter transformations * georob.exported.functions.R (pmm) small changes in f.aux * georob.private.functions.R (compute.estimating.equations) renamed to estimating.equations.thetahat * georob.private.functions.R (prepare.likelihood.calculations,georob.fit) extended variogram parameter transformations 2015-03-16 Andreas Papritz * georob.S3methods.R (profile, proflik.georob, profile.likfit) function for computing profile likelihood * georob.S3methods.R (residuals.georob, rstandard.georob, ) residuals of huberized observations * georob.S3methods.R (logLik, deviance) computing 'pseudo' likelihood for REML case * georob.exported.functions.R (georob) own function for psi * georob.private.functions.R (estimating.equations.thetahat, georob.fit, gradient.negative.restricted.loglikelihood, negative.restr.loglikelihood, prepare.likelihood.calculations) elimination of unused variables * georob.private.functions.R (f.psi.function) own function for psi 2015-04-07 Andreas Papritz * georob.exported.functions.R (param.transf, fwd.transf, dfwd.transf, bwd.transf) changes in transformation of anisotropy parameters * georob.private.functions.R (georob.fit, prepare.likelihood.calculations) changes in transformation of anisotropy parameters * georob.S3methods.R (summary.georob,) changes in transformation of anisotropy parameters * georob.S3methods.R (waldtest.georob) change of default for test statistic * variogram.R (sample.variogram, fit.variogram.model, summary.fitted.variogram, print.summary.fitted.variogram) correcting error when computing directional variograms 2015-06-30 Andreas Papritz * georob.exported.functions.R (georob, control.georob, control.nleqslv, control.optim, control.pmm, control.rq) functions and arguments renamed * georob.private.functions.R (compute.covariances) changes for improving efficiency * georob.private.functions.R (update.xihat) solving linear system of equation by cholesky decomposition * georob.private.functions.R (estimate.xihat) new method to determine convergence * predict.georob.R (crpsnorm, crpspd.resp.rob, ppd.resp.rob, predict.georob, qpd.resp.rob, var.pd.resp.rob) new functions and modifications for robust prediction of response * predict.georob.R (control.predict.georob) function renamed * georob.lgnpp.R (lgnpp) modifications for missing components 'lower' and 'upper' * georob.cv.R (cv.georob, plot.cv.georob, summary.cv.georob, validate.predictions) modifications for robust prediction of response 2015-07-17 Andreas Papritz * georob.cv.R (cv.georob) excluding blocks of observations * georob.exported.functions.R (georob, control.georob) change of control of computation of hessian for Gaussian (RE)ML, changes for singular design matrices, nlminb optimizer added (new function control.nlminb) * georob.private.functions.R (covariances.fixed.random.effects, estimate.zhat, update.zhat, estimating.equations.zhat, f.aux.gcr, f.aux.gamma, likelihood.calculations, f.aux.Qstar, negative.loglikelihood, gradient.negative.loglikelihood, f.aux.gradient.nll, f.aux.gradient.npll, f.reparam.fwd, f.reparam.bkw, partial.derivatives.variogram, f.aux.RSS, georob.fit) functions renamed, Gaussian (RE)ML estimation for reparametrized variogram, new functions (f.aux.gradient.npll, f.reparam.fwd, f.reparam.bkw, f.aux.RSS) * georob.private.functions.R (estimating.equantions.thetahat, f.aux.eeq) new function interface, improved efficiency 2015-07-22 Andreas Papritz * georob.cv.R (cv.georob) inactivation of modifications for robust prediction of response * predict.georob.R (predict.georob) inactivation of modifications for robust prediction of response 2015-07-22 Andreas Papritz * georob.S3methods.R (print.summary.georob) change in number of printed digits 2015-07-23 Andreas Papritz * georob.S3methods.R (add1.georob, drop1.georob, step.georob) changes for dropping terms from model with fixed variogram parameters * georob.private.functions.R (f.aux.gcr, likelihood.calculations, estimating.equations.thetahat, gradient.negative.loglikelihood, georob.fit, f.aux.Valphaxi) Valpha (correlation matrix without spatial nugget) no longer stored but computed from Valphaxi when needed 2015-07-27 Andreas Papritz * georob.private.functions.R (estimating.equations.thetahat, gradient.negative.loglikelihood, negative.loglikelihood, f.aux.eeq, f.aux.gradient.nll, f.aux.gradient.npll) * georob.exported.functions.R (control.georob, profilelogLik) new argument reparam for controlling variance estimation for Gaussian (RE)ML 2015-07-27 Andreas Papritz * georob.private.functions.R (estimating.equations.thetahat, gradient.negative.loglikelihood) changes for elimination of parallelized computation of gradient or estimating equations * georob.exported.functions.R (control.parallel) changes for elimination of parallelized computation of gradient or estimating equations 2015-08-19 Andreas Papritz * georob.private.functions.R (covariances.fixed.random.effects, estimating.equations.thetahat, georob.fit, f.psi.function) changes for computing covariances under long-tailed distribution of epsilon * georob.exported.functions.R (georob, control.georob) changes for computing covariances under long-tailed distribution of epsilon * georob.private.functions.R (rstandard.georob) correcting error when computing covariances of residuals 2015-08-27 Andreas Papritz * georob.predict.R (predict.georob) correcting error in processing output 2015-08-28 Andreas Papritz * georob.cv.R (cv.georob) computation of hessian suppressed * georob.S3methods.R (add1.georob, drop1.georob, waldtest.georob) computation of hessian suppressed; elimination of argument "fixed" from wildest.georob * georob.exported.functions.R (georob, control.georob) control arguments newly organized * georob.private.functions.R (georob.fit) correcting error when using georob.object 2015-12-02 Andreas Papritz * georob.cv.R (cv.georob) catching errors occurring during parallel model fits * georob.cv.R (validate.predictions) checking whether mandatory arguments were provided * georob.exported.functions.R (default.aniso, default.fit.param, default.fit.aniso, georob, control.georob) new way to control which variogram parameters are fitted * georob.predict.R (predict.georob) catching errors occurring during parallel computations * variogram.R (sample.variogram, sample.variogram.default, sample.variogram.formula, sample.variogram.gerob) generic and methods for computing sample variogram * variogram.R (fit.variogram.model) checking mandatory arguments, issuing warnings * variogram.R (plot.georob) changes for Tukey-Anscombe, QQnorm plots and for plotting variograms * georob.private.functions.R (f.aux.gcr,estimating.equations.theta, negative.loglikelihood, gradient.negative.loglikelihood, georob.fit) issuing warnings 2015-12-02 Andreas Papritz * variogram.R (fit.variogram.model) correcting error in setting default values for fit.param 2015-12-25 Andreas Papritz * variogram.R (plot.georob) changes for residual diagnostic plots 2015-12-29 Andreas Papritz * georob.cv.R (plot.cv.georob) minor changes for adding plots to existing diagnostics graphics 2016-05-22 Andreas Papritz * georob.S3methods.R (add1.georob, drop1.georob, step.georob) correction of error and extended functionality for refitting variorum parameters or keeping them fixed, changes for better computational efficiency 2016-05-27 Andreas Papritz * georob.S3methods.R (add1.georob), drop1.georob) diagnostics about convergence 2016-05-27 Andreas Papritz * georob.cv.R (cv.georob) allow recursive calls of mclapply 2016-07-15 Andreas Papritz * georob.S3methods (waldtest.georob) optimization * georob.exported.functions.R (profilelogLik) optimization* georob.exported.functions.R (profilelogLik) optimization * georob.exported.functions.R (gearbox) allowing use of lmrob for computing initial fixed effects for rank-deficient model matrix 2016-07-21 Andreas Papritz * georob.cv.R (cv.georob) changes for parallel computations * georob.exported.functions.R (georob, pmm, control.pcmp, profilelogLik) changes for parallel computations * georob.predict.R (control.predict.georob, predict.georob, f.robust.uk) changes for parallel computations * georob.private.functions.R (covariances.fixed.random.effects, estimate.zhat, f.aux.gcr, likelihood.calculations, estimating.equations.theta, negative.loglikelihood, gradient.negative.loglikelihood, georob.fit, f.aux.eeq, f.aux.gradient.nll, f.aux.gradient.npll, f.aux.Qstar, f.aux.Valphaxi) changes for parallel computations * georob.S3methods.R (ranef.georob, add1.georob, drop1.georob, step.georob) changes for parallel computations * georob.S3methods.R (fixef.georob) correcting wrong component name 2016-07-22 Andreas Papritz * georob.predict.R (predict.georob) SpatialPoints, SpatialPixels and SpatialGrid as newdata objects * georob.private.functions.R (georob.fit) corrected names of gradient components 2016-07-25 Andreas Papritz * cv.georob.R (plot.cv.georob) added line color and type for scatterplot smooths 2016-08-22 Andreas Papritz * cv.georob.R (cv.georob) correcting error when computing standard errors of cv kriging predictions * cv.georob.R (cv.georob) changes for nested variogram models * georob.exported.functions.R (georob, control.georob, profilelogLik) changes for nested variogram models * georob.exported.functions.R (bwd,transf) corrections for logitx if argument is +/-Inf * georob.lgnpp.R (lgnpp) changes for nested variogram models * georob.predict.R (predict.georob, f.robust.uk) changes for nested variogram models * georob.private.functions.R (f.aux.gcr, likelihood.calculations, partial.derivatives.variogram, estimating.equations.theta, negative.loglikelihood, gradient.negative.loglikelihood, georob.fit, f.aux.eeq, f.aux.gradient.nll, f.aux.gradient.npll, f.aux.Valphaxi, f.reparam.fwd, f.reparam.bwd, f.aux.tf.param.fwd, f.aux.print.gradient, f.call.set_x_to_value, f.call.set_allfitxxx_to_false, f.call.set_onefitxxx_to_value, f.call.set_allxxx_to_fitted_values, f.call.set_onexxx_to_value) changes for nested variogram models * georob.S3methods.R (print.georob, ranef.georob, rstandard.georob, summary.georob, print.summary.georob, waldtest.georob, logLik.georob, deviance.georob, extractAIC.georob, f.aux.add1.drop1, add1.georob, drop1.georob, step.georob) changes for nested variogram models * variogram.R (fit.variogram.model, print.fitted.variogram, summary.fitted.variogram, print.summary.fitted.variogram, plot.georob, lines.georob) changes for nested variogram models 2016-08-24 Andreas Papritz * georob.exported.functions.R (control.georob) change of default for argument error.family.cov.residuals * variogram.R (plot.sample.variogram) new argument lty 2016-09-08 Andreas Papritz * georob.private.functions.R (likelihood.calculations) correcting error for printing trial parameter values if they exceed safe bounds 2016-11-29 Andreas Papritz * georob.private.functions.R (likelihood.calculations,georob.fit, partial.derivatives.variogram) correcting error in 3d rotation matrix for geometrically anisotropic variograms * variogram.R (fit.variogram.model) correcting error in 3d rotation matrix for geometrically anisotropic variograms 2016-11-28 Andreas Papritz * georob.private.functions.R (georob.fit) checking ml.method and presence of intercept for intrinsic models * georob.predict.R (predict.georob,f.robust.uk) correcting error when computing predictions for intrinsic variograms 2016-11-29 Andreas Papritz * variogram.R (fit.variogram.model) correcting error in 3d rotation matrix for geometrically anisotropic variograms 2017-02-24 Andreas Papritz * georob.private.functions.R (georob.fit) warning for negative definite hessian 2017-05-09 Andreas Papritz * georob.exported.functions.R (georob, control.rq) small changes and error correction in interface to rq() for computing robust initial values 2017-07-26 Andreas Papritz * georob.private.functions.R (georob.fit) changes to allow non-zero snugget if there are no replicated observations 2017-10-20 Andreas Papritz * georob.S3methods.R (fixef.georob) new functions coef.georob and print.coef.georob 2017-10-24 Andreas Papritz * georob.predict.R (predict.georob) error message if names of coordinates in object and newdata are not the same 2018-01-05 Andreas Papritz * georob.exported.functions.R (pmm, profilelogLik) improved memory management in parallel computations * georob.cv.R (cv.georob) improved memory management in parallel computations * georob.predict.R (predict.georob) improved memory management in parallel computations * georob.private.functions.R (f.aux.gcr) improved memory management in parallel computations * georob.S3methods.R (step.georob, add1.georob, drop1.georob) improved memory management in parallel computations 2018-01-17 Andreas Papritz * georob.private.functions.R (f.call.set_allxxx_to_fitted_values) variogram.model is also updated 2018-01-24 Andreas Papritz * georob.predict.R (predict.georob) new optional arguments for specifying a variogram model different from the one contained in object. * georob.simulation.R (condsim.georob, control.condsim.georob) new functions for (un)conditional simulation 2018-08-27 Andreas Papritz * georob.S3methods.R (add1.georob, drop1.georob, step.georob) elimination of data argument 2018-11-25 Andreas Papritz * georob.simulation.R (f.aux.sim.1) elimination of grid.nodes argument 2019-03-29 Andreas Papritz * georob.private.functions.R (f.aux.gcr) call to RFvariogram{RandomFields, version 3.1} replaced by call to RFfctn{RandomFields, version 3.3} * georob.simulation.R (condsim) conditioning data is passed as SpatialPointsDataFrame to RFsimulate 2019-04-07 Andreas Papritz * georob.private.functions.R (f.aux.gcr) correction of error when computing semivariances for anisotropic variogram models (introduced on 2019-03-29) * variogram.R (control.fit.variogram.model) new function for providing sensible defaults to argument control of fit.variogram.model * variogram.R (fit.variogram.model) new control argument and possibility to choose between optim and nlminb for non-linear least squares 2019-05-25 Andreas Papritz * georob.S3methods.R (summary.georob) correction of error when printing confidence intervals of variogram parameters * georob.simulation.R (condsim) correction of error that occurred when preparing output consisting of a single realization 2019-10-04 Andreas Papritz * NAMESPACE correction of dependencies * DESCRIPTION correction of dependencies and licence information 2019-10-22 Andreas Papritz * georob.S3methods.R (summary.georob) terms component taken from georob object 2019-12-18 Andreas Papritz * georob.private.functions.R (f.diag) change in use of class() in and switch() * georob.simulation.R (condsim, control.condsim) sanity checks of specified function arguments and if() * georob.simulation.R (condsim) correction of errors when processing output from RFsimulate 2020-02-05 Andreas Papritz * DESCRIPTION deleting suggested orphaned package geoR * georob_vignette.Rnw changes for conditional use of object of suggest packages gstat and multcomp * wolfcamp data set included 2020-02-14 Andreas Papritz * all codes files renamed * georob_cv.R (cv.georob, plot.cv.georob, summary.cv.georob, validate.predictions) sanity checks of arguments and for if() and switch() * georob_exported_functions.R (georob, control.georob, bwd.transf, control.rq, control.nleqslv, control.optim, control.nlminb, control.pcmp, compress, expand, param.names, param.bounds, default.fit.param, default.fit.aniso, default.aniso, profilelogLik) sanity checks of arguments and for if() and switch() * georob_lgnpp.R (lgnpp) sanity checks of arguments and for if() and switch() * georob_predict.R (control.predict.georob, predict.georob, check.newdata) sanity checks of arguments and for if() and switch() * georob_S3methods.R (ranef.georob, summary.georob, waldtest.georob, logLik.georob, deviance.georob, extractAIC.georob, add1.georob, drop1.georob, step.georob) sanity checks of arguments and for if() and switch() * georob_simulation.R (control.condsim, condsim) sanity checks of arguments and for if() and switch() * georob_variogram.R (sample.variogram.default, plot.sample.variogram, control.fit.variogram.model, fit.variogram.model, summary.fitted.variogram, plot.georob, lines.georob) sanity checks of arguments and for if() and switch() * new data sets: wolfcamp, elevation 2020-03-27 Andreas Papritz * georob_exported_functions.R (georob) correction of error in sanity checks of arguments * georob_variogram.R (control.fit.variogram.model, fit.variogram.model, summary.fitted.variogram) computing Hessian of untransformed parameters * georob_private_functions.R (georob.fit) computing Hessian of untransformed parameters 2021-06-02 Andreas Papritz * georob_private_functions.R (georob.fit) correction of error in check of initial values of anisotropy parameters 2022-12-09 Andreas Papritz * validate.predictions.Rd: changes for KaTeX * predict.georob.Rd: changes for KaTeX * plot.georob.Rd: changes for KaTeX * param.defaults.Rd: changes for KaTeX * lgnpp.Rd: changes for KaTeX * georobSimulation.Rd: changes for KaTeX * georobS3methods.Rd: changes for KaTeX * georobPackage.Rd: changes for KaTeX * georobObject.Rd: changes for KaTeX * georobModelBuilding.Rd: changes for KaTeX * georob.Rd: changes for KaTeX * fit.variogram.model.Rd: changes for KaTeX * cv.georob.Rd: changes for KaTeX * control.georob.Rd: changes for KaTeX 2022-12-10 Andreas Papritz * new file inst/NEWS.Rd 2023-01-28 Andreas Papritz * georob_predict.R (georob.predict, simple.kriging.weights) RFoptions changed for RandomFieldsMLV3010 * georob_private_functions.R (georob.fit, f.aux.gcr) RFoptions changed for RandomFieldsMLV3010 * georob_S3methods.R (add1.georob, drop1.georob, step.georob) extracting data from object and using data in update * georob_simulation.R (condsim) RFoptions changed for RandomFieldsMLV3010, forcing socket clusters for parallelized computations 2023-11-17 Andreas Papritz * georob_exported_functions.R (param.bounds) corrections of errors in parameter bounds for models RMlgd and RMdampedcos * georob_exported_functions.R (georob.predict) elimination of calls to function RFoptions{RandomFields} * georob_private.functions.R (f.aux.gcr) elimination of calls to function RFoptions{RandomFields} * georob_private.functions.R (f.aux.gcr) substitution of function RFfctn{RandomFields} by new function generalized.correlation 2023-12-20/21 Andreas Papritz * georob_cv.R (cv.georob, plot.cv.georob) added on.exit(options(old.opt)), replaced makeCluster by makePSOCKcluster, class queries by inherits() * georob_exported_functions.R (pmm) added on.exit(options(old.opt)), deleted options(error = NULL) * georob_exported_functions.R (param.bounds) correction of upper bounds of alpha for RMfbm and RMgenfbm * georob_exported_functions.R (profilelogLik) checking class by inherits(), added on.exit(options(old.opt)), replaced makeCluster by makePSOCKcluster, replacement of identical(class(...), ...) by inherits(..., ...) * georob_lgnpp.R (lgnpp) checking class by inherits() * georob_predict.R (predict.georob, f.robust.uk, simple.kriging.weights) checking class by inherits(), added on.exit(options(old.opt)), replaced makeCluster by makePSOCKcluster, replacement of identical(class(...), ...) by inherits(..., ...) * georob_private_functions.R (covariances.fixed.random.effects, update.zhat, estimate.zhat, f.aux.gcr, georob.fit, f.aux.Qstar, f.aux.Valphaxi, f.stop.cluster, f.call.set_allfitxxx_to_false, f.call.set_onefitxxx_to_value, f.call.set_allxxx_to_fitted_values, f.call.set_onexxx_to_value) added on.exit(options(old.opt)), deleted options(error = NULL), replacement of identical(class(...), ...) by inherits(..., ...) * georob_S3methods.R (ranef.georob, resid.georob, rstandard.georob, summary.georob, deviance.georob, step.georob) replacement of identical(class(...), ...) by inherits(..., ...) * georob_S3methods.R (add1.georob, drop1.georob) added on.exit(options(old.opt)), replaced makeCluster by makePSOCKcluster, replacement of identical(class(...), ...) by inherits(..., ...), * georob_simulation.R (condsim) checking class by inherits(), added on.exit(options(old.opt)), deleted options(error = NULL), replacement of identical(class(...), ...) by inherits(..., ...) * georob_variogram.R (fit.variogram.model, summary.fitted.variogram) checking class by inherits() * georob_variogram.R (lines.georob) added on.exit(par(old.par)), replacement of identical(class(...), ...) by inherits(..., ...) 2024-01-21 Andreas Papritz * georob_exported_functions.R (control.pcmp) changed default for allow.recursive * georob_predict.R (f.robust.uk, simple.kriging.weights) more efficient calculation of lag.vectors for anisotropic variograms * georob_private_functions.R (georob.fit) more efficient calculation of lag.vectors for anisotropic variograms * georob_simulation.R (control.condsim) new arguments ce.method, cr.grid.expansion, mmax * georob_simulation.R (condsim) replacement of identical(class(...), ...) by inherits(..., ...), new function sim.chol.decomp for simulation with exact coordinates, new function sim.circulant.embedding for simulation on rectangular grid * georob_variogram.R (sample.variogram.default) more efficient calculation of lag.vectors for anisotropic variograms * DESCRIPTION eliminated import of package RandomFields * NAMESPACE eliminated import of package RandomFields, revised list of unexported, undocumented functions * reexportedfun.Rd new help page for re-exported functions that are imported from other packages * gencorr.Rd new help page for unexported function gencorr with concise description of implemented variogram models 2024-01-24 Andreas Papritz * georob_S3methods.R (summary.georob, print.summary.georob) compress and expand correlation matrices georob_private_functions.R (getCall.georob) elimination of this function 2024-02-01 Andreas Papritz * georob_cv.R (cv.georob) saving SOCKcluster.RData to tempdir() * georob_exported_functions.R (profilelogLik) saving SOCKcluster.RData to tempdir() * georob_exported_functions.R (gencorr) moved to code file for exported functions * georob_predict.R (predict.georob, simple.kriging.weights) saving SOCKcluster.RData to tempdir() * georob_private_functions.R (f.stop.cluster) new argument fname * georob_S3methods.R (add1.georob, drop1.georob) saving SOCKcluster.RData to tempdir() * georob_simulation.R (sim.circulant.embedding) minor changes in handling negative eigenvalues of base matrix, setting random seeds for parallel processing, saving SOCKcluster.RData to tempdir() * various Rd files: complented \value section and fixes to comply with CRAN policies 2024-02-09 Andreas Papritz * news.RD eliminated lonely item * georob_predict.R (predict.georob) correction of error in processing output * georob_variogram.R (plot.sample.variogram) returns now NULL instead of object x * georob_vignette.Rnw former section 5.3 moved to section 2.1, small changes in text, added doi to references * various Rd files substituted all \donttest{} statements in lengthy computations by interactive() which executes lenghty examples only in interactive sessions 2024-02-21 Andreas Papritz * georob_cv.R (cv.georob) conditionally prevent recursive parallelizations in pmm or f.aux.gcr * georob_exported_functions.R (georob) added sfStop() * georob_exported_functions.R (profilelogLik) conditionally prevent recursive parallelizations in pmm or f.aux.gcr * georob_predict.R (predict.georob, f.robust.uk, simple.kriging.weights) added sfStop() * georob_private_functions.R (f.call.prevent_recursive_parallelization) new function * georob_S3methods.R (ranef.georob, rstandard.georob) added sfStop() * georob_S3methods.R (add1.georob, drop1.georob) conditionally prevent recursive parallelizations in pmm or f.aux.gcr * georob_simulation.R (condsim, sim.chol.decomp, sim.circulant.embedding) added sfStop() 2024-03-08 Andreas Papritz * code file georob_private_functions.R replaced by 4 new code files georob_private_further_functions.R (covariances.fixed.random.effects, estimate.zhat, estimating.equations.theta, estimating.equations.z, f.aux.Qstar, f.aux.RSS, f.aux.eeq, f.aux.gradient.nll, f.aux.gradient.npll, f.aux.print.gradient, f.aux.tf.param.fwd, f.call.prevent_recursive_parallelization, f.call.set_allfitxxx_to_false, f.call.set_allxxx_to_fitted_values, f.call.set_onefitxxx_to_value, f.call.set_onexxx_to_value, f.call.set_x_to_value, f.call.set_x_to_value_in_fun, f.diag, f.reparam.bwd, f.reparam.fwd, f.stop.cluster, gradient.negative.loglikelihood, likelihood.calculations, negative.loglikelihood, update_zhat), georob_private_generalized_covariances.R (f.aux.Valphaxi, f.aux.gcr, partial.derivatives.variogram), georob_private_georob_fit.R (georob.fit) and georob_private_psi_functions_etc.R (f.psi.function)