version 0.3-17

cran · Feb 4, 2024 · 05a3c57 · 05a3c57
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diff --git a/ChangeLog b/ChangeLog
@@ -600,3 +600,90 @@ processing col and pch arguments
 2021-06-02 Andreas Papritz  <papritz@env.ethz.ch>
 
 * georob_private_functions.R (georob.fit) correction of error in check of initial values of anisotropy parameters
+
+
+2022-12-09 Andreas Papritz  <papritz@retired.ethz.ch>
+
+* 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  <papritz@retired.ethz.ch>
+
+* new file inst/NEWS.Rd
+
+
+2023-01-28 Andreas Papritz  <papritz@retired.ethz.ch>
+
+* 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  <papritz@retired.ethz.ch>
+
+* 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  <papritz@retired.ethz.ch>
+
+* 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  <papritz@retired.ethz.ch>
+
+* 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  <papritz@retired.ethz.ch>
+
+* 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  <papritz@retired.ethz.ch>
+
+* 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
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,31 +1,19 @@
 Package: georob
+Version: 0.3-17
+Date: 2024-02-01
 Type: Package
 Title: Robust Geostatistical Analysis of Spatial Data
-Version: 0.3-14
-Date: 2021-06-04
-Authors@R: c(
-  person( "Andreas", "Papritz", role = c( "cre", "aut" ), 
-          email =  "andreas.papritz@env.ethz.ch" ),
-  person( "Cornelia", "Schwierz", role = "ctb" ))
-Depends: R(>= 2.14.0), graphics, parallel, snowfall, sp(>= 0.9-60),
-        stats, utils
-Imports: abind, constrainedKriging(>= 0.2-1), fields, lmtest, methods,
-        nlme, nleqslv, quantreg, RandomFields(>= 3.3.6), robustbase(>=
-        0.90-2)
+Authors@R: c(person("Andreas", "Papritz", role = c("aut", "cre"), email =  "papritz@retired.ethz.ch" ))
+Description: Provides functions for efficiently fitting linear models with spatially correlated errors by robust (Kuensch et al. (2011) <doi:10.3929/ethz-a-009900710>) and Gaussian (Harville (1977) <doi:10.1080/01621459.1977.10480998>) (Restricted) Maximum Likelihood and for computing robust and customary point and block external-drift Kriging predictions (Cressie (1993) <doi:10.1002/9781119115151>), along with utility functions for variogram modelling in ad hoc geostatistical analyses, model building, model evaluation by cross-validation, (conditional) simulation of Gaussian processes (Davies and Bryant (2013) <doi:10.18637/jss.v055.i09>), unbiased back-transformation of Kriging predictions of log-transformed data (Cressie (2006) <doi:10.1007/s11004-005-9022-8>).
+Depends: R(>= 2.14), sp(>= 0.9-60)
+Imports: abind, constrainedKriging(>= 0.2-7), fields, graphics, lmtest,
+        methods, nlme, nleqslv, parallel, quantreg, robustbase(>=
+        0.90-2), snowfall, stats, utils
 Suggests: gstat, multcomp, lattice
-Description: Provides functions for efficiently fitting linear models with 
-         spatially correlated errors by robust and Gaussian (Restricted) 
-         Maximum Likelihood and for computing robust and customary point 
-         and block external-drift Kriging predictions, along with utility
-         functions for variogram modelling in ad hoc geostatistical analyses, 
-         model building, model evaluation by cross-validation, (conditional) 
-         simulation of Gaussian processes, unbiased back-transformation of 
-         Kriging predictions of log-transformed data.
 License: GPL (>= 2) | LGPL (>= 2)
 NeedsCompilation: no
-Packaged: 2021-06-04 08:33:43 UTC; papritz
-Author: Andreas Papritz [cre, aut],
-  Cornelia Schwierz [ctb]
-Maintainer: Andreas Papritz <andreas.papritz@env.ethz.ch>
+Packaged: 2024-02-01 20:55:20 UTC; papritz
+Author: Andreas Papritz [aut, cre]
+Maintainer: Andreas Papritz <papritz@retired.ethz.ch>
 Repository: CRAN
-Date/Publication: 2021-06-04 09:30:02 UTC
+Date/Publication: 2024-02-03 11:40:02 UTC
diff --git a/MD5 b/MD5
@@ -1,50 +1,52 @@
-2374eecd737af95aaca5c4c9d7ecdc15 *ChangeLog
-ed99f0e23c8ed6ba598298528ed33f72 *DESCRIPTION
-a3aebf8f010335965d39e5f3cb2a7a18 *NAMESPACE
-214fe19e899a57da46ba7210902a8496 *NEWS
-35145a52aef47b440a139180265668cc *R/georob_S3methods.R
-b79405d5d50fb0a1f9881b6c1bac83ed *R/georob_cv.R
-f4a04c80238549cdb1a37acdc75dd151 *R/georob_exported_functions.R
-c50c7a59c0bf26aa2a6293a30815aa89 *R/georob_lgnpp.R
-f3914a9f47ba0e95a9a2ab391a10d8e2 *R/georob_predict.R
-858fe9edaaef985b812b18ba9c25b2ad *R/georob_private_functions.R
-4b313284368ef8efbc231239e484f4b7 *R/georob_simulation.R
-a983a29c333707ccb370ae4cde83030f *R/georob_variogram.R
-60549b316e85404430eab3d4ffff7eab *build/partial.rdb
-e93790cb5644124cfdec6afcea7cf2ef *build/vignette.rds
+104be0120a5ebaf6c00a2cfdedce2f23 *ChangeLog
+aa44b84bfd8753c27fdcd6d6f53ebde1 *DESCRIPTION
+4a6618b3d6890d8f6696956f761b4766 *NAMESPACE
+51b09cd4f9df80e50e13648d0e03429b *R/georob_S3methods.R
+d70cf1eb48f1c7e9dcb760e4687ff976 *R/georob_cv.R
+e522d4a78513352d8e70c7059ff6ec18 *R/georob_exported_functions.R
+3cce1034058a322b25f15baac73787f4 *R/georob_lgnpp.R
+c50eabdfb35f9236bc2ff691d471516e *R/georob_predict.R
+7d4445c9ae57b0ec5e7f376af4eb519c *R/georob_private_functions.R
+4d66d0dd5989f08daea7c7744eb33af9 *R/georob_simulation.R
+601ce567888e61144637946deabf493a *R/georob_variogram.R
+8faf250d78a120ba4c7ea2186efddd24 *build/partial.rdb
+23abd7a74b7aa3765566dbcc4fb31153 *build/vignette.rds
 e7ee6102924977a7d244c83e6b392883 *data/datalist
 1872e62f43073c7b37f9e17f66cdf2db *data/elevation.rda
 23acabdbb64d4593da12a5f02131059c *data/wolfcamp.rda
-e43a88194fff5907b6bc75e2170d9b4e *inst/doc/georob_vignette.R
-6412a991720a3d7b781892c798968871 *inst/doc/georob_vignette.Rnw
-2b510be21c2feabdea73a171d26dc8c4 *inst/doc/georob_vignette.pdf
-36383f6da3fc5d7e3613015d80830fd1 *man/compress.Rd
-61467386f2424bb4e482e640f5831408 *man/control.georob.Rd
-f752a511c0b8f314d22fe25caf9da133 *man/cv.Rd
-f059b8f17d340a669619acf25b06d70d *man/cv.georob.Rd
-f021229d94ae71e9d62cc6fd7bf3a7dd *man/elevation.Rd
-4ad09fea2f41749d490b207f41f2a633 *man/fit.variogram.model.Rd
-21a810259d5f0b610d9eba0766d6a82c *man/georob.Rd
-1db467a015219af49286b93f9361c404 *man/georobModelBuilding.Rd
-7a2fdb9bcebba36d395ad04a41603dcb *man/georobObject.Rd
-fefa608e4ed3a8a6acdd72a78982b42f *man/georobPackage.Rd
-d61203a09231c75ffb3508dc26e66cb6 *man/georobS3methods.Rd
-f68e6a8c077ee5624e12d15bcc3e9ca3 *man/georobSimulation.Rd
-a366a544c5ac63b57e5be5d515c8664a *man/internal.functions.Rd
-cef6658ee54c7fc86bb85a228f410f3d *man/lgnpp.Rd
-24147ba5257d73d3c93c6479bc486e72 *man/param.defaults.Rd
-86f28f1f3513f428f0d8a7a476b13952 *man/param.names.Rd
-9bbfe504e007e71e80eda1d62e51952b *man/plot.georob.Rd
-a4f2e2e53f509a92c7cdc845e2e15a03 *man/pmm.Rd
-786b9692b7650c339499384cdc76c69b *man/predict.georob.Rd
-9341cc7beadc29ee728fa53b9f1f71f7 *man/profilelogLik.Rd
-3c1395bbe4af35e09e495a60c30b33e1 *man/sample.variogram.Rd
-45b349d63310e0a928c95b0e6508f739 *man/validate.predictions.Rd
-64f7faa156c2de377f90f83a08e7e37b *man/wolfcamp.Rd
+d0baaccfe321cfd5f469ae3a6b6b80d4 *inst/NEWS.Rd
+428f360a8741c866bbf4e513121743e7 *inst/doc/georob_vignette.R
+f004fee865e7ca01a516a1741664c2b2 *inst/doc/georob_vignette.Rnw
+50a85a4de97d8c8012fc2908f8b22d76 *inst/doc/georob_vignette.pdf
+085475baddb3ce7b2d8aa35012ecfa3d *man/compress.Rd
+0a09cbf473a10aa5fbfcd42b928be09e *man/control.georob.Rd
+c82ae1869b89223daab4d23e79540db6 *man/cv.Rd
+a25e69a82f2ec944ab7a72464e37dfc6 *man/cv.georob.Rd
+8be0f136c330e13b8db18d84288d81f0 *man/elevation.Rd
+66d2c9da5dafe21d595407efac08a3d1 *man/fit.variogram.model.Rd
+7cc305a9388e60e2df7445077b4eba15 *man/gencorr.Rd
+263b4513c3854ab51459173ccbdb4840 *man/georob.Rd
+b04ee6259026362fefe0018c44f2a250 *man/georobModelBuilding.Rd
+c239d1a69c7885238183244d0b547314 *man/georobObject.Rd
+4cd07dc145d05b927f03b99694ceb017 *man/georobPackage.Rd
+0a60462cb2d1f0b32a2bc2cecb93e30f *man/georobS3methods.Rd
+949ea9c0fd180be23ccdcef80743f0a1 *man/georobSimulation.Rd
+4b90dba5f88e9017d5fbb762f039510b *man/internal.functions.Rd
+290cefe6867c5bcd7236c687ba3116c9 *man/lgnpp.Rd
+070bc21690aabdb83c49b1cb71f7bb93 *man/param.defaults.Rd
+5cdc519388226f09c9d783d71de9edad *man/param.names.Rd
+aa3755e5b401e89277888d12b67469bf *man/plot.georob.Rd
+4f466e680405c7127464d7aa686db739 *man/pmm.Rd
+c6dbdd52779bcff4a2162ce29e089643 *man/predict.georob.Rd
+79ede11211a59630d0faea4a0ca57ea0 *man/profilelogLik.Rd
+6c742c878782272b758150896d309428 *man/reexportedfun.Rd
+13e429562dd62b76e68ab7ec2271d19e *man/sample.variogram.Rd
+df22a6aaa7550d19db18cb0e107d3331 *man/validate.predictions.Rd
+6360abb0c4d256e58836defab1fd65dc *man/wolfcamp.Rd
 bb27c0989db96d417b6420d1b941bf53 *vignettes/0-block-discretization.pdf
 43e94e7c726e507b341dc8dbbab2c3c3 *vignettes/0-overview-zinc-meuse.pdf
 fcb9c9341d601d8ed6e6be5066b5c0ba *vignettes/georob.bib
-6412a991720a3d7b781892c798968871 *vignettes/georob_vignette.Rnw
+f004fee865e7ca01a516a1741664c2b2 *vignettes/georob_vignette.Rnw
 ef97150509737b3d7c819a8f5d597538 *vignettes/natbib.bst
 b91b9277476564eb685ef863c43e64d3 *vignettes/r_coalash_objects.RData
 9b960e3179f9b687e97a99b14ead9e7b *vignettes/r_meuse_zinc_objects.RData
diff --git a/NAMESPACE b/NAMESPACE
@@ -8,7 +8,6 @@ importFrom( methods, slot)
 importFrom( nlme, fixef, fixed.effects, ranef, random.effects )
 importFrom( nleqslv, nleqslv )
 importFrom( quantreg, rq.fit )
-importFrom( RandomFields, RFsimulate, RFfctn, RFoldstyle, RFoptions)
 importFrom( robustbase, lmrob.control, lmrob.fit, Qn, robMD, summarizeRobWeights )
 # importFrom( nor1mix, norMix, pnorMix, qnorMix, var.norMix )
 
@@ -37,6 +36,7 @@ export(
   fixef,                            # ok export of generic fixef{nlme}
   fwd.transf,                       # ok
   fit.variogram.model,              # ok
+  gencorr,                          # ok
   georob,                           # ok 
   K,                                # ok export of K{constrainedKriging}, which is (indirectly) needed by f.point.block.cov{constrainedKriging}
   lgnpp,                            # ok
@@ -63,7 +63,7 @@ export(
 #   deviance.georob,                # ok
 #   drop1.georob,                   # ok
 #   drop1.georob,                   # ok
-#   exportAIC.georob,               # ok
+#   extractAIC.georob,              # ok
 #   fixed.effects.georob,           # ok
 #   fixef.georob,                   # ok
 #   lines.fitted.variogram,         # ok
@@ -108,7 +108,7 @@ export(
 ### crpspd.resp.rob                    # currently not used
 ## estimate.zhat
 ## estimating.equations.theta
-## estimating.equations.signal
+## estimating.equations.z
 ## f.aux.Qstar
 ## f.aux.RSS
 ## f.aux.Valphaxi
@@ -128,19 +128,20 @@ export(
 ## f.call.set_x_to_value_in_fun
 ## f.diag
 ## f.psi.function
-## f.reparam.bkw
+## f.reparam.bwd
 ## f.reparam.fwd
 ## f.robust.uk
 ## f.stop.cluster
 ## georob.fit
-## getCall.georob
 ## gradient.negative.loglikelihood
 ## likelihood.calculations
 ## negative.loglikelihood
 ## partial.derivatives.variogram
 ### ppd.resp.rob                       # currently not used
 ### qpd.resp.rob                       # currently not used
 ## safe_pchisq
+## sim.chol.decomp
+## sim.circulant.embedding
 ## simple.kriging.weights
 ### var.pd.resp.rob                    # currently not used
 ## update.zhat
@@ -156,6 +157,7 @@ S3method( drop1, georob  )
 S3method( extractAIC, georob  )
 S3method( fixed.effects, georob  )
 S3method( fixef, georob  )
+## S3method( getCall, georob  )
 S3method( lines, fitted.variogram )
 S3method( lines, georob )
 S3method( logLik, georob )

diff --git a/NEWS b/NEWS