2008-07-30 15:00  ribatet

	* R/smith.R: Fix a stupid error - starting values were sometimes
	  badly defined

2008-07-30 08:49  ribatet

	* R/fitmaxstable.R, R/schlather.R, R/smith.R, R/starting.values.R,
	  man/fitmaxstab.Rd: Replace the "warn.inf" argument by warn. Now
	  if TRUE, it warns also
	  when standard errors are erradic

2008-07-30 07:09  ribatet

	* R/fitmaxstable.R, man/fitmaxstab.Rd: Set fit.marge to FALSE as
	  default and passing it to TRUE if R formulas
	  are given

2008-07-30 07:06  ribatet

	* man/posterior.Rd: Add the sill and renaming the "scale" parameter
	  in the covariance
	  function as "range".

2008-07-30 07:05  ribatet

	* R/smith.R: Update due to the MINF value in /src/header.h

2008-07-30 07:04  ribatet

	* R/fitmaxstable.R, man/fitmaxstab.Rd: Moving the fit.marge
	  argument

2008-07-30 07:04  ribatet

	* man/univfit.Rd: Documentation/code mismatch (dots argument in
	  gpdmle)

2008-07-30 07:03  ribatet

	* R/covariance.R, R/gradients.R, R/mcmc.R, R/methods.R,
	  R/schlather.R, inst/doc/SpatialExtremesGuide.Rnw,
	  man/covariance.Rd, man/profile2d.maxstab.Rd: Add the sill and
	  renaming the "scale" parameter in the covariance
	  function as "range".

2008-07-30 07:00  ribatet

	* src/covariance.c, src/gradients.c, src/header.h, src/schlather.c:
	  Add the sill and renaming the "scale" parameter in the covariance
	  function as "range".

2008-07-29 10:04  ribatet

	* inst/doc/SpatialExtremesGuide.Rnw: Add the sill argument in the
	  covariance function - adjusting the code

2008-07-29 10:03  ribatet

	* R/covariance.R, R/methods.R, R/schlather.R, man/covariance.Rd,
	  src/covariance.c, src/gradients.c, src/header.h, src/schlather.c:
	  Add the sill component in the covariance function

2008-07-28 09:51  ribatet

	* src/header.h, src/pairwiselik.c, src/schlather.c: Minor change:
	  * MINF is now -1e120
	  * add comments

2008-07-28 09:50  ribatet

	* R/smith.R: Changing the starting values for the covariance matrix

2008-07-28 09:49  ribatet

	* R/univfit.R, man/univfit.Rd: Adding the ... argument to allow for
	  hand fixed parameter in the GEV/GPD

2008-07-26 11:38  ribatet

	* src/pairwiselik.c: Compute the log before as for really small x,
	  log(x) is not finite!

2008-07-26 11:19  ribatet

	* man/fitmaxstab.Rd: Passing std.err.type = "none" to save time
	  when running example

2008-07-26 11:19  ribatet

	* R/schlather.R, R/smith.R: Wasn't able to tweak appropriately
	  parscale

2008-07-26 11:18  ribatet

	* R/define.parscale.R: Wasn't able to tweak appropriately parscale

2008-07-25 14:07  ribatet

	* inst/doc/SpatialExtremesGuide.Rnw: Now uses the references.bib
	  file for citations

2008-07-25 14:07  ribatet

	* inst/doc/references.bib: Add a .bib file for vignette references

2008-07-25 14:02  ribatet

	* R/schlather.R, R/smith.R: Now the computation of starting values
	  uses the same optimizer than
	  for the model fitting.
	  Uses the function define.parscale to help optimization procedures

2008-07-25 14:02  ribatet

	* R/starting.values.R: Now the computation of starting values uses
	  the same optimizer than
	  for the model fitting.
	  Fix a bug in schlather: only the whitmat cov.mod was used for the
	  starting values...

2008-07-25 14:00  ribatet

	* src/pairwiselik.c: Minor change to optimize the code (smith's
	  model)

2008-07-25 14:00  ribatet

	* R/psplines.R, man/cv.Rd, man/rbpspline.Rd: Now we use the nlm
	  function to optimize the cv
	  When a one-dimensional p-spline is fitted, we arrange the output
	  so
	  that a simple "lines(fitted)" will draw the p-spline

2008-07-25 13:58  ribatet

	* R/define.parscale.R: Add a function to define appropriate scaling
	  values for the
	  optimization routine

2008-07-17 16:33  ribatet

	* R/smith.R: Removing the new definition of starting values as it
	  is too CPU
	  demanding

2008-07-17 16:32  ribatet

	* R/mcmc.R, man/posterior.Rd: Add the adjustment of the posterior
	  distribution. The output is now a
	  list $mc, $mc.adj

2008-07-17 16:31  ribatet

	* src/schlather.c, src/smith.c, src/smith3d.c: Removing useless
	  initializations

2008-07-17 16:30  ribatet

	* src/mcmc.c: Cleaning the gibbs code

2008-07-17 16:29  ribatet

	* man/fitmaxstab.Rd: Fix an error (example section) due to changes
	  in the code

2008-07-09 16:27  ribatet

	* inst/doc/SpatialExtremesGuide.Rnw: Some minor changes in the
	  vignette

2008-07-09 16:26  ribatet

	* R/smith.R: Try to define more relevant starting values as the
	  identity matrix may
	  be really poor

2008-07-09 16:25  ribatet

	* R/mcmc.R, man/posterior.Rd: Try to adjust the composite posterior
	  distribution

2008-07-09 13:08  ribatet

	* R/psplines.R: The optimize function gives a list with arg minimum
	  not value

2008-07-09 13:04  ribatet

	* R/mcmc.R: Add the adjuting method for the posterior distribution

2008-07-09 12:49  ribatet

	* R/psplines.R, man/cv.Rd, man/rbpspline.Rd: Change the upper bound
	  for the optimization stage of the smoothing
	  parameter.
	  rbpspline function now warns if the smoothing parameter estimate
	  is
	  equal to this upper bound.

2008-07-09 12:37  ribatet

	* R/selection.R: Multiply TIC by 2 so that it's more similar to AIC

2008-07-07 06:30  ribatet

	* R/schlather.R, R/smith.R: Add a "control" argument for the optim
	  function. It allows to
	  normalized auto-magically the parameters to avoid numerical
	  issues. If
	  users supply parscale, values won't be overwritten.

2008-07-07 06:30  ribatet

	* R/fitmaxstable.R, man/fitmaxstab.Rd: Add a "control" argument for
	  the optim function. It allows to
	  normalized auto-magically the parameters to avoid numerical
	  issues. If
	  users supply parscale, values won't be overwritten.

2008-07-07 06:28  ribatet

	* man/madogram.Rd: Fix an outdated link to a function

2008-07-07 06:26  ribatet

	* man/excofun.Rd:

2008-07-02 14:40  ribatet

	* R/extcoeff.R, R/fitmaxstable.R: Add some tests to check for wrong
	  use of the code

2008-06-30 15:13  ribatet

	* R/schlather.R, R/smith.R: Refining the "message" for the
	  optimization procedure

2008-06-30 15:13  ribatet

	* R/plots.R: Stop if we are not in a 2d case

2008-06-30 15:12  ribatet

	* R/extcoeff.R, man/extcoeffemp.Rd: Renaming excofun in
	  extcoeff.emp

2008-06-30 15:02  ribatet

	* inst/doc/SpatialExtremesGuide.Rnw: Keep on writing the vignette

2008-06-17 14:10  ribatet

	* inst/doc/SpatialExtremesGuide.Rnw: Adding Simone as a co-authors,
	  a model selection section and little changes

2008-06-17 14:09  ribatet

	* src/header.h, src/pairwiselik.c, src/schlather.c, src/smith.c,
	  src/smith3d.c, src/univllik.c: Using MINF as a C #define for non
	  feasible points

2008-06-17 14:08  ribatet

	* man/extcoeff.Rd: Improving the example

2008-06-17 14:07  ribatet

	* R/schlather.R, R/smith.R: Fix a bug while testing is.na

2008-06-17 08:28  ribatet

	* man/TIC.Rd: Can now compute TIC for several fitted models

2008-06-17 08:28  ribatet

	* R/utils.R, src/utils.c: No error when the GEV scale parameter is
	  <=0, it warns and return NA

2008-06-17 08:27  ribatet

	* R/starting.values.R: Removing the computations of the standard
	  errors when defining the
	  starting values

2008-06-17 08:26  ribatet

	* R/selection.R: Can now compute TIC for several fitted models

2008-06-17 08:25  ribatet

	* R/schlather.R, R/smith.R: Minor changes

2008-06-17 08:24  ribatet

	* R/predict.R, man/predict.maxstab.Rd: Allowing for return level
	  predictions

2008-06-17 08:23  ribatet

	* R/plots.R: Computes appropriate ranges using linear algebra
	  arguments

2008-06-17 08:18  ribatet

	* R/gradients.R, src/gradients.c, src/header.h: Allowing for
	  smith3d gradient computation

2008-06-17 08:16  ribatet

	* R/fitmaxstable.R, man/fitmaxstab.Rd: Passing std.err.type =
	  "score" as default now

2008-06-17 08:16  ribatet

	* R/covariance.R, src/covariance.c: Change the smooth upper bound
	  for the Whittle-Matern covariance
	  function

2008-06-13 12:04  ribatet

	* man/extcoeff.Rd: Default is now to plot 200 points - for
	  aesthetic purposes

2008-06-13 12:02  ribatet

	* src/smith3d.c: Allowing for 3 by 3 covariance matrices

2008-06-13 12:02  ribatet

	* src/header.h: Allowing for 3 by 3 covariance matrices

2008-06-13 12:02  ribatet

	* src/covariance.c: Allowing for 3 by 3 covariance matrices

2008-06-13 12:01  ribatet

	* man/excofun.Rd: Adding new arguments to control the display

2008-06-13 12:01  ribatet

	* R/smith.R: Allowing for 3 by 3 covariance matrices

2008-06-13 12:00  ribatet

	* R/schlather.R: Minor changes: typos

2008-06-13 12:00  ribatet

	* R/plots.R: Computes the x and y ranges appropriately - using
	  linear algebra

2008-06-13 11:59  ribatet

	* R/methods.R: Some minor changes subject to modifications of the
	  code (for example
	  allowing for 3 by 3 covariance matrices in the Smith's model)

2008-06-13 11:57  ribatet

	* R/extcoeff.R: Computes the x and y ranges appropriately - using
	  linear algebra

2008-06-12 08:01  ribatet

	* src/gradients.c: Removing uselesss comments

2008-06-12 08:00  ribatet

	* inst/doc/SpatialExtremesGuide.Rnw: Changing the examples: more
	  relevant now

2008-06-12 07:58  ribatet

	* man/covariance.Rd, man/internals.Rd, man/logLik.maxstab.Rd,
	  man/predict.maxstab.Rd: Changing the examples: more relevant now

2008-06-12 07:55  ribatet

	* R/extcoeff.R: Improving the madogram function and creating the
	  excofun one

2008-06-12 07:53  ribatet

	* man/TIC.Rd, man/excofun.Rd, man/madogram.Rd: Improving the
	  madogram function and creating the excofun one

2008-06-11 08:43  ribatet

	* R/extcoeff.R: Using unit Frechet margins for the madogram

2008-06-11 08:42  ribatet

	* R/extcoeff.R: Trying to write a function for a non parametric
	  estimation of the
	  extremal coefficient

2008-06-11 08:41  ribatet

	* man/predict.maxstab.Rd: Changing the example: more relevant now

2008-06-06 08:16  ribatet

	* R/extcoeff.R: A first attempt to produce madogram plots

2008-06-06 08:13  ribatet

	* R/smith.R: The analytical gradient is not passed in the optim
	  function anymore

2008-06-06 08:13  ribatet

	* R/utils.R: Modify the gev2frech and frech2gev functions to allow
	  for a null shape
	  parameter

2008-06-03 14:24  ribatet

	* R/utils.R, man/gev2frech.Rd: Add a frech2gev function

2008-06-02 08:41  ribatet

	* inst/doc/SpatialExtremesGuide.Rnw: Fix some typos and LaTeX
	  formatting

2008-06-02 08:40  ribatet

	* src/schlather.c, src/smith.c: Initializing array to 0s. Is it
	  really useful?

2008-06-02 08:40  ribatet

	* src/pairwiselik.c: Minor changes: optmizing purposes

2008-06-02 08:39  ribatet

	* src/covariance.c: Refining the C code.

2008-06-02 08:38  ribatet

	* R/fitmaxstable.R, R/gradients.R, R/mcmc.R, R/modeldef.R,
	  R/plots.R, R/predict.R, R/schlather.R, R/smith.R,
	  R/starting.values.R, R/univfit.R, man/fitmaxstab.Rd, man/map.Rd:
	  Convert arguments of a C code before invoking it - e.g. as.double
	  and
	  so on.
	  Allow for additional covariate when modelling the GEV margins

2008-05-31 15:46  ribatet

	* src/utils.c: Fix an error while writing the GEV CDF

2008-05-31 15:45  ribatet

	* src/header.h, src/smith.c: Substiute "icov" for "cov"

2008-05-30 17:58  ribatet

	* R/selection.R: Add a function for model selection

2008-05-30 17:56  ribatet

	* R/gradients.R, R/methods.R, R/schlather.R, R/smith.R,
	  R/starting.values.R, inst/doc/SpatialExtremesGuide.Rnw,
	  man/internals.Rd, src/gradients.c, src/pairwiselik.c,
	  src/schlather.c, src/smith.c, src/utils.c: Some improvements due
	  to applying these models on US data

2008-05-28 17:57  ribatet

	* inst/doc/SpatialExtremesGuide.Rnw: Keep on writing the vignette

2008-05-28 17:57  ribatet

	* R/gradients.R, R/schlather.R, src/gradients.c: Add the
	  computation of the gradient for the Schlather's model and a
	  polynomial response surface

2008-05-28 08:45  ribatet

	* inst/doc/SpatialExtremesGuide.Rnw: Keep on writing the vignette

2008-05-27 14:09  ribatet

	* src/header.h: Remove the gradient computations when the
	  parametrisation uses the
	  inverse of the covariance matrix

2008-05-27 14:08  ribatet

	* R/gradients.R, R/smith.R, src/gradients.c: Add the computation of
	  the standard errors for the Smith's model when
	  we use a polynomial response surface

2008-05-26 15:13  ribatet

	* inst/doc/SpatialExtremesGuide.Rnw: Keep on writing the vignette:
	  vignette output, error in the Smith's
	  gradient

2008-05-26 15:12  ribatet

	* R/fitmaxstable.R: Add a test if ``loc.form'', ``scale.form'' and
	  ``shape.form'' are
	  valid R formulas

2008-05-26 09:12  ribatet

	* src/pairwiselik.c: Add a test if the log pairwise likelihood is
	  infinite

2008-05-26 09:09  ribatet

	* inst/doc/SpatialExtremesGuide.Rnw: Keep on writing the vignette

2008-05-23 13:25  ribatet

	* inst/doc/SpatialExtremesGuide.Rnw: Keep on writing the vignette

2008-05-23 13:24  ribatet

	* man/covariance.Rd: The covariance function now produces a plot -
	  and thus takes more
	  arguments

2008-05-23 13:23  ribatet

	* R/schlather.R: Minor changes related to the modification of the
	  covariance function -
	  no plot.

2008-05-23 13:23  ribatet

	* R/covariance.R: The covariance function now produces a plot

2008-05-23 08:22  ribatet

	* R/starting.values.R: Changes (again) how the default x and y-axis
	  ranges are computed

2008-05-23 08:21  ribatet

	* src/covariance.c: Add a test if the Mahalanobis distance is
	  degenerate

2008-05-23 08:20  ribatet

	* src/pairwiselik.c: Replace log(a/b) by log(a) - log(b) for
	  potential numerical issues

2008-05-23 08:19  ribatet

	* inst/doc/SpatialExtremesGuide.Rnw: Keep on writing the vignette

2008-05-21 20:59  ribatet

	* R/plots.R: Change the default ranges for the x and y axis

2008-05-21 20:55  ribatet

	* inst/doc/SpatialExtremesGuide.Rnw: Keep on writing the vignette

2008-05-19 21:43  ribatet

	* man/posterior.Rd: Minor change: change the init values of the
	  Markov chain so that
	  convergence to the stationary distribution is more clear cut

2008-05-19 21:42  ribatet

	* man/extcoeff.Rd: Minor change: change the example

2008-05-19 21:41  ribatet

	* inst/doc/SpatialExtremesGuide.Rnw: Extend the documentation

2008-05-19 21:41  ribatet

	* src/header.h: Removing useless argument in a C function

2008-05-19 21:40  ribatet

	* R/utils.R, src/utils.c: Add a function that computes quantiles
	  from a GEV distribution

2008-05-19 21:39  ribatet

	* R/starting.values.R: Add a modification in the starting values
	  definition if there are any
	  negative scale parameter estimates.

2008-05-19 21:38  ribatet

	* R/smith.R: Minor changes: moving the coeff.ext function
	  definition to another
	  place.

2008-05-19 21:37  ribatet

	* R/predict.R: Add the coordinates in the output

2008-05-19 21:36  ribatet

	* R/methods.R: Change the message when we do not fit the marges

2008-05-19 21:36  ribatet

	* R/plots.R, man/map.Rd: Adding a new function "map" that produces
	  contour plots for the GEV
	  parameters as well as for return levels.

2008-05-18 21:32  ribatet

	* .: set property to ignore for the DESCRIPTION file

2008-05-18 21:30  ribatet

	* DESCRIPTION: Add a suggestion entry e.g. coda

2008-05-18 21:29  ribatet

	* man/internals.Rd: Removing entries for the functions that are now
	  documented

2008-05-18 21:28  ribatet

	* src/mcmc.c: Removing the use of the log-normal proposal
	  distribution for some
	  parameters.

2008-05-18 21:27  ribatet

	* src/header.h, src/schlather.c: There was an useless argument in
	  the schlather functions

2008-05-18 21:27  ribatet

	* inst/doc/SpatialExtremesGuide.Rnw: Add the Sweave package in the
	  preambule

2008-05-18 21:26  ribatet

	* R/schlather.R, R/smith.R: Minor changes: renaming the function
	  for the extremal coefficient.

2008-05-18 21:25  ribatet

	* R/mcmc.R: Changes to allow for mcmc computations while the
	  margins are not
	  fitted.
	  Smith model can now be considered.

2008-05-18 21:23  ribatet

	* man/gev2frech.Rd, man/posterior.Rd, man/prior.Rd, man/rb.Rd: Add
	  documentation files of already existing codes

2008-05-18 21:15  ribatet

	* R/plots.R, man/extcoeff.Rd: Add function (and doc) for plotting a
	  contour plot of the extremal
	  coefficient

2008-05-18 15:22  ribatet

	* src/covariance.c, src/gradients.c, src/header.h, src/mcmc.c,
	  src/pairwiselik.c, src/schlather.c, src/smith.c, src/utils.c: Fix
	  the bug in the gibbs sampler
	  Cleaning C codes - structures are now avoided

2008-05-18 15:21  ribatet

	* R/mcmc.R: Fix the bug in the gibbs sampler

2008-05-18 15:20  ribatet

	* inst/removeCodes: Remove this folder useless as svn is
	  implemented now

2008-05-09 08:31  ribatet

	* inst/doc/SpatialExtremesGuide.pdf: Removing the pdf vignette

2008-05-09 08:31  ribatet

	* inst/doc/SpatialExtremesGuide.pdf: New vignette - but will be
	  ignored soon

2008-05-09 08:18  ribatet

	* R/mcmc.R, src/mcmc.c: Some improvements in the mcmc procedures.
	  The bug is still present
	  though - "REAL() can only be applied to a 'numeric', not a 'list'
	  or
	  not a 'integer' or whatever...

2008-05-09 08:14  ribatet

	* man/covariance.Rd, man/predict.maxstab.Rd,
	  man/predict.pspline.Rd, man/print.maxstab.Rd: Changes in the
	  example section

2008-05-09 08:13  ribatet

	* R/starting.values.R: Removing unnecessary materials

2008-05-09 08:13  ribatet

	* R/schlather.R, R/smith.R: Some improvements in detecting
	  optimizations problems

2008-05-09 08:12  ribatet

	* R/fitmaxstable.R, man/fitmaxstab.Rd: Changing the argument. Now
	  the Smith's or Schlather's
	  characterisations are directly selected from the cov.mod
	  argument.

2008-05-07 15:57  ribatet

	* inst/derivatives.aux, inst/derivatives.log, inst/derivatives.pdf,
	  inst/derivatives.tex: Removing unnecessary files

2008-05-07 15:57  ribatet

	* inst/auto: Removing unnecessary files

2008-05-07 15:55  ribatet

	* man, src: Ignoring the header.h and internals.Rd files

2008-05-07 15:54  ribatet

	* inst/doc: Ignoring the pdf file

2008-05-07 15:54  ribatet

	* inst/doc, inst/doc/SpatialExtremesGuide.Rnw,
	  inst/doc/SpatialExtremesGuide.pdf: Add a inst/doc directory for
	  package vignette

2008-05-07 15:53  ribatet

	* man/internals.Rd, src/header.h: Passing src/header.h and
	  man/internals.Rd with "ignore" prop. to svn

2008-05-07 15:51  ribatet

	* src/utils.c: Improve how obs. are transformed to unit Frechet

2008-05-07 15:50  ribatet

	* src/schlather.c: Minor changes: adding some comments (non
	  feasible cases)

2008-05-07 15:50  ribatet

	* src/pairwiselik.c: Improve how the pairwise likelihood is
	  computed
	  Cleaning the codes

2008-05-07 15:49  ribatet

	* src/gradients.c: New function to compute the gradient for the
	  Schlather's model

2008-05-07 15:48  ribatet

	* src/covariance.c: Improve how covariance functions are computed -
	  more stable

2008-05-07 15:47  ribatet

	* R/utils.R: gev2frech can return 0 values

2008-05-07 15:46  ribatet

	* R/starting.values.R: Changing the way starting values are
	  computed. Now it's "quite"
	  impossible the log-likelihood is infinite at starting values

2008-05-07 15:45  ribatet

	* R/modeldef.R, R/schlather.R, R/smith.R: Improving the way how
	  formulas are interpreted

2008-05-07 15:44  ribatet

	* R/mcmc.R, R/methods.R: Changing the names of the param "icovxx"
	  --> "covxx"

2008-05-07 15:42  ribatet

	* R/gradients.R: Add the gradient computation for the schlather's
	  model.
	  Renaming function gradxxx to .gradxxxx

2008-05-05 08:48  ribatet

	* src/schlather.c: Use the rb penalization matrix as the default

2008-05-05 08:46  ribatet

	* R/schlather.R: Use "BFGS" as the default method for optimization

2008-05-05 08:37  ribatet

	* src/pairwiselik.c: Remove useless computations in the pairwise
	  likelihood

2008-04-28 15:01  ribatet

	* ., DESCRIPTION, R, R/covariance.R, R/fitmaxstable.R,
	  R/gradients.R, R/mcmc.R, R/methods.R, R/modeldef.R, R/predict.R,
	  R/profile.R, R/psplines.R, R/schlather.R, R/smith.R,
	  R/starting.values.R, R/univfit.R, R/utils.R, R/zzz.R, inst,
	  inst/auto, inst/auto/derivatives.el, inst/derivatives.aux,
	  inst/derivatives.log, inst/derivatives.pdf, inst/derivatives.tex,
	  inst/removeCodes, inst/removeCodes/oldcodes.R,
	  inst/removeCodes/oldcodes.c, man, man/covariance.Rd, man/cv.Rd,
	  man/distances.Rd, man/fitmaxstab.Rd, man/internals.Rd,
	  man/logLik.maxstab.Rd, man/modeldef.Rd, man/predict.maxstab.Rd,
	  man/predict.pspline.Rd, man/print.maxstab.Rd,
	  man/print.pspline.Rd, man/profile.maxstab.Rd,
	  man/profile2d.maxstab.Rd, man/rbpspline.Rd, man/univfit.Rd, src,
	  src/covariance.c, src/gradients.c, src/header.h, src/mcmc.c,
	  src/pairwiselik.c, src/penalizations.c, src/schlather.c,
	  src/smith.c, src/univllik.c, src/utils.c: Initial Import

