THIS IS THE CHANGELOG OF THE "phenology" PACKAGE

            CHANGES IN VERSION 4.2.3  (2015-06-29)
            
* New models for fitRMU()
* New functions plot.fitRMU(), logLik.fitRMU(), fitRMU_MHmcmc_p() and fitRMU_MHmcmc()
* Test if names of timeseries has a _ character and change it with a warning
* phenology_MHmcmc_p() returns a data.frame and no more a matrix
* The lastest version can always been installed using:
    install.packages("http://www.ese.u-psud.fr/epc/conservation/CRAN/phenology.tar.gz", repos=NULL, type="source")
* Require package HelpersMG version higher or equal than 1.2

            CHANGES IN VERSION 4.2    (2015-05-09)
            
* New function fitRMU()
* Correct add_phenology() description
* Correct a bug if no fixed parameter is included

            CHANGES IN VERSION 4.1    (2015-04-08)

* growlnotify(), MHalgoGen(), as.mcmc.mcmcComposite(), as.par.mcmcComposite(), summary.mcmcComposite(), plot.mcmcComposite(), plot_add(), ScalePreviousPlot(), plot_errbar(), ChangeCoordinate(), barplot_errbar(), chr(), asc(), ind_long_lat(), getTide(), clean.knitr(), local.search(), map.scale2(), compassRose2(), convert.tz(), insidesearch(), moon_phase(), compare_AIC(), read_folder() are transfered into new package HelpersMG
* Desription conforms to new CRAN specification

            CHANGES IN VERSION 4.0.5    (2015-02-15)
            
* Better managment of hidden function .MHalgoGen for very long MCMC profiling.
* Prevent an error in MCMC search when likelihood cannot be estimated.
* convert.tz(x, ) return an object of the same class than x.
* Length_ and Peak_ parameters can be series-specific.

            CHANGES IN VERSION 4.0.4    (2015-01-29)
            
* The hidden function .MHalgoGen has three new parameters for very long MCMC profiling to resume search for computer crash.
* Correct a bug for add_phenology() when month_ref is indicated
* Correct a cosmetic bug in print.phenologyout()
* Length parameter can now be associated with a beach
* New function insidesearch() to search for a string in files within a folder

            CHANGES IN VERSION 4.0    (2014-10-05)
            
* Remove phenology-swot() and keep only phenology() for web application
* Function convert.ts() renamed convert.tz()
* New tests for add_phenology()
* The parameter trace for mcmc can take an integer value to tell how many intermediate results must be shown
* Simplification of ind_lat_lon()

            CHANGES IN VERSION 3.71-3.72    (2014-08-24)

* Breaks for plot mcmc objects with uniform distribution use min and max as limits
* New parameter to help scaling prior vs posterior in plot mcmc objects
* Better examples for MCMC
* phenology_MHmcmc_p() check is initial values are out of range
* Correct bug for phenology_MHmcmc_p() with pMin, pMinE, pMinB
* Correct bug for ind_long_lat() using indices
* New way to use RNetCDF and XML packages which are only suggested
* New function convert.ts() to convert POSIXlt or POSIXct date-time from one timezone to an other

            CHANGES IN VERSION 3.70    (2014-07-07)

* Correct of bug in toggle_Min_PMin()

            CHANGES IN VERSION 3.69    (2014-06-21)

* New function map.scale2() and compassRose2() to change the colors of text and lines

            CHANGES IN VERSION 3.66-3.68    (2014-06-04)

* New function clean.knitr() to clean folder after knitr compile
* New function local.search() to search a file on local disk
* XML package is no more required but suggested
* New function logLik() for phenology class

            CHANGES IN VERSION 3.64-3.65    (2014-04-27)
            
* Add compatibility of ind_lat_lon() with RNetCDF package
* Change in ind_lat_lon() to make it more general

            CHANGES IN VERSION 3.63    (2014-04-06)
            
* Correct two bugs in function getTide() (when levels are negative and when system cannot use utf-8)
* add_phenology() now keeps the name of timeseries added
* New parameter silent=TRUE/FALSE for add_phenology()

            CHANGES IN VERSION 3.61-3.62    (2014-03-14)
            
* New function getTide()
* Shiny server

            CHANGES IN VERSION 3.60    (2014-03-08)
            
* New parameter in function ind_long_lat() to give the explicit name of longitude and latitude in ncdf file. Defaults are "lon" and "lat". Correction of bug.
* New shiny server (experimental)

            CHANGES IN VERSION 3.59    (2014-02-26)
            
* Remove dependency to ncdf4 package and make function ind_long_lat() compatible also with RNetCDF and ncdf packages

            CHANGES IN VERSION 3.57    (2014-02-23)
            
* Parameter folder of function read_folder() accept or a file or a folder
* New parameter wildcard for function read_folder()

            CHANGES IN VERSION 3.56    (2013-12-09)
            
* new function ind_long_lat()

            CHANGES IN VERSION 3.55    (2013-11-21)
            
* New function MinBMinE_to_Min()
* new parameter growlnotify for fit_phenology and plot.phenology
* correcton of a bug to prevent PMinE to become negatif

            CHANGES IN VERSION 3.53-3.54    (2013-10-23)
            
* New functions asc() and chr() to manipulate UTF-8 codes
* Function ScalePreviousPlot() returns also the range, the center and the position of labels

            CHANGES IN VERSION 3.52    (2013-08-05)
            
* New function used to toggle between Min and PMin parameters
* new parameter legend=TRUE for plot.mcmcComposite()

            CHANGES IN VERSION 3.51    (2013-07-10)
            
* New version of the update check at startup

            CHANGES IN VERSION 3.50    (2013-07-10)
            
* Correct a bug for scale of prior in plot.mcmcComposite()
* If prior is uniform, changed the scale to show all prior
* Parameters x.plus, x.minus, y.plus, and y.minus in plot_errbar to define absolut position of ends of error bars.
* Minor change in print.phenologyout()
* Add add=FALSE parameter to plot_errbar()
* New function barplot_errbar()

            CHANGES IN VERSION 3.49    (2013-06-23)

* Minor change in add_phenology()
* New function plot_add()
* New function ScalePreviousPlot()
* New function plot_errbar()
* New function ChangeCoordinate()


            CHANGES IN VERSION 3.47    (2013-06-03)
            
* New format of examples to be compatible with R 3.10

            CHANGES IN VERSION 3.46    (2013-04-08)
            
* New parameter accept for phenology_MHmcmc_p() to run the function in batch mode
* Correct the resolution for prior curve in plot()

            CHANGES IN VERSION 3.45    (2013-02-23)
            
* Correction for onAttach() to allow the package to load if internet is present but does not anwser as expected.
* compare_AIC() can use list of several object and then the AIC is summed.
* New functions as.mcmc.Composite() and as.par.mcmcComposite().
* compare_AIC() shows only 3 digits.
* compare_AIC() can uses list object summarizing data.


            CHANGES IN VERSION 3.44    (2013-01-28)
            
* add parameter progressbar = TRUE/FALSE for plot and map_phenology() to be used with Sweave
* plot_phenology() and plot_map() removed
* correct a bug when xlim or ylim were used with plot.phenology()
* remove the pdf option for plot.phenology
* correction of bug in the .MHalgoGen() function
* correct a display bug for maximum likelihood in map_phenology()

            CHANGES IN VERSION 3.42-3.43    (2013-01-02)
            
* first likelihood is stored in mcmcComposite
* check for update at load time
* compare_AIC() can use any list with elements named AIC or aic
* better managment of options for plot
* New funtions L_to_LBLE() and LBLE_to_L()
* add_format() has been renamed as add_phenology()
* add_phenology() and fit_phenology() by default opens a box to choose a file and try to read the file directly
* better managment for file reading in phenology_swot()
* if fit_phenology() is executed without formated data or parameterfit, it runs add_phenology() or par_init() first.
* phenology() stores data in phenology environment.

            CHANGES IN VERSION 3.41    (2012-11-25)
            
* add function phenology_swot() for rapid fit of nesting season
* if standard error of parameters is not available, produce NA for SE of nest counts rather than 0

            CHANGES IN VERSION 3.40    (2012-10-06)

* add Bayesian analysis

            CHANGES IN VERSION 3.36    (2012-07-22)

* change the function compare_AIC() to be used also with package embryogrowth

            CHANGES IN VERSION 3.35    (2012-06-06)

* new function adapt_parameters to extract only the useful parameters form a set
* the output from a plot can be used with several timeseries analyzed at the same time
* add a new class: phenologyout that is created by plot_phenology
* add the print.phenologyout and summary.phenologyout function
* the moons are now displayed at the top of the graph, not superimposed

            CHANGES IN VERSION 3.34    (2012-05-31)

* remove the use of the phenology.env environment

            CHANGES IN VERSION 3.33    (2012-05-31)

* internal changes

            CHANGES IN VERSION 3.32    (2012-05-23)

* new option for add_format: adjust_ref=TRUE
* change on the way that Begin, Peak and End are calculated within par_init

            CHANGES IN VERSION 3.31    (2012-05-14)

* internal change to get no warnings during build

            CHANGES IN VERSION 3.30    (2012-05-13)

* create two new classes: phenology and phenologymap
* create the plot, print, summary methods for these new classes
* it is possible to add several datasets at one time with add=list(d1, d2, d3)
* for add_format, it is possible to add several format for date with format = c("%d/%m/%Y", "%d/%m/%y"). All formats are tested.
* added function read_folder() to open all files from a folder and create a list to be used with add_format function
* correct an error for the outputs of plot_phenology with several series
* the main calendar dates for each series are shown at the end of the fit
* these dates are stored in the result under the name $Dates

            CHANGES IN VERSION 3.29    (2012-04-09)

* added function moon_phase()
* added moon=FALSE parameter for fit_phenology()
* added moon=TRUE for examples of shift_sinusoid()
* plot_phenology() return a list of lists with the outputs
* added function compare_AIC()


