THIS IS THE CHANGELOG OF THE "phenology" PACKAGE

Please note that only the most significant changes are reported here.

            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()