THIS IS THE CHANGELOG OF THE "phenology" PACKAGE

            CHANGES IN VERSION 7.3 (2019-01-04)

* Lnegbin can be run without parallel computing (sometimes parallel computing is slower than normal computing) - 7.1.1 (2018-08-03)
* lower and upper bounds for parameters can be set up in fit_phenology() - 7.1.1 (2018-08-03)
* L-BFGS-B rather than BFGS is used for fitting in fit_phenology() - 7.1.1 (2018-08-03)
* It is possible to save all the progress of fit with fit_phenology() - 7.1.2 (2018-08-03)
* Better organization of list for intermediate save in fit_phenology() - 7.1.3 (2018-08-05)
* fixed.parameters beginning by sd# are used in summary() and plot() - 7.1.4 (2018-09-24)
* New version in CRAN - 7.2 (2018-09-25)
* Solve an error if detectcores returns NA ou NULL - 7.2.1 (2018-10-12)
* Solve a problem when lnCF() returns Inf - 7.2.2 (2018-10-24)
* Solve a problem with multicores computers in ECFOCF_f() - 7.2.3 (2018-10-24)
* xaxt parameter can be used for plot.ECFOCF with result="prob" - 7.2.4 (2018-10-30)
* fixed.parameters beginning by se# (no more sd#) are used in summary() and plot() - 7.2.5 (2018-11-03)
* New parameter method for fit_phenology() - 7.2.5 (2018-11-03)
* Solve a rare problem in fitRMU() when the number for one year is null - 7.2.6 (2018-11-14)
* Possible to set a bimodal nesting season in fit_phenology() - 7.2.7 (2018-11-14)
* A new function to plot the formated tagloss data - 7.2.8 (2018-12-11)
* tagloss_daymax() can return max (default), min, mean, all the number of days individuals have been followed - 7.2.9 (2018-12-13)
* New function Tagloss_cumul() to estimate cumulative daily tag-loss rate - 7.2.9 (2018-12-17)
* Rivalan et al 2005 and Casale et al 2017 model can be used for tagloss modeling - 7.2.10 (2018-12-18)

            CHANGES IN VERSION 7.1 (2018-07-10)

* New set of functions for Internesting Periods for marine turtles - 7.1
* Minor change in .Lnegbin to prevent rare case when probabilities are too small - 7.1
* fitRMU() accept null SD for a beach - 7.1
* Takes into account Cauchy-Schwartz inequality to estimate SD in fitRMU - 7.1
* It is possible to not indicate SE of nesting season counts in fitRMU - 7.1
* A proportional model for SD is possible for fitRMU - 7.1
* Solve a rare warning in plot.phenology - 7.1

            CHANGES IN VERSION 7.0.4 (2018-04-25)

* New set of functions for Clutch Frequency for marine turtles - 7.0
* Minor change in par_init() - 7.0.1
* Force PMinE et PMinB to be positive - 7.0.1
* New non-parameteric model for CF - 7.0.2
* New parameter show.scale for plot.ECFOCF() - 7.0.3
* New attribute final in TableOCFECF - 7.0.4

            CHANGES IN VERSION 6.0-6.0.3  (2017-10-17)

* New set of functions for Tagloss - 6.0
* Correct a bug in add_phenology() when a list is used to enter new data - 6.0
* Confidence interval for Peak_Series, Length_Series are shown - 6.0
* Minor change in Tagloss - 6.0
* New option "cumul" to plot tagloss result - 6.0
* Simplification to specify partial models in tagloss - 6.0
* If N20 == 0, does not produce an error - 6.0
* Random distribution of individuals in groups send in cores for parallel computing - 6.0
* Minor change in Tagloss_L - 6.0.1
* New function loglik for Tagloss - 6.0.2
* Correct examples - 6.0.3

            CHANGES IN VERSION 5.5  (2017-05-14)

* Use of SEfromHessian - 5.5

            CHANGES IN VERSION 5.4.1  (2017-04-07)

* New version for CRAN - 5.4
* phenology() is compatible with shiny 1.0.1 - 5.4.1

            CHANGES IN VERSION 5.3.15  (2017-03-03)

* New version for CRAN - 5.3
* par_init() better handle PMin - 5.3.1
* New function AutoFitPhenology() - 5.3.2
* Parallel computing in windows - 5.3.3
* Adaptive mcmc - 5.3.3
* Correction of parallel computing in windows - 5.3.4-5.3.5
* parametersfixed is renammed fixed.parameters in fit_phenology(), par_init() and plot.phenology() - 5.3.6
* parametersfit is renammed fitted.parameters in fit_phenology() - 5.3.6
* Plot is renammed show.plot in plot.phenology() - 5.3.6
* summary() returns an estimate of global nesting if mcmc object is indicated - 5.3.7
* summary() returns the details day by day of quantiles -5.3.8
* plot() can plot now the result of a mcmc object as quantiles - 5.3.8
* Correct diverse bugs in phenology_MHmcmc() and map_phenology() - 5.3.9
* summary.phenology() and plot.phenology() rewritten from scratch - 5.3.10
* summary.phenology() uses matrix of variances-covariances for confidence interval - 5.3.10
* fit_phenology() uses optimx() - 5.3.11
* web version updated - 5.3.12
* Remove dependency to zoo package but add optimx and numDeriv - 5.3.12
* Change the function to estimate random number with vcov using lmf package - 5.3.13
* summary.phenologyout() is more complete - 5.3.14
* autfitphenology() can be used again - 5.3.15

            CHANGES IN VERSION 5.2.1-5.2.5  (2016-08-15)

* New version of shiny phenology() - 5.2.1
* New version of shiny phenology() - 5.2.2
* New parameter plot=TRUE for plot.phenology() - 5.2.2
* Restore shiny version within the package - 5.2.3
* Multilanguage version of phenology() - 5.2.4
* Spanish version of phenology() - 5.2.5

            CHANGES IN VERSION 5.2  (2016-07-17)

* Correction for likelihod_phenology() - 5.1.1
* Estimation of likelihoods for different beaches is ran in parallel - 5.1.1
* Can add a list read using read_folder() - 5.1.2
* phenology() function works again - 5.1.3
* plot.phenologymap() plot only one heat map - 5.1.4
* plot_phi() and plot_delta() are more flexible - 5.1.4
* Moon is not shown if xlim is used for plot.phenology() - 5.1.4
* Shiny application phenology() is better handeld - 5.2

            CHANGES IN VERSION 5.1  (2016-05-02)

* Minor changes in documentation

            CHANGES IN VERSION 5.0.3  (2016-04-09)

* Add cofactors for daily effects in fit_phenology() - 5.0.0
* method_incertitude are changed to 'convolution' or 'combinatory' - 5.0.0
* Correct a bug for cofactor analysis - 5.0.1
* Minor change in the output of plot() - 5.0.2
* Add a zero parameter for fit_phenology() - 5.0.3
* Bug correction for for cofactor analysis - 5.0.3

            CHANGES IN VERSION 4.4-4.4.1  (2016-01-13)

* The "sum" method_incertitude uses an exact method for the negative binomial distribution
* The "binomial" method has been removed
* Optimisation of the function .Lnegbin to be more rapid and to return also the likelihood of each observation
* Require package HelpersMG version higher or equal than 1.3.4

            CHANGES IN VERSION 4.3.1-4.3.6  (2015-12-09)

* Object returns from MHmcmc has the correct class mcmcComposite - 4.3.1
* Bisextile years are possible - 4.3.2
* Theta can be a fixed parameter - 4.3.3
* se for some parameters can be indicated manually in plot - 4.3.4
* Better gestion of bisextil years in plot - 4.3.4
* se indicated manually in plot replaced the previous ones if they exist - 4.3.5
* plot.ftiRMU has a new parameter to change the order of series - 4.3.5
* fit_phenology can produce positive likelihood without error - 4.3.6
* correct a bug introduced in 4.3.5 for se managment - 4.3.6
* print.phenologyout() can show data with very small se - 4.3.6

            CHANGES IN VERSION 4.3  (2015-07-29)

* Minor changes in fitRMU() and bugs corrections

            CHANGES IN VERSION 4.2.3-4.2.4  (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()


