THIS IS THE CHANGELOG OF THE "embryogrowth" PACKAGE

Please note that only the most significant changes are reported here.
All the changes are indicated inside the R code.

          CHANGES IN VERSION 5.1    (2014-10-05)

* New version of STRES_TSD and help for this database is more clear
* Future changes in STRES_TSD will not be longer be reported here
* tsd() can now uses also incubation period
* Equation Hulin (from Hulin et al 2009) is implemented in tsd()
* Equation Double-Richards (from Girondot, submited) is implemented in tsd()
* Packages numDeriv and entropy are now only suggested
* New parameters lty.temperatures and lwd.temperatures for plot.NestsResult()
* Predict.tsd() without temperatures or durations uses original temperatures or durations
* New function plot.tsd() 
* New possibility to use Bayesian estimate for tsd()
* Remove parallel computing for windows in MCMC
* New functions minmax.periodic() and temperature.periodic()

          CHANGES IN VERSION 5.0    (2014-08-15)

* New bibliographic references and first version in CRAN
* Remove parallel computing option for Windows
* Remove local update

          CHANGES IN VERSION 4.14    (2014-06-14)

* Correct bug for Richards equation in tsd and predict.tsd() works faster

          CHANGES IN VERSION 4.09-4.13    (2014-06-11)

* New function logLik() applied to NestsResult and tsd
* New version of STRES_TSD
* No return line from plot()
* x-axis is returned correctly after plotR_hist()

          CHANGES IN VERSION 4.05-4.08    (2014-06-03)

* predict.tsd() is more rapid and can be used without CI
* New version of STRES_TSD
* remove dependency of many packages
* new parameter lwd and lwdCI for plotR() and plotR_hist() 

          CHANGES IN VERSION 4.04    (2014-04-14)

* Correct a warning in plotR() when Scale is used
* Correct a bug in plot.nestresult() when for special length of time series

          CHANGES IN VERSION 4.01-4.03    (2014-03-05)

* 1000 iterations are allowed for tsd() and test if convergence is reached
* new way to define initial P value for tsd()
* new automatic xlim for tsd() function to show all TRT 
* many changes in shiny code. Remove visibility of ShinyEmbryogrowth()

          CHANGES IN VERSION 4.00    (2014-03-02)

* shiny application is included. Call it using ShinyEmbryogrowth()

          CHANGES IN VERSION 3.02    (2014-03-01)

* mcmc results for anchored parameters use 10000 iterations
* Correct a warning when there is no variability in TSP

          CHANGES IN VERSION 3.01    (2014-02-12)

* Possible to save intermediate results during fitting

          CHANGES IN VERSION 3.00    (2014-02-08)

* Possibility to define R by anchor of loess fitting

          CHANGES IN VERSION 2.30    (2014-02-02)

* New version with corrected rK value
* weight parameter is store in result of searchR() and used for mcmc
* Add the function switch.transition()
* New function merge.mcmcComposite() to merge two objects mcmcComposite

          CHANGES IN VERSION 2.28    (2014-01-24)

* Correct a bug in movingincubation()

          CHANGES IN VERSION 2.27    (2014-01-23)

* Correct a bug in movingincubation()
* Predict method for tsd

          CHANGES IN VERSION 2.26    (2014-01-22)

* Add SE for weight temperature by growth during TSP and mean temperature during TSP
* Add SE for borders of TSP
* Store weighted temperature by growth during TSP for movingincubation()

          CHANGES IN VERSION 2.25    (2014-01-21)

* Calculate mean temperature in middle-third of incubation and weight temperature by growth during TSP

          CHANGES IN VERSION 2.24    (2014-01-16)

* New function to change from 4p to 6p parameters functions and reverse

          CHANGES IN VERSION 2.23    (2014-01-08)

* Correct a bug for linear or exponential derivative and parallel computing
* Add mar parameter for plot.NestResults()

           CHANGES IN VERSION 2.22    (2013-12-22)

* TRT is calculated for Hill and Richards equations in tsd() function
* Limits and their standard errors are calculated in tsd()

           CHANGES IN VERSION 2.21    (2013-11-22)

* GSD, Hill and Richards equations are included in tsd() function
* Many improvments for tsd() function

           CHANGES IN VERSION 2.19-2.20    (2013-09-26)

* In MovingIncubation(), a timesseries at the end of incubation can be provided to model the metabolic heating
* SE of parameters are used if replicate.CI is different from 0

           CHANGES IN VERSION 2.18    (2013-09-09)

* Correction of bug in generateIL.df and info.nests
* generateIL.df renamed GenerateConstInc
* New parameter xlimR to show only part of R function in plotR and plotR_hist

           CHANGES IN VERSION 2.17    (2013-08-20)

* hist.nests and hist.nestsresults return a list with the complete set of temperatures

           CHANGES IN VERSION 2.16    (2013-07-01)

* New function generateIL.df

           CHANGES IN VERSION 2.15    (2013-06-25)

* New parameter OutPlot for plot.NestsResult()

           CHANGES IN VERSION 2.15    (2013-06-24)

* Correct a bug for mean temperature of a nest

           CHANGES IN VERSION 2.14    (2013-06-23)

* New version of uploading to ESE server after building package
* New parameter col for Entropy
* Output of tsd() takes into account that the regressor could be not the temperature

           CHANGES IN VERSION 2.11    (2013-06-11)

* Better format for examples

           CHANGES IN VERSION 2.10    (2013-04-08)
           
* New parameter for embryogrowth_MHmcmc_p() to automatically accept proposed priors
* New parameter echo for likelihoodR()

           CHANGES IN VERSION 2.09    (2013-04-04)
           
* Correct a bug in mean.temperature and mean.temperature.TSP in info.nest() and plot()
* Add a parameter to plotR() to manage where to display information "mean" and "confidence interval"

           CHANGES IN VERSION 2.08    (2013-04-04)
           
* Correct a bug in plotR_hist() if parameters for plotR() were used
* Add the progress parameter in info.nests
* Calculte the mean temperature during all incubation in info.nest() and plot()

           CHANGES IN VERSION 2.07    (2013-02-21)
           
* Parameter weight is added in FormatNests(), searchR() and likelihoodR()
* Correct the test in SearchR() to be sure that fixed and fitted parameters are not duplicated
* New function weightmaxentropy() which searches for the relative weights for each nest to maximize entropy
* New database fitted with weight

            CHANGES IN VERSION 2.06    (2013-02-15)
           
* Correct Movingincubation() to take into account the _L list return by .SSM()
* Correct plot.NestsResult() for truncated numbers
* as.par.mcmcComposite() and as.mcmc.mcmcComposite() are transfered to the package phenology.
* Loading of package does not failed if the description is not available online.
* Movingincubation() returns a dataframe with time and length of TSP

            CHANGES IN VERSION 2.05    (2013-01-27)
           
* many minor changes in plot.NestsResult for better ylimS managment and to prevent an error when no SD is available

           CHANGES IN VERSION 2.04    (2013-01-09)
           
* tsd() show the complete curve depending on xlim parameter
* plot.NestsResult returns a list with two objects: summary with the summary statistics for each nest and traces with the change of length or mass for each nest

           CHANGES IN VERSION 2.00-2.03    (2013-01-02)
           
* Embryo growth can be modeled using two sets of equations, one for early development and one for late development
* as.mcmc() can be used with mcmcComposite objects
* library zoo is required to use na.locf()
* Add the function tsd() to fit data of temperature-dependent sex determination
* Correction of bug for show.box and ylimH parameters in plotR() and plotR_hist()

           CHANGES IN VERSION 1.23    (2012-11-11)

* New parameter for plot(NestsResult): ref.stage=TRUE ou FALSE
* Modeled size at the end of incubation and likelihood for each nest are returned by plot()

           CHANGES IN VERSION 1.22    (2012-11-09)

* New function MovingIncubation() to run the model day by day on a timeseries
* summary() for Nests objects
* Add simplify=TRUE for FormatNests()
* mcmc data for 6p: result_mcmc_6p_80
* Correct scale of x axis for histogram and add legend for Y axis in plotR_hist()
* Legends are not drawn twice in plotR() with lists
* Initial point is taken into account for as.par.mcmcComposite()

           CHANGES IN VERSION 1.20-1.21    (2012-11-01)

* Update can use install_url() from package devtools
* New function GenerateTest(series, size, previous) to generate test parameter for searchR()
* Color of embryo mass in plot can be changed using a vector of colors

           CHANGES IN VERSION 1.14-1.19    (2012-10-31)

* Remove the use of .EGR.env environment for searchR() in 1.14 and in plot() in 1.17
* Package can load when no internet connection is available
* Add a function testParallel() to evaluate if the option parallel is interesting for the running system
* Add class mcmcComposite to result of embryogrowth_MHmcmc()
* Add BatchSE and TimeSeriesSE elements of the output of embryogrowth_MHmcmc()
* New function plotR_hist() to display both RGraph and hist of temperatures
* Rename as_mcmc() to as.mcmc2.mcmcComposite()
* New function as.par.mcmcComposite() to get parameters at maximum likelihood from mcmcComposite object
* Add a parameter force=TRUE or FALSE to force update

           CHANGES IN VERSION 1.11-1.13     (2012-10-23)

* Rename extractMCMC() to as_mcmc()
* Correct a bias when the temperature reaches a maximum or minimum
* Allow parallel computing to be disabled

           CHANGES IN VERSION 1.10      (2012-10-21)

* Uses parallel computing for searchR() and embryogrowth_MHmcmc()

           CHANGES IN VERSION 1.09      (2012-10-19)

* New functions: extractMCMC() to be used with mcmcComposite objects to get an object to be use with coda package
* New functions: embryogrowthUpdate() to update package
* Package version is checked at package loading
* Add the defaults plot parameters for plotR()
* Possible to plot several growth rates using list objects
* Correct a bias when the temperatures always increase or decrease during incubation

           CHANGES IN VERSION 1.08      (2012-10-07)

* Use mcmc methods from phenology package

           CHANGES IN VERSION 1.07      (2012-10-06)

* Remove plotnest() and plotMHmcmc() function to keep only plot().
* If optimization is not finished after maxiter, it shows the value of fitted parameters and continues.
* Change mcmcNests class to mcmcComposite.
* plot.Nests() returns also the mean temperature within the TSP.
* The package is renamed embryogrowth
* The objects wihtin the mcmcComposite object are mcmc and mcmc.list objects
* Add a method summary of mcmcComposite object
 
 CHANGES IN VERSION 1.04      (2012-05-28 -> 2012-07-28)

* Add the possibility to use fixed parameters
* Add the three new class: mcmcNests, Nests and NestsResult
* Add Bayesian MCMC script and plot of MCMC
* Many minor changes for speed improvment
* Some bug corrections
* Change T12H for 6-parameters equation to DT
* Catch the error of singularity of matrix
* Better managment of test size if the temperatures are changed

           CHANGES IN VERSION 1.05      (2012-07-30)

* The MHMCMC algorithm can now be used by other packages.
* hist.NestsResult uses the same script as hist.Nests
* plot gives information on the position of first and second third and Sum of Square difference between these and the position of stages 21 and 26.

            CHANGES IN VERSION 1.00-1.03 (2012-05-27)

* first versions as a package. New functions added sequentially.








