News

THIS IS THE CHANGELOG OF THE "embryogrowth" PACKAGE

        CHANGES IN VERSION 7.4.1 (2018-09-26)

• New function to study data logger precision: uncertainty.datalogger - 7.3

• Correct a bug in predict.HatchingSuccess - 7.3

• Correct a bug in STRN - 7.3.1

• Add the temperatures object in STRN output - 7.3.2

• New functions calibrate.datalogger - 7.3.3

• Simplification of calibrate.datalogger() and uncertainty.datalogger() - 7.3.4

• uncertainty.datalogger() by default uses only one measurement - 7.4.1

        CHANGES IN VERSION 7.2.3 (2018-02-07)
  

• New functions to study hatching success - 7.2

• Temperature.max is a new output of info.nests() - 7.2.1

• Change the examples of info.nests() - 7.2.2

• New Generic_ProportionDevelopment item in TSP.list - 7.2.3

        CHANGES IN VERSION 7.1.1 (2018-01-24)
  

• Add an example to plot the temperatures - 7.1.1

      CHANGES IN VERSION 7.1-7.1.1    (2017-11-19)
  

• If no SD for test, use SSE criteria to fit - 7.1

• New example in searchR to fit data using method of proportion of development - 7.1

• Small improvment in plot.NestsResult() - 7.1

• Better control of the beginning and end of the TSP within the corresponding stages - 7.1

      CHANGES IN VERSION 7.0    (2017-09-25)
  

• 2D reaction norm - 7.0

• Cholesky decomposition is used to estimate a pseudo-variance matrix for SE - 7.0

• AICc and BIC are estimated for the sexualisation thermal reaction norm - 7.0

• SE or hessian are used for movingincubation - 7.0

• Podocnemis expansa stages - 7.0

      CHANGES IN VERSION 6.5-6.5.18    (2017-05-09)
  

• New version for CRAN - 6.5

• Correction of some examples - 6.5.1

• Cleaning DatabaseTSD - 6.5.1

• New parameter pipping_emergence is the number of days between pipping and emergence. It is used to establish the 1/3 and 2/3 of the incubation - 6.5.2

• predict.tsd() can be used with only one probs - 6.5.3

• STRN() used the new version of predict.tsd() - 6.5.3

• STRN_MHmcmc() is corrected to be used with fixed.parameters of STRN() - 6.5.3

• First tentative to include hygrometry in the model as cofactor of Rho25 parameter. The new parameters are Rho25_b and Rho25_b_L - 6.5.3

• predict.tsd() works without temperatures or durations - 6.5.4

• New prallel parameter for STRN() and STRN_MHmcmc() - 6.5.5

• fixed.parameters from STRN is used now in info.nests() - 6.5.6

• New examples for STRN() and STRN_MHmcmc() - 6.5.6

• Minor bug for fixed.parameters in info.nests() - 6.5.7

• tsd(), P_TRT() and plot.tsd() can be used when some parameters are badly fitted - 6.5.8

• plot.tsd() is more robust to unusual situations - 6.5.9

• New outMCMC data - 6.5.10

• STRN() is faster if some timeseries have no information for sex - 6.5.11

• Database of embryological stages is more complete - 6.5.12

• New exemple for stages dataset - 6.5.13

• plot() of series can use the hessian matrix - 6.5.13

• Better control of the confidence interval shown is plot() using the CI parameter - 6.5.14

• Minor change in stages dataset - 6.5.15

• Hessian matrix for STRN() is estimated - 6.5.16

• info.nests() can use Hessian matrix for STRN() - 6.5.17

• Minor change in info.nests() - 6.5.18

      CHANGES IN VERSION 6.4-6.4.56    (2017-03-09)
  

• New version for CRAN - 6.4

• Correction of the y legend for plotR() - 6.4.1 & 6.4.2

• ylim parameter for plotR() works again - 6.4.2

• Bug correction : GRTRN_MHmcmc() works also with only one parameter - 6.4.3

• New parameter for SSM model: epsilon (SSM = SSM + epsilon) - 6.4.4

• Correct some examples - 6.4.5

• Nicer arrow for plot - 6.4.6

• New examples - 6.4.7

• Separate parameters for plotR and hist in plotR_hist() - 6.4.7

• New examples - 6.4.8 & 6.4.9

• Legend for hist() and plotR_hist() has been changed to Temperature density - 6.4.10

• Arrows in plot() are no more masked - 6.4.11

• Possibility to setup nonsymmetrical confidence interval using quantiles in ChangeSSM() - 6.4.12

• The non-symmetrical confidence interval can be used for randomization using info.nests() - 6.4.12

• New functions plotRdensity() and plotRdensity_hist() - 6.4.12

• New examples - 6.4.13

• If a mcmc object is used in info.nests() or plot.NestsResult(), it will be used directly - 6.4.14

• New asymmetric normal model - 6.4.15

• trace can be changed during mcmc search after a stop and previous use - 6.4.16

• New trigonometric model - 6.4.16

• Correct scaleY for plotRdensity() - 6.4.17

• Weibull model is correct and functional - 6.4.17

• BIC is calculated after searchR() - 6.4.17

• Correct a bug in info.nests() for replicate.CI=1 and resultmcmc - 6.4.18

• mcmc for normal function in SSM - 6.4.18

• new function nobs.NestResult() to be used with BIC() - 6.4.18

• New mcmc results for trigo and Weibull models - 6.4.19

• Adaptive mcmc is implemented for GTRN and STRN - 6.4.20

• Adaptive mcmc is implemented for TSD - 6.4.21

• Parallel computing implemented for windows - 6.4.22 & 6.4.23 & 6.4.24

• New version of resultNest_mcmc_4p_normal - 6.4.25

• Prevent an error in rare case in tsd - 6.4.26

• New examples in resultNest_mcmc_4p_normal - 6.4.26

• New data for Weibull model with 3 parameters - 6.4.27

• New data for SSM6p model - 6.4.28

• Bug correction when metric.end.incubation == NA - 6.4.28

• Transition parameters work for Weibull model - 6.4.29

• Can use several size for transition model in the same plot - 6.4.29

• set.par with plotR works again- 6.4.30

• cex.lab = 1, cex.axis = 1 for plotRdensity - 6.4.31

• New plotR2() will be a replacement for plotR, plotR_hist, plotRdensity and plotRdensity_hist - 6.4.32

• Cleaning the code: remove old SEforR, plotR, plotR_hist, plotRdensity and plotRdensity_hist - 6.4.33

• MovingIncubation() scheme for parallel is better and mcmc objects can be used instead of SE - 6.4.34

• Correct some problems with parallel in info.nests() in windows - 6.4.34

• polygon option for plotR() - 6.4.35

• mar and breaks parameter for plotR() - 6.4.36

• correct a bug in info.nests() for windows when parallel=FALSE - 6.4.37

• Legends are homogenized for various plots - 6.4.37

• New results in info.nests()$summary: CTEA.TSP_CTEA.2ndT, CTEA.TSP_CTEA.2ndT.se, CTEW.TSP_CTEW.2ndT, CTEW.TSP_CTEW.2ndT.se - 6.4.37

• New option parallel for MovingIncubation() and plot.NestsResult() to use or not parallel computing - 6.4.37

• New parameter SexualisationTRN.mcmc to generate variability of SexualisationTRN - 6.4.37

• If + or -Inf is produced in SSM, does not produce error - 6.4.38

• Dallwitz 3 parameters is simpler to implement - 6.4.39

• Correct a problem with mar parameter in plotR() - 6.4.40

• SE as matrix can be used with plotR() - 6.4.41

• New parameter log.hist canbe used to show log axis for histogram - 6.4.42

• Minor change for plot.tsd() - 6.4.43

• new parameter fixed.parameters for STRN() - 6.4.44

• Fix a bug in MovingIncubation() - 6.4.45

• Implementation of delta method for confidence interval - 6.4.46

• temperature.heterogeneity accepts a vector of two values being sd_low and sd_high - 6.4.47

• Change the suggest packages - 6.4.48

• Better management of curves and polygon in plotR() - 6.4.49

• Minor change to prevent warnings() in plotR() - 6.4.50

• Correct tsd_MHmcmc() - 6.4.51

• SE returns by tsd() was not SE but variance - 6.4.52

• New parameter mar for plot.tsd() - 6.4.52

• New function trt() - 6.4.53

• New function P_TRT() more general than trt(); trt() is removed - 6.4.54

• Confidence interval for plot.tsd() uses the hessian matrix - 6.4.54

• durations is added for P_TRT() - 6.4.55

• SD for temperatures or durations is added for P_TRT() - 6.4.55

• predict.tsd can use mcmc or hessian matrix - 6.4.55

• minor change in predict.tsd - 6.4.56

      CHANGES IN VERSION 6.3.1-6.3.11    (2016-09-15)
  

• New shiny function web.tsd() - 6.3.1

• Restore web.tsd() - 6.3.2

• Minor modification of shiny application - 6.3.3

• plotR() returns R values in the unmodified scale - 6.3.4

• Modification of the scale of R graph produced by plotR() - 6.3.4

• errbar.tick does not produce warnings() in plot.tsd() - 6.3.5

• No error if show.anchors is used with plotR_hist() - 6.3.6

• Info.nest() returns also MassWeighted.temperature.mean - 6.3.7

• Solve some rare cases when info.nest()$summary returns NA - 6.3.7

• Correct description for test parameter in searchR() - 6.3.8

• Add parameter show.legend in plotR() - 6.3.9

• Correct a bug for STRN() when one of the timeseries had no known sex ratio - 6.3.10

• cex.axis in plot.tsd() and plot.NestResult() is used for x-axis - 6.3.11

      CHANGES IN VERSION 6.3    (2016-07-17)
  

• Minor update of plot.NestResult() to show TSP at the top of temperatures - 6.2.1

• Caretta caretta stages are no more defaults for plot.NestResult() - 6.2.1

• equation Hulin for tsd() is more robust - 6.2.2

• fixedparameter is used for mcmc - 6.2.2

• A matrix for SE can be used in plotR() for anchored parameters to use quantiles - 6.2.3

• New parameter x.SE to control the envelope of R - 6.2.3

• cex.axis and cex.lab works for temperature scale in plotR_hist - 6.2.4

• tsd indicates durations or temperatures correctly depending on data input - 6.2.5

• plot.tsd indicates durations or temperatures correctly - 6.2.6

• It is possible to show anchors in plotR() and plotR_hist() - 6.2.7

• New columns and information in STSR_TSD database - 6.2.8

• STRN() has been changed to be more reliable if the order of nests is changed - 6.2.8

• Bug correction in info.nests() - 6.2.9

• New option to not show observations in plot.tsd() - 6.2.9

• New parameter parallel for info.nests() and GTRN_MHmcmc() to control the use of parallel version within R (preparation for SparkR version) - 6.2.10

• batchsize option has been removed from GTRN_MHmcmc() - 6.2.10

• New example for movingincubation() - 6.2.11

• Introduction of Weibull function to fit thermal reaction norm - 6.2.11

• New parameter metabolic.heating in info.nests() - 6.2.11

• New parameter metabolic.heating in movingincubation() - 6.2.12

• range.CI parameter of predict.tsd() is replaced by quantiles - 6.2.13

• New temperature.heterogeneity parameter in info.nests() and movingincubation() - 6.2.14

• Changes in documentation - 6.2.15

• Better managment of error in SE during SearchR() - 6.2.16

• New function SEforR() to estimate SE for a set of parameters based on Fisher information matrix - 6.2.16

• Estimation of anchored model is more rapid - 6.2.16

• New parameter XlimSE for plotR and plotR is simplified - 6.2.17

• New model for anchors (polynomial fit) - 6.2.18

• New parameter hessian to return the hessian matrix in SEforR() - 6.2.18

• New model for anchors (linear fit) - 6.2.19

• Correct a bug in STRN() that prevent SE estimation - 6.2.19

• Object returns by STRN() is more complete and can be used by compare_AIC - 6.2.20

• info.nests() can use an object created by STRN() for the parameter SexualisationTRN - 6.2.20

• Call to MCMC is simplified - 6.2.21

• info.nests() use a parameter x rather than parameters - 6.2.21

• info.nests() can use both x and parameters to provide back compatibility - 6.2.22

• plotR() and plotR_hist() return a list with confidence intevals - 6.2.23

• Correct a bug in info.nests() (Thanks to Taylor R. Roberge to identifiy it) - 6.2.24

• xlimR of plotR() or plotR_hist() can be a vector of values - 6.2.24

• New example for plotR() using xlimR as a vector - 6.2.25

• shiny version has been removed as it was not maintained anymore - 6.3

      CHANGES IN VERSION 6.2    (2016-01-08)
  

• Update of documentation

      CHANGES IN VERSION 6.1.3-6.1.5    (2015-12-04)
  

• plot.NestResult() and plotR_hist() can be used with layout() or mfrow() - 6.1.3

• New database stages for embryonics stages, mass and SCL. Will be expanded in next versions - 6.1.4

• Solve a problem with mcmc - 6.1.5

      CHANGES IN VERSION 6.1.2    (2015-10-22)
  

• Correct a problem with info.nest when timeseries are of different length during resampling of parameters

• Correct a problem with info.nest when fill is not NULL

      CHANGES IN VERSION 6.1.1    (2015-10-16)
  

• Correct a problem occuring only with windows version

      CHANGES IN VERSION 6.1    (2015-10-11)
  

• Correction of movingincubation() to work with the new version of info.nests()

• In info.nests(), when temperatures are changed, if all NestResult$test parameters are the same and test is NULL, the test parameter is taken from NestResult$test

• metric.end.incubation in info.nests() and plot.NestsResult() is recycled if necessary

• plot.NestsResult() uses info.nests(), new parameter show.metric

• if metric.end.incubation is NA, the embryo metrics for TSP are scaled by metric of hatchlings at the end of incubation

• if metric.end.incubation is NULL, the embryo metrics for TSP are scaled by the maximum metric of mean in test parameters

• if metric.end.incubation is a value, it is used directly for scale

• New data for info.nests(): MiddleThird.MassWeighted.temperature.mean and .se

• Correct a bug for info.nests() if there is only one temperature

• Correct a bug for searchR() that prevent return a result in rare occasions

• metric and summary can be used when partial incubations are observed using metric.end.incubation=x with x being the final size

• Correct a bug for fill parameter in info.nests()

• New data for embryological stages: Emys orbicularis.mass and Emys obicularis.SCL. They are store in TSP.list

• Rename Caretta caretta embryological stages: Caretta caretta.SCL

• After plotR_hist(), the y-scale is the scale for R graph (previously it was the one for histogram)

• Only the function lsoda is imported from deSolve to prevent a warning during check

      CHANGES IN VERSION 6.0.1    (2015-06-30)
  

• Change info.nests() for R 3.2 compatibility

• Minor changes in FormatNests(); test if names are unique

• Correct a bug for Hill model of TSD

• Add optimx as an option for searchR()

• The latest version can always been installed using: install.packages("http://www.ese.u-psud.fr/epc/conservation/CRAN/embryogrowth.tar.gz", repos=NULL, type="source")

• $SD is store also in mcmc objects. This SD is the SE for points estimates.

      CHANGES IN VERSION 6.0    (2015-04-15)
  

• FormatNests() can convert old format database using data=xxx with xxx being the old format database

• info.nests() is much more complete

• polynom package is now in dependencies

• New columns IndiceK in FormatNests() output to accelerate SearchR()

• predict.tsd() uses the new model for CI estimation

• plot.tsd() does not make any estimation; it just plot the object created by tsd()

• New method for confidence interval in tsd()

• If stopattest=TRUE is used in .fonctionfit() the time for end of incubation is estimated using polynomial interpolation

• Hmisc package is no more required

• new parameters SE and fixed.parameters in tsd()

• The anchored parameters can use Celcius degrees

• Many changes in .fonctionfit .STRNfit (hidden fonctions)

• searchR() is more rational for initial tests of weights and better manage parallel runs

• Add a progression bar for predict.tsd()

• MHmcmcAlgo(), minmax.periodic(), temperature.periodic() and info.sun() functions are transfered to new package: HelpersMG

• STRN() does not use replicate.CI for info.nests()

• Add parameters= for GenerateAnchor() and GRTRN_MHmcmc_p()

• The weight scheme for CTE called weigthed mean temperature during TSP can use another thermal reaction norm: the thermal reaction norm for sexualisation (STRN). The new CTE is named TSD.mean.temperature

• New CTE named TSD.weighted.mean.temperature. It includes both the thernal reaction norm for growth rate and the thermal reaction norm for sexualisation.

• New function STRN() to fit the Sexualisation thermal reaction norm

• New function STRN_MHmcmc() to model the enveloppe of the STRN

• New parameters to continue MCMC run from previous run in GRTRN_MHmcmc(), STRN_MHmcmc() and tsd_MHmcmc()

• Correct a bug to estimate the mean temperature within the TSP

• If weight is included in FormatNests, it is used in searchR()

• Correct a bug when plotR() is called without result parameter

• Correct a bug for info.nest() with SE

• Temperatures or durations can be associated with SE for predict.tsd()

• TestParallel() function display the user time of system.time()

• Package polynom is required for anchored model

• Anchored model uses now Lagrange polynoms rather than loess fitting method

• When anchored model is negative, it is fixed to 0

• New function sun.info()

• minmax.periodic() can use different minimum or maximum time each day. Correct a bug for SD in minmax.periodic

      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.

Reference manual