Tools to Analyze the Thermal Reaction Norm of Embryo Growth

Tools to analyze the embryo growth and the sexualisation thermal reaction norms. See for tsd functions; see for thermal reaction norm of embryo growth.


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

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install.packages("embryogrowth")

8.2 by Marc Girondot, 2 months ago


Browse source code at https://github.com/cran/embryogrowth


Authors: Marc Girondot <[email protected]>


Documentation:   PDF Manual  


GPL-2 license


Depends on deSolve, optimx, numDeriv, parallel, HelpersMG

Suggests entropy, shiny, coda, polynom, car, lmf, gam, pbapply


See at CRAN