Tools to Analyze the Thermal Reaction Norm of Embryo Growth

Tools to analyze the embryo growth and the sexualisation thermal reaction norms.


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")

7.6 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


See at CRAN