THIS IS THE CHANGELOG OF THE "embryogrowth" PACKAGE CHANGES IN VERSION 9.1 (2023-10-24) * New CRAN version - 9.1 (2023-04-03) CHANGES IN VERSION 9.0.2 (2023-10-24) * New CRAN version - 9.0 (2023-04-03) * New stages for Lepidochelys olivacea - 9.0.1 (2023-09-12) * Correction of priors for TSD when durations are used - 9.0.2 (2023-10-02) * New data for Trachemys in databaseTSD - 9.1 (2023-10-24) CHANGES IN VERSION 8.7.3 (2023-03-16) * New CRAN version - 8.7 (2022-09-06) * Solve a rare problem in FormatNests() - 8.7.1 (2023-02-17) * New parameter xlimR in plotR() - 8.7.2 (2023-02-22) * Change the limits for L-BFGS-B parameters in HatchingSuccess.fit() - 8.7.3 (2023-03-16) * SexualisationTRN can use the polynom format 9.0 (2023-04-07) CHANGES IN VERSION 8.6-7 (2022-08-22) * New CRAN version - 8.6 (2022-07-14) * Fix align for html5 - 8.6-7 (2022-08-22) CHANGES IN VERSION 8.5-17 (2022-07-13) * New CRAN version - 8.5 (2022-05-28) * The hatching success model can be defined only with one parameter, MaxHS or MeanHS - 8.5-1 (2022-05-29) * Fixed.parameters are used in plot of HatchingSuccess - 8.5-11 (2022-06-06) * Tentatively solve a problem in movingincubation in Windows when parallel is TRUE - 8.5-16 (2022-07-13) CHANGES IN VERSION 8.4-10 (2022-05-05) * New CRAN version - 8.4 (2022-04-04) * Better managment of class - 8.4-1 (2022-04-21) * Side effect of new class managment for STRN_MHmcmc() is corrected - 8.4-9 (2022-05-05) CHANGES IN VERSION 8.3-26 (2022-04-02) * New CRAN version - 8.3 (2022-01-31) * Minor change for figure in documentation - 8.3-1 (2022-02-17) * New url to update the package before to be uploaded to CRAN - 8.3-5 (2022-02-24) * Check for update at startup - 8.3-6 (2022-03-28) * New parameter SD for final size when proportion of development is used - 8.3-7 (2022-03-28) * New parameters Threshold_High and Threshold_Low - 8.3-17 (2022-04-01) * Function TRN_MHmcmc_p() has been simplified - 8.3-20 (2022-04-02) CHANGES IN VERSION 8.2-15 (2022-01-26) * New CRAN version - 8.2 (2021-06-29) * Add option "pseudohessianfrommcmc" for movingincubation - 8.2-1 (2021-10-06) * plotR() return a list with two elements, scaleY and xy - 8.2-4 (2021-11-19) * plot.tsd() return a data.frame with model - 8.2-6 (2022-01-11) CHANGES IN VERSION 8.1-7 (2021-08-20) * New CRAN version - 8.1 (2021-06-29) * tsd() accepts replicate.CI being null - 8.1-1 (2021-07-13) * MovingIncubation() accepts metabolic.heating being different from 0 - 8.1-5 (2021-08-19) CHANGES IN VERSION 8.0-42 (2021-06-03) * fixed.parameters works again in tsd - 8.0-0 (2020-10-20) * Fix a bug for AICc and BIC estimation in tsd function - 8.0-1 (2020-10-31) * Calculate AICc and BIC in HatchingSuccess.fit - 8.0-2 (2020-11-23) * HatchingSuccess.fit is compatible with IP.mean - 8.0-2 (2020-11-23) * Polishing STRN - 8.0-3 (2020-12-10) * Correction for deviance test in tsd() - 8.0-4 * nobs.HatchingSuccess() is corrected - 8.0-5 * BIG CHANGE: test and stopattest parameters are renamed hatchling.metric and stop.at.hatchling.metric - 8.0-6 * BIG EXPERIMENTAL CHANGE: New method to estimate growth of embryos to limit the impact of Runge-Kutta approximation - 8.0-7-8.0-9 * New ways to estimate CTE in info.nests() to be closer from the biological interpretation - 8.0-10 * P_TRT works when S is positive in flexit model - 8.0-11 (2021-02-01) * Change of description in STRN_MHmcmc() - 8.0-12 (2021-02-03) * durations can be used with predict.tsd - 8.0-13 (2021-02-04) * SE FALSE does not roduce error in tsd - 8.0-14 (2021-03-15) * Minor change in info.nests() - 8.0-15 (2021-04-07) * Results in info.nests() are ordered - 8.0-16 (2021-04-08) * New parameter max.time in MovingIncubation() - 8.0-17 (2021-04-13) * Change in info.nests to ensure that size is always increasing - 8.0-18 (2021-04-14) * Change in TRN_MHmcmc_p() to use only runif distribution - 8.0-19 (2021-04-15) * Minor change in description of DatabaseTSD(), info.nests() and GRTRN_MHmcmc() - 8.0-20 (2021-04-16) * Updated version of examples in searchR() - 8.0-21 (2021-04-19) * Minor change in info.nests() when fill is the same as existing temperatures - 8.0-21 (2021-04-19) * Cchange in info.nests() to estimate the TSP - 8.0-22 (2021-04-19) * Minor change in STRN() - 8.0-23 (2021-04-20) * Simplification and enhancement of STRN() - 8.0-24 (2021-04-27) * Prevent a case in which LengthTSP can be negative in STRN() - 8.0-25 (2021-04-29) * Add embryogrowth logo - 8.0-26 (2021-05-01) * Minor changes in info.nests() - 8.0-27 (2021-05-03) * Add hessian parameter in STRN() - 8.0-28 (2021-05-04) * Minor changes in info.nests() - 8.0-29 (2021-05-03) * Minor changes in info.nests() - 8.0-30 & 8.0-31 & 8.0-32 & 8.0-33 (2021-05-11) * Minor changes in movingincubation() - 8.0-34 & 8.0-35 (2021-05-11) * Minor changes in info.nests() - 8.0-36 (2021-05-12) * fill parameter in STRN() - 8.0-37 (2021-05-13) * Minor change in plotR - 8.0-38 (2021-05-14) * Minor changes in info.nests() - 8.0-39 (2021-05-16) * Minor changes in info.nests() - 8.0-40 (2021-05-17) * Add option dynamic in info.nests() - 8.0-41 (2021-05-18) * Solve too long vector in info.nests() - 8.0-42 (2021-06-03) CHANGES IN VERSION 7.7 (2020-01-15) * Correct a strange erratic problem in P_TRT() - 7.6.1 * Correct a problem when replicate.CI was not taken into account with resultmcmc in P_TRT() - 7.6.2 * Parameter CI replaced by GTRN.CI in info.nests() - 7.6.3 * Better management of replicate.CI in info.nests() - 7.6.3 * Minor changes in info.nests() and moving.incubation() - 7.6.4 * Major changes in hatching success model - 7.6.5 * Correct a bug in predict.HatchingSuccess() with MCMC - 7.6.6 * New version of TSD database - 7.6.7 * New function movement() - 7.7 * replicate.NullDeviance was not taken into account in tsd() - 7.7 * New CRAN version - 7.7 (2020-01-15) * TSP.begin and TSP.end are used in STRN - 7.7.1 (2020-02-22) * MassWeighted is replaced by GrowthWeighted in info.nests() - 7.7.2 (2020-02-23) * New outputs in info.nests() with GrowthRateWeighted - 7.7.2 (2020-02-23) * Minor changes in plot.tsd() and P_TRT() - 7.7.3 (2020-06-10) * Add flexit in tsd in shiny - 7.7.4 (2020-06-27) * when mcmc result is given with P_TRT() and the number of replicate.ci is equal to the number of iteration, no resampling is done - 7.7.5 (2020-08-12) * Improvement of the hatchling success model - 7.8 (2020-09-17) * Improvement of databaseTSD for Eretmochelys imbricata - 7.8.1 & 7.8.2 (2020-09-23 & 2020-09-24) * New hessian parameter in HatchingSuccess.fit - 7.8.3 (2020-10-07) * tsd function can now fit TSDII or FMF pattern - 7.9 (2020-10-11) * DatabaseTSD.version() returns the date of the most recent update of the database TSD - 7.9 (2020-10-19) CHANGES IN VERSION 7.6 (2019-08-30) * 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 * New version of TSD database - 7.4.2 * Better fit control in tsd() - 7.4.3 * New algorithm to search for confidence interval of TRT bounds in tsd() - 7.4.4 * New approximation for Hulin, Richards, and double-Richards equations in tsd() - 7.4.5 * New example in info.nests() - 7.4.6 * fixed.parameters in fitHS() - 7.4.7 * TSP.borders parameter in STRN() - 7.4.8 * Correct a bug when weights were used - 7.4.9 * STRN can fit the TSD model - 7.5, 7.5.1, 7.5.2, 7.5.3 * movingincubation() can show again a progress bar - 7.5.4 * P_TRT() can manipulate very large TRT - 7.5.5 * New example in info.nests() to use the PM method of Massey et al. 2019 - 7.5.6 * info.nests() returns PM.mean and PM.se from Massey et al. 2019 - 7.5.7 * Correct a bug in info.nests()$metric when more than one nest were used - 7.5.7 * New outputs for summary of info.nests() PM.TimeWeight.mean and PM.TimeWeight.se - 7.5.8 * Bug correction in info.nests() - 7.5.9 * New flexit model for tsd() - 7.5.10 * New mcmc function for hatching success - 7.5.11 * Rename all Hatching Success functions for better homogeneity; new plot function - 7.5.12 * Better implementation of flexit model for tsd - 7.5.14-7.5.15 * Solve a case when predict.tsd() returns 0 or 1 whereas some observations are present - 7.5.16 * Better implementation of flexit model for tsd - 7.5.17 * Fix a bug in STRN_MHmcmc - 7.5.18 * Better implementation of flexit model for tsd - 7.5.19 * flexit model for tsd comes from HelpersMG package - 7.5.20 * traceML parameter for GRTRN_MHmcmc, HatchingSuccess.MHmcmc, tsd_MHmcmc, and STRN_MHmcmc- 7.5.21 (2019-08-20) * Solve a problem in plot.tsd() when SE for S, K1 or K2 are very high - 7.5.22 & 7.5.23 (2019-08-22) * TRT is no more estimated for Hulin and Double-A-logistic models of tsd() - 7.5.24 * Add deviance test for tsd() - 7.5.25 * Correct deviance estimation for tsd() - 7.5.26 * Correct TRT estimation for A-logistic model for extrem K value- 7.5.27 * New CRAN version - 7.6 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.