Changes in version 2025.12.22 (2025-12-22) o New CRAN version - 10.3 (2025-08-08) o Begin, End of TSP and End of incubation are better managed in info.nests() - 10.3.1 (2025-08-21) o Solve a rare case with a problem in info.nests() - 10.3.2 (2025-08-21) o New CRAN Version - 10.4 (2025-09-10) o Minor change in plotR() to prevent an error when the number of replicates in mcmc quantiles when the number of row in object is lower than replicate.CI - 10.4.1 (2025-09-17) o New numerotation using the date - 2025.09.18 (2025-09-18) o New SD parameter for tsd() model - 2025.11.19 (2025-11-19) o The SD parameter in tsd() model can be used for mcmc - 2025.12.06 (2025.12.06) o New ROSIE database - 2025.12.22 (2025.12.22) Changes in version 10.2 (2025-06-16) o New CRAN version - 10.2 (2025-06-16) o Better color managment for HeterogeneityNests - 10.2.1 (2025-06-30) o Remove default values for metric size in searchR() - 10.2.2 (2025-07-08) o Minor change in HeterogeneityNests() - 10.2.3 (2025-07-15) o Authorize lwd and lty in absolute time in plot.Nest2() - 10.2.4 (2025-07-21) o WAIC option is included for Hatching.Success() - 10.2.5 (2025-08-06) o Cosmetic change in plot.HatchingSuccess() - 10.2.6 (2025-08-07) Changes in version 10.1 o New CRAN version - 10.1 (2025-05-06) o New parameter for plot.tsd: show.observations.sd - 10.1.1 (2025-05-25) o New parameter for plot.Nest2 to change the labels - 10.1.2 (2025-05-29) o Add xaxt parameter for plotR - 10.1.3 (2025-06-03) o Update ROSIE database - 10.1.4 (2025-06-03) o Bug correction for absolute plot in plot.Nest2 - 10.1.5 (2025-06-09) o can show only full or half heterogeneity - 10.1.6 (2025-06-09) Changes in version 10.0 o New internal format for Nests objects - 10.0 (2025-02-10) o Bug for HeterogeneityNests() - 10.0.1 (2025-02-28) o WAIC for GRTRN_MHmcmc() - 10.0.4 (2025-03-06) o WAIC for STRN_MHmcmc() - 10.0.5 (2025-03-08) o WAIC for tsd() - 10.0.6 (2025-03-08) o New experimental stairs model for tsd() - 10.0.7 (2025-03-28) o Priors default in tsd_MHmcmc_p() can use different densities - 10.0.8 (2025-03-30) o Bug corrected to show the uncertainty in prediction of growth of embryo - 10.0.9 (2025-03-31) o flexit** model of tsd() is updated - 10.0.10 (2025-04-02) o Take into account replicate.CI in info.nest() when stop.at.hatchling.metric = TRUE - 10.0.11 (2025-04-04) o New stages version for TSP - 10.0.12 (2025-04-04) o Show the number of cores that will be used in searchR() - 10.0.13 (2025-04-09) o New information in movments() function - 10.0.14 (2025-04-30) o New options for x-scale in plot() - 10.0.14 (2025-04-30) o Correct a warning in hist() - 10.0.15 (2025-05-05) Changes in version 9.5.4 o New CRAN version - 9.5 (2024-08-23) o formatNests() accept a new information: the laying time for each nest - 9.5.3 (2025-02-04) o formatNests() can store information (UnitTime, Longitude, Latitude, Informations) for each nest - 9.5.4 (2025-02-06) Changes in version 9.4.2 o New CRAN version - 9.1 (2023-04-03) o Solve a problem in tsd() when the vcov matrix is not positive - 9.1.1 (2023-11-05) o Solve problems in movement() function - 9.1.2 (2023-11-07) o Experimental: Add a new possibility to estimate likelihood is tsd() for sex ratio when n is not known - 9.1.3 (2023-11-08) o New out possibility for info.nests() to be able to use Bayesian Model Averaging - 9.1.4 (2023-11-10) o Experimental: Add a new possibility to estimate likelihood in tsd() for sex ratio when n is not known - 9.1.5 (2023-11-08) o RMU.2010 and RMU.2023 are included in databaseTSD - 9.1.6 (2023-12-01) o New equation flexit* - 9.2 (2023-12-29) o New references- 9.2 (2024-02-05) o Minor change for initial parameters in tsd - 9.2.1 (2024-03-20) o Solve a problem in STRN when sex ratio was missing for some timeseries - 9.2.2 (2024-03-30) o STRN can use a flexit* model - 9.2.2 (2024-03-30) o 2 new columns in databaseTSD: incubation.temperature.set and incubation.temperature.corrected - 9.2.3 (2024-04-07) o Dermochelys coriacea information in databaseTSD were corrected - 9.2.4 (2024-04-30) o New option to use ggplot2 to produce tsd graph - 9.3.0 (2024-05-16) o New examples for tsd graph - 9.3.1 (2024-05-18) o Dermochelys coriacea information in databaseTSD were corrected - 9.3.3 (2024-05-22) o Dermochelys coriacea information in databaseTSD and listTSP were corrected - 9.4 (2024-05-26) o logit model is implemented in tsd - 9.4.1 (2024-06-24) Changes in version 9.0.2 o New CRAN version - 9.0 (2023-04-03) o New stages for Lepidochelys olivacea - 9.0.1 (2023-09-12) o Correction of priors for TSD when durations are used - 9.0.2 (2023-10-02) o New data for Trachemys in databaseTSD - 9.1 (2023-10-24) Changes in version 8.7.3 o New CRAN version - 8.7 (2022-09-06) o Solve a rare problem in FormatNests() - 8.7.1 (2023-02-17) o New parameter xlimR in plotR() - 8.7.2 (2023-02-22) o Change the limits for L-BFGS-B parameters in HatchingSuccess.fit() - 8.7.3 (2023-03-16) o SexualisationTRN can use the polynom format 9.0 (2023-04-07) Changes in version 8.6-7 o New CRAN version - 8.6 (2022-07-14) o Fix align for html5 - 8.6-7 (2022-08-22) Changes in version 8.5-17 o New CRAN version - 8.5 (2022-05-28) o The hatching success model can be defined only with one parameter, MaxHS or MeanHS - 8.5-1 (2022-05-29) o Fixed.parameters are used in plot of HatchingSuccess - 8.5-11 (2022-06-06) o Tentatively solve a problem in movingincubation in Windows when parallel is TRUE - 8.5-16 (2022-07-13) Changes in version 8.4-10 o New CRAN version - 8.4 (2022-04-04) o Better managment of class - 8.4-1 (2022-04-21) o Side effect of new class managment for STRN_MHmcmc() is corrected - 8.4-9 (2022-05-05) Changes in version 8.3-26 o New CRAN version - 8.3 (2022-01-31) o Minor change for figure in documentation - 8.3-1 (2022-02-17) o New url to update the package before to be uploaded to CRAN - 8.3-5 (2022-02-24) o Check for update at startup - 8.3-6 (2022-03-28) o New parameter SD for final size when proportion of development is used - 8.3-7 (2022-03-28) o New parameters Threshold_High and Threshold_Low - 8.3-17 (2022-04-01) o Function TRN_MHmcmc_p() has been simplified - 8.3-20 (2022-04-02) Changes in version 8.2-15 o New CRAN version - 8.2 (2021-06-29) o Add option "pseudohessianfrommcmc" for movingincubation - 8.2-1 (2021-10-06) o plotR() return a list with two elements, scaleY and xy - 8.2-4 (2021-11-19) o plot.tsd() return a data.frame with model - 8.2-6 (2022-01-11) Changes in version 8.1-7 o New CRAN version - 8.1 (2021-06-29) o tsd() accepts replicate.CI being null - 8.1-1 (2021-07-13) o MovingIncubation() accepts metabolic.heating being different from 0 - 8.1-5 (2021-08-19) Changes in version 8.0-42 o fixed.parameters works again in tsd - 8.0-0 (2020-10-20) o Fix a bug for AICc and BIC estimation in tsd function - 8.0-1 (2020-10-31) o Calculate AICc and BIC in HatchingSuccess.fit - 8.0-2 (2020-11-23) o HatchingSuccess.fit is compatible with IP.mean - 8.0-2 (2020-11-23) o Polishing STRN - 8.0-3 (2020-12-10) o Correction for deviance test in tsd() - 8.0-4 o nobs.HatchingSuccess() is corrected - 8.0-5 o BIG CHANGE: test and stopattest parameters are renamed hatchling.metric and stop.at.hatchling.metric - 8.0-6 o BIG EXPERIMENTAL CHANGE: New method to estimate growth of embryos to limit the impact of Runge-Kutta approximation - 8.0-7-8.0-9 o New ways to estimate CTE in info.nests() to be closer from the biological interpretation - 8.0-10 o P_TRT works when S is positive in flexit model - 8.0-11 (2021-02-01) o Change of description in STRN_MHmcmc() - 8.0-12 (2021-02-03) o durations can be used with predict.tsd - 8.0-13 (2021-02-04) o SE FALSE does not roduce error in tsd - 8.0-14 (2021-03-15) o Minor change in info.nests() - 8.0-15 (2021-04-07) o Results in info.nests() are ordered - 8.0-16 (2021-04-08) o New parameter max.time in MovingIncubation() - 8.0-17 (2021-04-13) o Change in info.nests to ensure that size is always increasing - 8.0-18 (2021-04-14) o Change in TRN_MHmcmc_p() to use only runif distribution - 8.0-19 (2021-04-15) o Minor change in description of DatabaseTSD(), info.nests() and GRTRN_MHmcmc() - 8.0-20 (2021-04-16) o Updated version of examples in searchR() - 8.0-21 (2021-04-19) o Minor change in info.nests() when fill is the same as existing temperatures - 8.0-21 (2021-04-19) o Cchange in info.nests() to estimate the TSP - 8.0-22 (2021-04-19) o Minor change in STRN() - 8.0-23 (2021-04-20) o Simplification and enhancement of STRN() - 8.0-24 (2021-04-27) o Prevent a case in which LengthTSP can be negative in STRN() - 8.0-25 (2021-04-29) o Add embryogrowth logo - 8.0-26 (2021-05-01) o Minor changes in info.nests() - 8.0-27 (2021-05-03) o Add hessian parameter in STRN() - 8.0-28 (2021-05-04) o Minor changes in info.nests() - 8.0-29 (2021-05-03) o Minor changes in info.nests() - 8.0-30 & 8.0-31 & 8.0-32 & 8.0-33 (2021-05-11) o Minor changes in movingincubation() - 8.0-34 & 8.0-35 (2021-05-11) o Minor changes in info.nests() - 8.0-36 (2021-05-12) o fill parameter in STRN() - 8.0-37 (2021-05-13) o Minor change in plotR - 8.0-38 (2021-05-14) o Minor changes in info.nests() - 8.0-39 (2021-05-16) o Minor changes in info.nests() - 8.0-40 (2021-05-17) o Add option dynamic in info.nests() - 8.0-41 (2021-05-18) o Solve too long vector in info.nests() - 8.0-42 (2021-06-03) Changes in version 7.7 o Correct a strange erratic problem in P_TRT() - 7.6.1 o Correct a problem when replicate.CI was not taken into account with resultmcmc in P_TRT() - 7.6.2 o Parameter CI replaced by GTRN.CI in info.nests() - 7.6.3 o Better management of replicate.CI in info.nests() - 7.6.3 o Minor changes in info.nests() and moving.incubation() - 7.6.4 o Major changes in hatching success model - 7.6.5 o Correct a bug in predict.HatchingSuccess() with MCMC - 7.6.6 o New version of TSD database - 7.6.7 o New function movement() - 7.7 o replicate.NullDeviance was not taken into account in tsd() - 7.7 o New CRAN version - 7.7 (2020-01-15) o TSP.begin and TSP.end are used in STRN - 7.7.1 (2020-02-22) o MassWeighted is replaced by GrowthWeighted in info.nests() - 7.7.2 (2020-02-23) o New outputs in info.nests() with GrowthRateWeighted - 7.7.2 (2020-02-23) o Minor changes in plot.tsd() and P_TRT() - 7.7.3 (2020-06-10) o Add flexit in tsd in shiny - 7.7.4 (2020-06-27) o 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) o Improvement of the hatchling success model - 7.8 (2020-09-17) o Improvement of databaseTSD for Eretmochelys imbricata - 7.8.1 & 7.8.2 (2020-09-23 & 2020-09-24) o New hessian parameter in HatchingSuccess.fit - 7.8.3 (2020-10-07) o tsd function can now fit TSDII or FMF pattern - 7.9 (2020-10-11) o 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) o New function to study data logger precision: uncertainty.datalogger - 7.3 o Correct a bug in predict.HatchingSuccess - 7.3 o Correct a bug in STRN - 7.3.1 o Add the temperatures object in STRN output - 7.3.2 o New functions calibrate.datalogger - 7.3.3 o Simplification of calibrate.datalogger() and uncertainty.datalogger() - 7.3.4 o uncertainty.datalogger() by default uses only one measurement - 7.4.1 o New version of TSD database - 7.4.2 o Better fit control in tsd() - 7.4.3 o New algorithm to search for confidence interval of TRT bounds in tsd() - 7.4.4 o New approximation for Hulin, Richards, and double-Richards equations in tsd() - 7.4.5 o New example in info.nests() - 7.4.6 o fixed.parameters in fitHS() - 7.4.7 o TSP.borders parameter in STRN() - 7.4.8 o Correct a bug when weights were used - 7.4.9 o STRN can fit the TSD model - 7.5, 7.5.1, 7.5.2, 7.5.3 o movingincubation() can show again a progress bar - 7.5.4 o P_TRT() can manipulate very large TRT - 7.5.5 o New example in info.nests() to use the PM method of Massey et al. 2019 - 7.5.6 o info.nests() returns PM.mean and PM.se from Massey et al. 2019 - 7.5.7 o Correct a bug in info.nests()$metric when more than one nest were used - 7.5.7 o New outputs for summary of info.nests() PM.TimeWeight.mean and PM.TimeWeight.se - 7.5.8 o Bug correction in info.nests() - 7.5.9 o New flexit model for tsd() - 7.5.10 o New mcmc function for hatching success - 7.5.11 o Rename all Hatching Success functions for better homogeneity; new plot function - 7.5.12 o Better implementation of flexit model for tsd - 7.5.14-7.5.15 o Solve a case when predict.tsd() returns 0 or 1 whereas some observations are present - 7.5.16 o Better implementation of flexit model for tsd - 7.5.17 o Fix a bug in STRN_MHmcmc - 7.5.18 o Better implementation of flexit model for tsd - 7.5.19 o flexit model for tsd comes from HelpersMG package - 7.5.20 o traceML parameter for GRTRN_MHmcmc, HatchingSuccess.MHmcmc, tsd_MHmcmc, and STRN_MHmcmc- 7.5.21 (2019-08-20) o 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) o TRT is no more estimated for Hulin and Double-A-logistic models of tsd() - 7.5.24 o Add deviance test for tsd() - 7.5.25 o Correct deviance estimation for tsd() - 7.5.26 o Correct TRT estimation for A-logistic model for extrem K value- 7.5.27 o New CRAN version - 7.6 Changes in version 7.2.3 o New functions to study hatching success - 7.2 o Temperature.max is a new output of info.nests() - 7.2.1 o Change the examples of info.nests() - 7.2.2 o New Generic_ProportionDevelopment item in TSP.list - 7.2.3 Changes in version 7.1-7.1.1 o If no SD for test, use SSE criteria to fit - 7.1 o New example in searchR to fit data using method of proportion of development - 7.1 o Small improvment in plot.NestsResult() - 7.1 o Better control of the beginning and end of the TSP within the corresponding stages - 7.1 Changes in version 7.1.1 o Add an example to plot the temperatures - 7.1.1 Changes in version 7.0 (2017-09-26) o 2D reaction norm - 7.0 o Cholesky decomposition is used to estimate a pseudo-variance matrix for SE - 7.0 o AICc and BIC are estimated for the sexualisation thermal reaction norm - 7.0 o SE or hessian are used for movingincubation - 7.0 o Podocnemis expansa stages - 7.0 Changes in version 6.5-6.5.18 o New version for CRAN - 6.5 o Correction of some examples - 6.5.1 o Cleaning DatabaseTSD - 6.5.1 o 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 o predict.tsd() can be used with only one probs - 6.5.3 o STRN() used the new version of predict.tsd() - 6.5.3 o STRN_MHmcmc() is corrected to be used with fixed.parameters of STRN() - 6.5.3 o 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 o predict.tsd() works without temperatures or durations - 6.5.4 o New prallel parameter for STRN() and STRN_MHmcmc() - 6.5.5 o fixed.parameters from STRN is used now in info.nests() - 6.5.6 o New examples for STRN() and STRN_MHmcmc() - 6.5.6 o Minor bug for fixed.parameters in info.nests() - 6.5.7 o tsd(), P_TRT() and plot.tsd() can be used when some parameters are badly fitted - 6.5.8 o plot.tsd() is more robust to unusual situations - 6.5.9 o New outMCMC data - 6.5.10 o STRN() is faster if some timeseries have no information for sex - 6.5.11 o Database of embryological stages is more complete - 6.5.12 o New exemple for stages dataset - 6.5.13 o plot() of series can use the hessian matrix - 6.5.13 o Better control of the confidence interval shown is plot() using the CI parameter - 6.5.14 o Minor change in stages dataset - 6.5.15 o Hessian matrix for STRN() is estimated - 6.5.16 o info.nests() can use Hessian matrix for STRN() - 6.5.17 o Minor change in info.nests() - 6.5.18 Changes in version 6.4-6.4.56 o New version for CRAN - 6.4 o Correction of the y legend for plotR() - 6.4.1 & 6.4.2 o ylim parameter for plotR() works again - 6.4.2 o Bug correction : GRTRN_MHmcmc() works also with only one parameter - 6.4.3 o New parameter for SSM model: epsilon (SSM = SSM + epsilon) - 6.4.4 o Correct some examples - 6.4.5 o Nicer arrow for plot - 6.4.6 o New examples - 6.4.7 o Separate parameters for plotR and hist in plotR_hist() - 6.4.7 o New examples - 6.4.8 & 6.4.9 o Legend for hist() and plotR_hist() has been changed to Temperature density - 6.4.10 o Arrows in plot() are no more masked - 6.4.11 o Possibility to setup nonsymmetrical confidence interval using quantiles in ChangeSSM() - 6.4.12 o The non-symmetrical confidence interval can be used for randomization using info.nests() - 6.4.12 o New functions plotRdensity() and plotRdensity_hist() - 6.4.12 o New examples - 6.4.13 o If a mcmc object is used in info.nests() or plot.NestsResult(), it will be used directly - 6.4.14 o New asymmetric normal model - 6.4.15 o trace can be changed during mcmc search after a stop and previous use - 6.4.16 o New trigonometric model - 6.4.16 o Correct scaleY for plotRdensity() - 6.4.17 o Weibull model is correct and functional - 6.4.17 o BIC is calculated after searchR() - 6.4.17 o Correct a bug in info.nests() for replicate.CI=1 and resultmcmc - 6.4.18 o mcmc for normal function in SSM - 6.4.18 o new function nobs.NestResult() to be used with BIC() - 6.4.18 o New mcmc results for trigo and Weibull models - 6.4.19 o Adaptive mcmc is implemented for GTRN and STRN - 6.4.20 o Adaptive mcmc is implemented for TSD - 6.4.21 o Parallel computing implemented for windows - 6.4.22 & 6.4.23 & 6.4.24 o New version of resultNest_mcmc_4p_normal - 6.4.25 o Prevent an error in rare case in tsd - 6.4.26 o New examples in resultNest_mcmc_4p_normal - 6.4.26 o New data for Weibull model with 3 parameters - 6.4.27 o New data for SSM6p model - 6.4.28 o Bug correction when metric.end.incubation == NA - 6.4.28 o Transition parameters work for Weibull model - 6.4.29 o Can use several size for transition model in the same plot - 6.4.29 o set.par with plotR works again- 6.4.30 o cex.lab = 1, cex.axis = 1 for plotRdensity - 6.4.31 o New plotR2() will be a replacement for plotR, plotR_hist, plotRdensity and plotRdensity_hist - 6.4.32 o Cleaning the code: remove old SEforR, plotR, plotR_hist, plotRdensity and plotRdensity_hist - 6.4.33 o MovingIncubation() scheme for parallel is better and mcmc objects can be used instead of SE - 6.4.34 o Correct some problems with parallel in info.nests() in windows - 6.4.34 o polygon option for plotR() - 6.4.35 o mar and breaks parameter for plotR() - 6.4.36 o correct a bug in info.nests() for windows when parallel=FALSE - 6.4.37 o Legends are homogenized for various plots - 6.4.37 o 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 o New option parallel for MovingIncubation() and plot.NestsResult() to use or not parallel computing - 6.4.37 o New parameter SexualisationTRN.mcmc to generate variability of SexualisationTRN - 6.4.37 o If + or -Inf is produced in SSM, does not produce error - 6.4.38 o Dallwitz 3 parameters is simpler to implement - 6.4.39 o Correct a problem with mar parameter in plotR() - 6.4.40 o SE as matrix can be used with plotR() - 6.4.41 o New parameter log.hist canbe used to show log axis for histogram - 6.4.42 o Minor change for plot.tsd() - 6.4.43 o new parameter fixed.parameters for STRN() - 6.4.44 o Fix a bug in MovingIncubation() - 6.4.45 o Implementation of delta method for confidence interval - 6.4.46 o temperature.heterogeneity accepts a vector of two values being sd_low and sd_high - 6.4.47 o Change the suggest packages - 6.4.48 o Better management of curves and polygon in plotR() - 6.4.49 o Minor change to prevent warnings() in plotR() - 6.4.50 o Correct tsd_MHmcmc() - 6.4.51 o SE returns by tsd() was not SE but variance - 6.4.52 o New parameter mar for plot.tsd() - 6.4.52 o New function trt() - 6.4.53 o New function P_TRT() more general than trt(); trt() is removed - 6.4.54 o Confidence interval for plot.tsd() uses the hessian matrix - 6.4.54 o durations is added for P_TRT() - 6.4.55 o SD for temperatures or durations is added for P_TRT() - 6.4.55 o predict.tsd can use mcmc or hessian matrix - 6.4.55 o minor change in predict.tsd - 6.4.56 Changes in version 6.3.1-6.3.11 o New shiny function web.tsd() - 6.3.1 o Restore web.tsd() - 6.3.2 o Minor modification of shiny application - 6.3.3 o plotR() returns R values in the unmodified scale - 6.3.4 o Modification of the scale of R graph produced by plotR() - 6.3.4 o errbar.tick does not produce warnings() in plot.tsd() - 6.3.5 o No error if show.anchors is used with plotR_hist() - 6.3.6 o Info.nest() returns also MassWeighted.temperature.mean - 6.3.7 o Solve some rare cases when info.nest()$summary returns NA - 6.3.7 o Correct description for test parameter in searchR() - 6.3.8 o Add parameter show.legend in plotR() - 6.3.9 o Correct a bug for STRN() when one of the timeseries had no known sex ratio - 6.3.10 o cex.axis in plot.tsd() and plot.NestResult() is used for x-axis - 6.3.11 Changes in version 6.3 (2016-07-19) o Minor update of plot.NestResult() to show TSP at the top of temperatures - 6.2.1 o Caretta caretta stages are no more defaults for plot.NestResult() - 6.2.1 o equation Hulin for tsd() is more robust - 6.2.2 o fixedparameter is used for mcmc - 6.2.2 o A matrix for SE can be used in plotR() for anchored parameters to use quantiles - 6.2.3 o New parameter x.SE to control the envelope of R - 6.2.3 o cex.axis and cex.lab works for temperature scale in plotR_hist - 6.2.4 o tsd indicates durations or temperatures correctly depending on data input - 6.2.5 o plot.tsd indicates durations or temperatures correctly - 6.2.6 o It is possible to show anchors in plotR() and plotR_hist() - 6.2.7 o New columns and information in STSR_TSD database - 6.2.8 o STRN() has been changed to be more reliable if the order of nests is changed - 6.2.8 o Bug correction in info.nests() - 6.2.9 o New option to not show observations in plot.tsd() - 6.2.9 o 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 o batchsize option has been removed from GTRN_MHmcmc() - 6.2.10 o New example for movingincubation() - 6.2.11 o Introduction of Weibull function to fit thermal reaction norm - 6.2.11 o New parameter metabolic.heating in info.nests() - 6.2.11 o New parameter metabolic.heating in movingincubation() - 6.2.12 o range.CI parameter of predict.tsd() is replaced by quantiles - 6.2.13 o New temperature.heterogeneity parameter in info.nests() and movingincubation() - 6.2.14 o Changes in documentation - 6.2.15 o Better managment of error in SE during SearchR() - 6.2.16 o New function SEforR() to estimate SE for a set of parameters based on Fisher information matrix - 6.2.16 o Estimation of anchored model is more rapid - 6.2.16 o New parameter XlimSE for plotR and plotR is simplified - 6.2.17 o New model for anchors (polynomial fit) - 6.2.18 o New parameter hessian to return the hessian matrix in SEforR() - 6.2.18 o New model for anchors (linear fit) - 6.2.19 o Correct a bug in STRN() that prevent SE estimation - 6.2.19 o Object returns by STRN() is more complete and can be used by compare_AIC - 6.2.20 o info.nests() can use an object created by STRN() for the parameter SexualisationTRN - 6.2.20 o Call to MCMC is simplified - 6.2.21 o info.nests() use a parameter x rather than parameters - 6.2.21 o info.nests() can use both x and parameters to provide back compatibility - 6.2.22 o plotR() and plotR_hist() return a list with confidence intevals - 6.2.23 o Correct a bug in info.nests() (Thanks to Taylor R. Roberge to identifiy it) - 6.2.24 o xlimR of plotR() or plotR_hist() can be a vector of values - 6.2.24 o New example for plotR() using xlimR as a vector - 6.2.25 o shiny version has been removed as it was not maintained anymore - 6.3 Changes in version 6.2 (2016-01-08) o Update of documentation Changes in version 6.1.3-6.1.5 o plot.NestResult() and plotR_hist() can be used with layout() or mfrow() - 6.1.3 o New database stages for embryonics stages, mass and SCL. Will be expanded in next versions - 6.1.4 o Solve a problem with mcmc - 6.1.5 Changes in version 6.1.2 o Correct a problem with info.nest when timeseries are of different length during resampling of parameters o Correct a problem with info.nest when fill is not NULL Changes in version 6.1.1 (2015-10-16) o Correct a problem occuring only with windows version Changes in version 6.1 (2015-10-12) o Correction of movingincubation() to work with the new version of info.nests() o 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 o metric.end.incubation in info.nests() and plot.NestsResult() is recycled if necessary o plot.NestsResult() uses info.nests(), new parameter show.metric o if metric.end.incubation is NA, the embryo metrics for TSP are scaled by metric of hatchlings at the end of incubation o if metric.end.incubation is NULL, the embryo metrics for TSP are scaled by the maximum metric of mean in test parameters o if metric.end.incubation is a value, it is used directly for scale o New data for info.nests(): MiddleThird.MassWeighted.temperature.mean and .se o Correct a bug for info.nests() if there is only one temperature o Correct a bug for searchR() that prevent return a result in rare occasions o metric and summary can be used when partial incubations are observed using metric.end.incubation=x with x being the final size o Correct a bug for fill parameter in info.nests() o New data for embryological stages: Emys orbicularis.mass and Emys obicularis.SCL. They are store in TSP.list o Rename Caretta caretta embryological stages: Caretta caretta.SCL o After plotR_hist(), the y-scale is the scale for R graph (previously it was the one for histogram) o Only the function lsoda is imported from deSolve to prevent a warning during check Changes in version 6.0.1 o Change info.nests() for R 3.2 compatibility o Minor changes in FormatNests(); test if names are unique o Correct a bug for Hill model of TSD o Add optimx as an option for searchR() o 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") o $SD is store also in mcmc objects. This SD is the SE for points estimates. Changes in version 6.0 (2015-04-15) o FormatNests() can convert old format database using data=xxx with xxx being the old format database o info.nests() is much more complete o polynom package is now in dependencies o New columns IndiceK in FormatNests() output to accelerate SearchR() o predict.tsd() uses the new model for CI estimation o plot.tsd() does not make any estimation; it just plot the object created by tsd() o New method for confidence interval in tsd() o If stopattest=TRUE is used in .fonctionfit() the time for end of incubation is estimated using polynomial interpolation o Hmisc package is no more required o new parameters SE and fixed.parameters in tsd() o The anchored parameters can use Celcius degrees o Many changes in .fonctionfit .STRNfit (hidden fonctions) o searchR() is more rational for initial tests of weights and better manage parallel runs o Add a progression bar for predict.tsd() o MHmcmcAlgo(), minmax.periodic(), temperature.periodic() and info.sun() functions are transfered to new package: HelpersMG o STRN() does not use replicate.CI for info.nests() o Add parameters= for GenerateAnchor() and GRTRN_MHmcmc_p() o 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 o New CTE named TSD.weighted.mean.temperature. It includes both the thernal reaction norm for growth rate and the thermal reaction norm for sexualisation. o New function STRN() to fit the Sexualisation thermal reaction norm o New function STRN_MHmcmc() to model the enveloppe of the STRN o New parameters to continue MCMC run from previous run in GRTRN_MHmcmc(), STRN_MHmcmc() and tsd_MHmcmc() o Correct a bug to estimate the mean temperature within the TSP o If weight is included in FormatNests, it is used in searchR() o Correct a bug when plotR() is called without result parameter o Correct a bug for info.nest() with SE o Temperatures or durations can be associated with SE for predict.tsd() o TestParallel() function display the user time of system.time() o Package polynom is required for anchored model o Anchored model uses now Lagrange polynoms rather than loess fitting method o When anchored model is negative, it is fixed to 0 o New function sun.info() o minmax.periodic() can use different minimum or maximum time each day. Correct a bug for SD in minmax.periodic Changes in version 5.1 (2014-10-06) o New version of STRES_TSD and help for this database is more clear o Future changes in STRES_TSD will not be longer be reported here o tsd() can now uses also incubation period o Equation Hulin (from Hulin et al 2009) is implemented in tsd() o Equation Double-Richards (from Girondot, submited) is implemented in tsd() o Packages numDeriv and entropy are now only suggested o New parameters lty.temperatures and lwd.temperatures for plot.NestsResult() o Predict.tsd() without temperatures or durations uses original temperatures or durations o New function plot.tsd() o New possibility to use Bayesian estimate for tsd() o Remove parallel computing for windows in MCMC o New functions minmax.periodic() and temperature.periodic() Changes in version 5.0 (2014-08-15) o New bibliographic references and first version in CRAN o Remove parallel computing option for Windows o Remove local update Changes in version 4.14 o Correct bug for Richards equation in tsd and predict.tsd() works faster Changes in version 4.09-4.13 o New function logLik() applied to NestsResult and tsd o New version of STRES_TSD o No return line from plot() o x-axis is returned correctly after plotR_hist() Changes in version 4.05-4.08 o predict.tsd() is more rapid and can be used without CI o New version of STRES_TSD o remove dependency of many packages o new parameter lwd and lwdCI for plotR() and plotR_hist() Changes in version 4.04 o Correct a warning in plotR() when Scale is used o Correct a bug in plot.nestresult() when for special length of time series Changes in version 4.01-4.03 o 1000 iterations are allowed for tsd() and test if convergence is reached o new way to define initial P value for tsd() o new automatic xlim for tsd() function to show all TRT o many changes in shiny code. Remove visibility of ShinyEmbryogrowth() Changes in version 4.00 o shiny application is included. Call it using ShinyEmbryogrowth() Changes in version 3.02 o mcmc results for anchored parameters use 10000 iterations o Correct a warning when there is no variability in TSP Changes in version 3.01 o Possible to save intermediate results during fitting Changes in version 3.00 o Possibility to define R by anchor of loess fitting Changes in version 2.30 o New version with corrected rK value o weight parameter is store in result of searchR() and used for mcmc o Add the function switch.transition() o New function merge.mcmcComposite() to merge two objects mcmcComposite Changes in version 2.28 o Correct a bug in movingincubation() Changes in version 2.27 o Correct a bug in movingincubation() o Predict method for tsd Changes in version 2.26 o Add SE for weight temperature by growth during TSP and mean temperature during TSP o Add SE for borders of TSP o Store weighted temperature by growth during TSP for movingincubation() Changes in version 2.25 o Calculate mean temperature in middle-third of incubation and weight temperature by growth during TSP Changes in version 2.24 o New function to change from 4p to 6p parameters functions and reverse Changes in version 2.23 o Correct a bug for linear or exponential derivative and parallel computing o Add mar parameter for plot.NestResults() Changes in version 2.22 o TRT is calculated for Hill and Richards equations in tsd() function o Limits and their standard errors are calculated in tsd() Changes in version 2.21 o GSD, Hill and Richards equations are included in tsd() function o Many improvments for tsd() function Changes in version 2.19-2.20 o In MovingIncubation(), a timesseries at the end of incubation can be provided to model the metabolic heating o SE of parameters are used if replicate.CI is different from 0 Changes in version 2.18 o Correction of bug in generateIL.df and info.nests o generateIL.df renamed GenerateConstInc o New parameter xlimR to show only part of R function in plotR and plotR_hist Changes in version 2.17 o hist.nests and hist.nestsresults return a list with the complete set of temperatures Changes in version 2.16 o New function generateIL.df Changes in version 2.15 o New parameter OutPlot for plot.NestsResult() o Correct a bug for mean temperature of a nest Changes in version 2.14 o New version of uploading to ESE server after building package o New parameter col for Entropy o Output of tsd() takes into account that the regressor could be not the temperature Changes in version 2.11 o Better format for examples Changes in version 2.10 o New parameter for embryogrowth_MHmcmc_p() to automatically accept proposed priors o New parameter echo for likelihoodR() Changes in version 2.09 o Correct a bug in mean.temperature and mean.temperature.TSP in info.nest() and plot() o Add a parameter to plotR() to manage where to display information "mean" and "confidence interval" Changes in version 2.08 o Correct a bug in plotR_hist() if parameters for plotR() were used o Add the progress parameter in info.nests o Calculte the mean temperature during all incubation in info.nest() and plot() Changes in version 2.07 o Parameter weight is added in FormatNests(), searchR() and likelihoodR() o Correct the test in SearchR() to be sure that fixed and fitted parameters are not duplicated o New function weightmaxentropy() which searches for the relative weights for each nest to maximize entropy o New database fitted with weight Changes in version 2.06 o Correct Movingincubation() to take into account the _L list return by .SSM() o Correct plot.NestsResult() for truncated numbers o as.par.mcmcComposite() and as.mcmc.mcmcComposite() are transfered to the package phenology. o Loading of package does not failed if the description is not available online. o Movingincubation() returns a dataframe with time and length of TSP Changes in version 2.05 o 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 o tsd() show the complete curve depending on xlim parameter o 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 o Embryo growth can be modeled using two sets of equations, one for early development and one for late development o as.mcmc() can be used with mcmcComposite objects o library zoo is required to use na.locf() o Add the function tsd() to fit data of temperature-dependent sex determination o Correction of bug for show.box and ylimH parameters in plotR() and plotR_hist() Changes in version 1.23 o New parameter for plot(NestsResult): ref.stage=TRUE ou FALSE o Modeled size at the end of incubation and likelihood for each nest are returned by plot() Changes in version 1.22 o New function MovingIncubation() to run the model day by day on a timeseries o summary() for Nests objects o Add simplify=TRUE for FormatNests() o mcmc data for 6p: result_mcmc_6p_80 o Correct scale of x axis for histogram and add legend for Y axis in plotR_hist() o Legends are not drawn twice in plotR() with lists o Initial point is taken into account for as.par.mcmcComposite() Changes in version 1.20-1.21 o Update can use install_url() from package devtools o New function GenerateTest(series, size, previous) to generate test parameter for searchR() o Color of embryo mass in plot can be changed using a vector of colors Changes in version 1.14-1.19 o Remove the use of .EGR.env environment for searchR() in 1.14 and in plot() in 1.17 o Package can load when no internet connection is available o Add a function testParallel() to evaluate if the option parallel is interesting for the running system o Add class mcmcComposite to result of embryogrowth_MHmcmc() o Add BatchSE and TimeSeriesSE elements of the output of embryogrowth_MHmcmc() o New function plotR_hist() to display both RGraph and hist of temperatures o Rename as_mcmc() to as.mcmc2.mcmcComposite() o New function as.par.mcmcComposite() to get parameters at maximum likelihood from mcmcComposite object o Add a parameter force=TRUE or FALSE to force update Changes in version 1.11-1.13 o Rename extractMCMC() to as_mcmc() o Correct a bias when the temperature reaches a maximum or minimum o Allow parallel computing to be disabled Changes in version 1.10 o Uses parallel computing for searchR() and embryogrowth_MHmcmc() Changes in version 1.09 o New functions: extractMCMC() to be used with mcmcComposite objects to get an object to be use with coda package o New functions: embryogrowthUpdate() to update package o Package version is checked at package loading o Add the defaults plot parameters for plotR() o Possible to plot several growth rates using list objects o Correct a bias when the temperatures always increase or decrease during incubation Changes in version 1.08 o Use mcmc methods from phenology package Changes in version 1.07 o Remove plotnest() and plotMHmcmc() function to keep only plot(). o If optimization is not finished after maxiter, it shows the value of fitted parameters and continues. o Change mcmcNests class to mcmcComposite. o plot.Nests() returns also the mean temperature within the TSP. o The package is renamed embryogrowth o The objects wihtin the mcmcComposite object are mcmc and mcmc.list objects o Add a method summary of mcmcComposite object Changes in version 1.05 o The MHMCMC algorithm can now be used by other packages. o hist.NestsResult uses the same script as hist.Nests o 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 1.04 o Add the possibility to use fixed parameters o Add the three new class: mcmcNests, Nests and NestsResult o Add Bayesian MCMC script and plot of MCMC o Many minor changes for speed improvment o Some bug corrections o Change T12H for 6-parameters equation to DT o Catch the error of singularity of matrix o Better managment of test size if the temperatures are changed Changes in version 1.00-1.03 o first versions as a package. New functions added sequentially.