NEWS

embryogrowth 9.5 (2024-08-23)

New CRAN version - 9.5 (2024-08-23)

embryogrowth 9.4.2

New CRAN version - 9.1 (2023-04-03)
Solve a problem in tsd() when the vcov matrix is not positive - 9.1.1 (2023-11-05)
Solve problems in movement() function - 9.1.2 (2023-11-07)
Experimental: Add a new possibility to estimate likelihood is tsd() for sex ratio when n is not known - 9.1.3 (2023-11-08)
New out possibility for info.nests() to be able to use Bayesian Model Averaging - 9.1.4 (2023-11-10)
Experimental: Add a new possibility to estimate likelihood is tsd() for sex ratio when n is not known - 9.1.5 (2023-11-08)
RMU.2010 and RMU.2023 are included in databaseTSD - 9.1.6 (2023-12-01)
New equation flexit* - 9.2 (2023-12-29)
New references- 9.2 (2024-02-05)
Minor change for initial parameters in tsd - 9.2.1 (2024-03-20)
Solve a problem in STRN when sex ratio was missing for some timeseries - 9.2.2 (2024-03-30)
STRN can use a flexit* model - 9.2.2 (2024-03-30)
2 new columns in databaseTSD: incubation.temperature.set and incubation.temperature.corrected - 9.2.3 (2024-04-07)
Dermochelys coriacea information in databaseTSD were corrected - 9.2.4 (2024-04-30)
New option to use ggplot2 to produce tsd graph - 9.3.0 (2024-05-16)
New examples for tsd graph - 9.3.1 (2024-05-18)
Dermochelys coriacea information in databaseTSD were corrected - 9.3.3 (2024-05-22)
Dermochelys coriacea information in databaseTSD and listTSP were corrected - 9.4 (2024-05-26)
logit model is implemented in tsd - 9.4.1 (2024-06-24)

embryogrowth 9.0.2

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)

embryogrowth 8.7.3

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)

embryogrowth 8.6-7

New CRAN version - 8.6 (2022-07-14)
Fix align for html5 - 8.6-7 (2022-08-22)

embryogrowth 8.5-17

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)

embryogrowth 8.4-10

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)

embryogrowth 8.3-26

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)

embryogrowth 8.2-15

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)

embryogrowth 8.1-7

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)

embryogrowth 8.0-42

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)

embryogrowth 7.7

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)

embryogrowth 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

embryogrowth 7.2.3

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

embryogrowth 7.1-7.1.1

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

embryogrowth 7.1.1

Add an example to plot the temperatures - 7.1.1

embryogrowth 7.0 (2017-09-26)

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

embryogrowth 6.5-6.5.18

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

embryogrowth 6.4-6.4.56

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

embryogrowth 6.3.1-6.3.11

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

embryogrowth 6.3 (2016-07-19)

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

embryogrowth 6.2 (2016-01-08)

Update of documentation

embryogrowth 6.1.3-6.1.5

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

embryogrowth 6.1.2

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

embryogrowth 6.1.1 (2015-10-16)

Correct a problem occuring only with windows version

embryogrowth 6.1 (2015-10-12)

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

embryogrowth 6.0.1

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.

embryogrowth 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

embryogrowth 5.1 (2014-10-06)

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()

embryogrowth 5.0 (2014-08-15)

New bibliographic references and first version in CRAN
Remove parallel computing option for Windows
Remove local update

embryogrowth 4.14

Correct bug for Richards equation in tsd and predict.tsd() works faster

embryogrowth 4.09-4.13

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()

embryogrowth 4.05-4.08

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()

embryogrowth 4.04

Correct a warning in plotR() when Scale is used
Correct a bug in plot.nestresult() when for special length of time series

embryogrowth 4.01-4.03

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()

embryogrowth 4.00

shiny application is included. Call it using ShinyEmbryogrowth()

embryogrowth 3.02

mcmc results for anchored parameters use 10000 iterations
Correct a warning when there is no variability in TSP

embryogrowth 3.01

Possible to save intermediate results during fitting

embryogrowth 3.00

Possibility to define R by anchor of loess fitting

embryogrowth 2.30

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

embryogrowth 2.28

Correct a bug in movingincubation()

embryogrowth 2.27

Correct a bug in movingincubation()
Predict method for tsd

embryogrowth 2.26

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()

embryogrowth 2.25

Calculate mean temperature in middle-third of incubation and weight temperature by growth during TSP

embryogrowth 2.24

New function to change from 4p to 6p parameters functions and reverse

embryogrowth 2.23

Correct a bug for linear or exponential derivative and parallel computing
Add mar parameter for plot.NestResults()

embryogrowth 2.22

TRT is calculated for Hill and Richards equations in tsd() function
Limits and their standard errors are calculated in tsd()

embryogrowth 2.21

GSD, Hill and Richards equations are included in tsd() function
Many improvments for tsd() function

embryogrowth 2.19-2.20

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

embryogrowth 2.18

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

embryogrowth 2.17

hist.nests and hist.nestsresults return a list with the complete set of temperatures

embryogrowth 2.16

New function generateIL.df

embryogrowth 2.15

New parameter OutPlot for plot.NestsResult()
Correct a bug for mean temperature of a nest

embryogrowth 2.14

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

embryogrowth 2.11

Better format for examples

embryogrowth 2.10

New parameter for embryogrowth_MHmcmc_p() to automatically accept proposed priors
New parameter echo for likelihoodR()

embryogrowth 2.09

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"

embryogrowth 2.08

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()

embryogrowth 2.07

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

embryogrowth 2.06

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

embryogrowth 2.05

many minor changes in plot.NestsResult for better ylimS managment and to prevent an error when no SD is available

embryogrowth 2.04

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

embryogrowth 2.00-2.03

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()

embryogrowth 1.23

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()

embryogrowth 1.22

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()

embryogrowth 1.20-1.21

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

embryogrowth 1.14-1.19

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

embryogrowth 1.11-1.13

Rename extractMCMC() to as_mcmc()
Correct a bias when the temperature reaches a maximum or minimum
Allow parallel computing to be disabled

embryogrowth 1.10

Uses parallel computing for searchR() and embryogrowth_MHmcmc()

embryogrowth 1.09

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

embryogrowth 1.08

Use mcmc methods from phenology package

embryogrowth 1.07

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

embryogrowth 1.05

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.

embryogrowth 1.04

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

embryogrowth 1.00-1.03

first versions as a package. New functions added sequentially.