NEWS

phenology 10.1 (2024-08-23)

New CRAN version - 10.1 (2024-08-23)

phenology 9.1.2-10.0.3

New CRAN version - 9.1 (2023-10-16)
Add season parameter in summary.phenology() - 9.1.1 (2023-11-03)
Add season parameter in plot.phenology() - 9.1.2 (2023-11-05)
Possibility to implement a detection probability model in phenology - 10.0 (2023-11-21)
Check if some series in phenology have names that can be confound, for example beach and beach1 can be considered the same in some situations - 10.0.2 (2024-7-4)
In a phenology, if A is not NA, the observed data is excluded from summary - 10.0.3 (2024-7-4)

phenology 9.0.14

New CRAN version - 9.0 (2023-04-01)
better management of errors in phenology_MHmcmc_p() - 9.0.1 (2023-04-28)
Can use multiple peaks - 9.0.2 (2023-05-10)
Possible to manipulate parameters using model_before within fit_phenology - 9.0.3-9.0.5 (2023-05-24)
MinB, MinE, Min, PMin, PMinB, and PMinE can have .x sub-parameters - 9.0.6 (2023-06-01)
Saddlepoint approximation of sum of negative binomial is used if more than 5 days are summed - 9.0.7 (2023-07-13)
Possible to control the approximation of sum of negative binomial in fit_phenology - 9.0.8 (2023-07-21)
normalize = FALSE for pSnbinom - 9.0.9 (2023-07-31)
If NaN is returned by pSnegbin in .Lnegbin, it will returned 1E9 - 9.0.10 (2023-08-05)
If the value in the column CountType is a number, it is used as a maximum number - 9.0.11 (2023-08-07)
Solve a problem with map_phenology() - 9.0.12 (2023-08-20)
Solve a problem with result_Gratiot1 and result_Gratiot2 - 9.0.13 (2023-10-04)
Solve a problem with colnames in add_phenology - 9.0.14 (2023-10-11)

phenology 8.0.6

New CRAN version - 8.0 (2022-12-12)
New model to use a minimum observed number - 8.0 (2022-12-12)
The Zero Counts model applies now at the level of daily counts, not automatically to the entire timeseries. It is a big change that makes previous formated datasets no more compatible with this version - 8.0 (2022-12-13)
Minor change in .Lnegbin - 8.0.1 (2022-12-29)
.Lnegbin uses furman, Vellaisamy&Upadhye or approximate.negativebinomial method adaptively for Snbinom to prevent overflow - 8.0.2 (2022-12-29)
Correction of examples in fit_phenology() - 8.0.3 (2022-12-29)
silent parameters from fit_phenology() is used also for SEfromHessian() in the function - 8.0.4 (2023-01-08)
Prevent error when theta is very large - 8.0.5 (2023-03-10)
Hessian is FALSE by default in fit_phenology() - 8.0.6 (2023-03-20)
Change the default parameters for phenology_MHmcmc() - 8.0.6 (2023-03-20)
Restore functional shiny version - 8.0.7 (2023-04-01)

phenology 7.9 (2022-09-06)

New CRAN version - 7.9 (2022-09-06)

phenology 7.8-4

Show intermediate fitted values in fit_phenology() - 7.8-1 (2022-08-22)
Customized probs values in CI.RMU - 7.8-3 (2022-09-06)

phenology 7.8 (2022-07-15)

New CRAN version - 7.6 (2020-10-22)
Minor changes in the documentation - 7.6-1 (2020-12-14)
Tagloss_format() cleans data before to format them - 7.6-2 (2020-12-14)
New function Tagloss_mcmc_p() - 7.6-3 (2020-12-18)
Minor changes in Tagloss_model - 7.6-4 (2020-12-21)
Growlnotify option is removed - 7.6-5 (2021-01-13)
par_init() is compatible with convolution method- 7.6-6 (2021-01-13)
Solve a rare case when Theta converges to 0 - 7.7-1 (2021-01-20)
Use the new parameter method for RandomFromHessianOrMCMC - 7.7-2 (2021-01-26)
Prevent a warning in CI.RMU - 7.7-3 (2021-03-12)
Correct a bug in plot.fitRMU - 7.7-3 (2021-03-12)
New MCMC functions for fitCF - 7.7-4 (2021-03-19)
Correct a bug in CI.RMU - 7.7-5 & 7.7-6 (2021-03-23)
More precisions in Description of fitCF() - 7.7-7 (2021-03-24)
Minor change in fitCF() - 7.7-8 (2021-03-27)
Parallel version of OCFECF_f() for windows - 7.7-9 (2021-03-27)
Minor change for OCFECF_f() for windows - 7.7-10-7.7.12 (2021-03-31)
Prevent a warning in OCFECF_f() and lnCF() - 7.7-13 (2021-04-01)
New function generateCF() - 7.7-14 & 7.7-15 (2021-04-21)
Tagloss_model() can use mcmc and Hessian - 7.7-16 (2021-04-23)
Parameter_Global_Year() corrects names f series if they have _ - 7.7-17 (2021-04-26)
Add phenology logo - 7.7-18 (2021-05-01)
Add names.legend, col and border parameters in plot.fitRMU - 7.7-19 (2021-06-22)
Correct CI.RMU if some years are missing - 7.7-20 (2021-06-23)
New parametrization for phenology based on Omeyer et al. In prep - 7.7-25 (2021-09-02)
Minor change in the documentation of fitRMU() - 7.7-29 (2021-09-14)
Minor change in the documentation of add_phenology() - 7.7-30 (2021-10-15)
Minor change in format_par() to take into account strange name of beach - 7.7-32 (2021-11-01)
Named vector for zero_counts in fit_phenology() is possible - 7.7-41 (2021-11-03)
If method is NULL in fitRMU(), the initial parameters is returned - 7.7-42 (2021-11-06)
fitRMU uses optim and no more optimx - 7.7-43 (2021-11-06)
summary.phenology() returns also the sum of series - 7.7-46 (2021-11-16)
New option for add_phenology(): check.overlapping.dates - 7.7-53 (2022-01-18)
New option for fit_phenology(): stop.fit - 7.7-57 (2022-01-28)
Minor change in summary.phenology() - 7.7-59 (2022-01-29)
Forking=FALSE is used for Lnegbin due to a bug in Rstudio - 7.7-65 (2022-02-01)
options are used to tell to fit_phenology() and map_phenology() how to use parallel computing - 7.7-68 (2022-02-02)
Bug correction in rare case in fit_phenology() - 7.7-71 (2022-02-06)
Minor change in plot.IP - 7.7-76 (2022-02-19)
Prevent an error when meanECF is very small in IPFit() - 7.7-78 (2022-02-20)
New url to update the package before to be uploaded to CRAN - 7.7-80 (2022-02-24)
Minor change for dunif prior in fitRMU_MHmcmc_p - 7.7-82 (2022-03-25)
Minor change in plot.ECFOCF() that can use resultMCMC for CF plot - 7.7-108 (2022-03-26)
dgamma can be used as predefined density for fitRMU_MHmcmc_p() - 7.7-114 (2022-04-09)
Better managment of classes in the package - 7.7-120 (2022-04-09)
plot.fitRMU with proportions of numbers can use replicate.CI and then use median - 7.7-121 (2022-04-24)
New function ExponentialRegression() - 7.7-127 (2022-05-03)

phenology 7.5.25

New parameter max.scale for plot.TableECFOCF() - (2019-02-05)
New function Tagloss_mcmc() for Bayesian analysis of tag loss rate - 7.3.2 (2019-02-19)
New set of functions of remigration interval - 7.4 (2019-03-09)
peak_2018 will be applied to series XX2018 and XY2018 - 7.4.1 (2019-05-07)
Bug correction in fitRMU_MHmcmc_p() - 7.4.2 (2019-06-10)
New model for the proportions of fitRMU() - 7.4.3 (2019-06-11)
Modification of the first and second order probability of fitRMU() - 7.4.4 & 7.4.5 (2019-06-25)
add_phenology() can use recursively sep.dates parameter - 7.4.6 (2019-08-14)
solve a problem with fit_phenology() in parallel in windows - 7.4.7 (2019-08-14)
Add parameters for column names to be used in add_phenology() - 7.4.7 (2019-08-14)
Simplification of add_phenology() - 7.4.8 (2019-08-15)
Series with 0 observations are not included by add_phenology() - 7.4.9 (2019-08-15)
Better description of format errors in add_phenology() - 7.4.10 (2019-08-16)
previous can be NULL when using add_phenology() - 7.4.11 (2019-08-17)
If likelihood change is lower than 1e-6, fit_phenology() stops - 7.4.12 (2019-08-19)
traceML parameter in phenology_MHmcmc(), Tagloss_mcmc, and fitRMU_MHmcmc - 7.4.13 & 7.4.14 (2019-08-20)
Solve a problem in fit_phenology() that prevents ending - 7.4.15 (2019-08-21)
Brent method can be used in fit_phenology() - 7.4.16 (2019-08-26)
Plot.phenology() works without SE being estimated - 7.4.17 (2019-08-28)
Correct y-axis if only range of dates are available in plot.phenology() - 7.4.18 (2019-08-28)
fitRMU() is more rapid - 7.4.19 (2019-09-03)
Minor correction in phenology_MHmcmc_p() - 7.4.20 (2019-09-04)
Better prediction of priors in phenology_MHmcmc_p() - 7.4.21 (2019-09-10)
New parameter default.density in phenology_MHmcmc_p() - 7.4.22 (2019-09-12)
New parameter expandRange0Observation in add_phenology() - 7.4.23 (2019-09-13)
Series with 0 observation can be used directly in phenology_MHmcmc_p() - 7.4.24 (2019-09-17)
New function phenology2fitRMU() - 7.4.25 (2019-09-18)
summary.phenology() returns also variance and mean for ML and MCMC - 7.4.26 (2019-09-20)
New column density in RMU.names parameter of fitRMU() - 7.4.26 (2019-09-20)
Possibility to use gamma distribution in fitRMU() - 7.4.26 (2019-09-20)
Confidence interval can be shown in painted polygon in plot.phenology() - 7.4.26 (2019-09-20)
New parameter limit.sd in phenology2fitRMU()- 7.4.27 (2019-09-23)
Names of series can have the separator of year in their name in phenology2fitRMU()- 7.4.28 (2019-10-01)
print.phenologyout() shows all the series - 7.4.29 (2019-10-01)
Remove - character from beach name as it makes interference with fitRMU() - 7.4.30 (2019-10-02)
Require HelpersMG >=3.8 for a better control of xSnbbinom() - 7.5 (2019-10-06)
New function Parameter_Global_Year() to change parameters for phenology analysis - 7.5 (2019-10-07)
New function fixed.parameters0() - 7.5 (2019-10-12)
Optimization of .Lnegbin() by using .dialy_count() less often - 7.5 (2019-10-15)
Only convolution method in fit_phenology() is maintained - 7.5 (2019-10-15)
New function CI.RMU() - 7.5 (2019-10-17)
plot.fitRMU() completely changed - 7.5 (2019-10-17)
fitRMU() can use unusual parameter names - 7.5 (2019-10-20)
New model.SD in fitRMU() being "rookery.proportional" - 7.5.1 (2019-10-27)
CI.RMU() is much faster - 7.5.1 (2019-10-27)
Shiny version is corrected to be used with new add_phenology() function - 7.5.1 (2019-10-27)
Bug in CI.RMU() for replicate = 1 - 7.5.2 (2019-10-30)
Prevent some cases with theta = 0 - 7.5.3 (2019-11-05)
Cosmetic change in add_phenology() - 7.5.4 (2019-11-08)
phenology2fitRMU() without sd works correctly - 7.5.5 (2019-11-10)
Print phenology is possible with old fit (v. < 6) - 7.5.6 7.5.7 (2019-11-14)
Minor change in CI.RMU - 7.5.8 (2019-11-28)
Solve a case when some years have no information for year-specific in CI.RMU() - 7.5.9 (2019-12-23)
Fit continues if likelihood changed a lot in fitRMU - 7.5.10 (2019-12-24)
Correct a bug in fitRMU() for exponential when all years are not present - 7.5.11 (2019-12-26)
fitRMU_MHmcmc_p() works with new fitRMU() model - 7.5.12 (2020-01-01)
Years without data are not shown in plot.fitRMU() with what="Total" - 7.5.13 (2020-01-02)
Estimate of likelihood for phenology model is faster - 7.5.14 (2020-05-15)
phenology2fitRMU() is more fexible - 7.5.15 (2020-05-18)
Correct a bug in fitRMU() - 7.5.16 (2020-05-18)
Estimate of likelihood for phenology model is more accurate - 7.5.17 (2020-05-18)
Minor change in CI.RMU() - 7.5.18 (2020-05-20)
Summary and plot can use flat hessian - 7.5.19 (2020-05-22)
Two kinds of cofactors can be used in fit_phenology() - 7.5.20 (2020-05-24)
Big changes in summary.phenology() - 7.5.21 (2020-05-25) Note that sd# and se# (standard errors for fixed parameters) are not working
map_phenology is parallelized - 7.5.22 & 7.5.23 (2020-06-03)
Change introduced in as.numeric in R 4.0.0 - 7.5.24 (2020-06-27)
Change in .Lnegbin to prevent NA output when NA is present in input data - 7.5.25 (2020-08-14)

phenology 7.2 (2018-09-27)

New version in CRAN - 7.2 (2018-09-25)
Solve an error if detectcores returns NA ou NULL - 7.2.1 (2018-10-12)
Solve a problem when lnCF() returns Inf - 7.2.2 (2018-10-24)
Solve a problem with multicores computers in ECFOCF_f() - 7.2.3 (2018-10-24)
xaxt parameter can be used for plot.ECFOCF with result="prob" - 7.2.4 (2018-10-30)
fixed.parameters beginning by se# (no more sd#) are used in summary() and plot() - 7.2.5 (2018-11-03)
New parameter method for fit_phenology() - 7.2.5 (2018-11-03)
Solve a rare problem in fitRMU() when the number for one year is null - 7.2.6 (2018-11-14)
Possible to set a bimodal nesting season in fit_phenology() - 7.2.7 (2018-11-14)
A new function to plot the formated tagloss data - 7.2.8 (2018-12-11)
tagloss_daymax() can return max (default), min, mean, all the number of days individuals have been followed - 7.2.9 (2018-12-13)
New function Tagloss_cumul() to estimate cumulative daily tag-loss rate - 7.2.9 (2018-12-17)
Rivalan et al 2005 and Casale et al 2017 model can be used for tagloss modeling - 7.2.10 (2018-12-18)

phenology 7.1 (2018-07-10)

New set of functions for Internesting Periods for marine turtles - 7.1
Minor change in .Lnegbin to prevent rare case when probabilities are too small - 7.1
fitRMU() accept null SD for a beach - 7.1
Takes into account Cauchy-Schwartz inequality to estimate SD in fitRMU - 7.1
It is possible to not indicate SE of nesting season counts in fitRMU - 7.1
A proportional model for SD is possible for fitRMU - 7.1
Solve a rare warning in plot.phenology - 7.1
Lnegbin can be run without parallel computing (sometimes parallel computing is slower than normal computing) - 7.1.1 (2018-08-03)
lower and upper bounds for parameters can be set up in fit_phenology() - 7.1.1 (2018-08-03)
L-BFGS-B rather than BFGS is used for fitting in fit_phenology() - 7.1.1 (2018-08-03)
It is possible to save all the progress of fit with fit_phenology() - 7.1.2 (2018-08-03)
Better organization of list for intermediate save in fit_phenology() - 7.1.3 (2018-08-05)
fixed.parameters beginning by sd# are used in summary() and plot() - 7.1.4 (2018-09-24)

phenology 7.0.4

New set of functions for Clutch Frequency for marine turtles - 7.0
Minor change in par_init() - 7.0.1
Force PMinE et PMinB to be positive - 7.0.1
New non-parameteric model for CF - 7.0.2
New parameter show.scale for plot.ECFOCF() - 7.0.3
New attribute final in TableOCFECF - 7.0.4

phenology 6.0-6.0.3

New set of functions for Tagloss - 6.0
Correct a bug in add_phenology() when a list is used to enter new data - 6.0
Confidence interval for Peak_Series, Length_Series are shown - 6.0
Minor change in Tagloss - 6.0
New option "cumul" to plot tagloss result - 6.0
Simplification to specify partial models in tagloss - 6.0
If N20 == 0, does not produce an error - 6.0
Random distribution of individuals in groups send in cores for parallel computing - 6.0
Minor change in Tagloss_L - 6.0.1
New function loglik for Tagloss - 6.0.2
Correct examples - 6.0.3

phenology 5.5

Use of SEfromHessian - 5.5

phenology 5.4.1

New version for CRAN - 5.4
phenology() is compatible with shiny 1.0.1 - 5.4.1

phenology 5.3.15

New version for CRAN - 5.3
par_init() better handle PMin - 5.3.1
New function AutoFitPhenology() - 5.3.2
Parallel computing in windows - 5.3.3
Adaptive mcmc - 5.3.3
Correction of parallel computing in windows - 5.3.4-5.3.5
parametersfixed is renammed fixed.parameters in fit_phenology(), par_init() and plot.phenology() - 5.3.6
parametersfit is renammed fitted.parameters in fit_phenology() - 5.3.6
Plot is renammed show.plot in plot.phenology() - 5.3.6
summary() returns an estimate of global nesting if mcmc object is indicated - 5.3.7
summary() returns the details day by day of quantiles -5.3.8
plot() can plot now the result of a mcmc object as quantiles - 5.3.8
Correct diverse bugs in phenology_MHmcmc() and map_phenology() - 5.3.9
summary.phenology() and plot.phenology() rewritten from scratch - 5.3.10
summary.phenology() uses matrix of variances-covariances for confidence interval - 5.3.10
fit_phenology() uses optimx() - 5.3.11
web version updated - 5.3.12
Remove dependency to zoo package but add optimx and numDeriv - 5.3.12
Change the function to estimate random number with vcov using lmf package - 5.3.13
summary.phenologyout() is more complete - 5.3.14
autfitphenology() can be used again - 5.3.15

phenology 5.2.1-5.2.5

New version of shiny phenology() - 5.2.1
New version of shiny phenology() - 5.2.2
New parameter plot=TRUE for plot.phenology() - 5.2.2
Restore shiny version within the package - 5.2.3
Multilanguage version of phenology() - 5.2.4
Spanish version of phenology() - 5.2.5

phenology 5.2 (2016-07-18)

Correction for likelihod_phenology() - 5.1.1
Estimation of likelihoods for different beaches is ran in parallel - 5.1.1
Can add a list read using read_folder() - 5.1.2
phenology() function works again - 5.1.3
plot.phenologymap() plot only one heat map - 5.1.4
plot_phi() and plot_delta() are more flexible - 5.1.4
Moon is not shown if xlim is used for plot.phenology() - 5.1.4
Shiny application phenology() is better handeld - 5.2

phenology 5.1 (2016-05-02)

Minor changes in documentation

phenology 5.0.3

Add cofactors for daily effects in fit_phenology() - 5.0.0
method_incertitude are changed to 'convolution' or 'combinatory' - 5.0.0
Correct a bug for cofactor analysis - 5.0.1
Minor change in the output of plot() - 5.0.2
Add a zero parameter for fit_phenology() - 5.0.3
Bug correction for for cofactor analysis - 5.0.3

phenology 4.4-4.4.1

The "sum" method_incertitude uses an exact method for the negative binomial distribution
The "binomial" method has been removed
Optimisation of the function .Lnegbin to be more rapid and to return also the likelihood of each observation
Require package HelpersMG version higher or equal than 1.3.4

phenology 4.3.1-4.3.6

Object returns from MHmcmc has the correct class mcmcComposite - 4.3.1
Bisextile years are possible - 4.3.2
Theta can be a fixed parameter - 4.3.3
se for some parameters can be indicated manually in plot - 4.3.4
Better gestion of bisextil years in plot - 4.3.4
se indicated manually in plot replaced the previous ones if they exist - 4.3.5
plot.ftiRMU has a new parameter to change the order of series - 4.3.5
fit_phenology can produce positive likelihood without error - 4.3.6
correct a bug introduced in 4.3.5 for se managment - 4.3.6
print.phenologyout() can show data with very small se - 4.3.6

phenology 4.3

Minor changes in fitRMU() and bugs corrections

phenology 4.2.3-4.2.4

New models for fitRMU()
New functions plot.fitRMU(), logLik.fitRMU(), fitRMU_MHmcmc_p() and fitRMU_MHmcmc()
Test if names of timeseries has a _ character and change it with a warning
phenology_MHmcmc_p() returns a data.frame and no more a matrix
The lastest version can always been installed using: install.packages("http://www.ese.u-psud.fr/epc/conservation/CRAN/phenology.tar.gz", repos=NULL, type="source")
Require package HelpersMG version higher or equal than 1.2

phenology 4.2 (2015-05-10)

New function fitRMU()
Correct add_phenology() description
Correct a bug if no fixed parameter is included

phenology 4.1 (2015-04-09)

growlnotify(), MHalgoGen(), as.mcmc.mcmcComposite(), as.par.mcmcComposite(), summary.mcmcComposite(), plot.mcmcComposite(), plot_add(), ScalePreviousPlot(), plot_errbar(), ChangeCoordinate(), barplot_errbar(), chr(), asc(), ind_long_lat(), getTide(), clean.knitr(), local.search(), map.scale2(), compassRose2(), convert.tz(), insidesearch(), moon_phase(), compare_AIC(), read_folder() are transfered into new package HelpersMG
Desription conforms to new CRAN specification

phenology 4.0.5

Better managment of hidden function .MHalgoGen for very long MCMC profiling.
Prevent an error in MCMC search when likelihood cannot be estimated.
convert.tz(x, ) return an object of the same class than x.
Length_ and Peak_ parameters can be series-specific.

phenology 4.0.4 (2015-02-11)

The hidden function .MHalgoGen has three new parameters for very long MCMC profiling to resume search for computer crash.
Correct a bug for add_phenology() when month_ref is indicated
Correct a cosmetic bug in print.phenologyout()
Length parameter can now be associated with a beach
New function insidesearch() to search for a string in files within a folder

phenology 4.0 (2014-10-06)

Remove phenology-swot() and keep only phenology() for web application
Function convert.ts() renamed convert.tz()
New tests for add_phenology()
The parameter trace for mcmc can take an integer value to tell how many intermediate results must be shown
Simplification of ind_lat_lon()

phenology 3.71-3.72

Breaks for plot mcmc objects with uniform distribution use min and max as limits
New parameter to help scaling prior vs posterior in plot mcmc objects
Better examples for MCMC
phenology_MHmcmc_p() check is initial values are out of range
Correct bug for phenology_MHmcmc_p() with pMin, pMinE, pMinB
Correct bug for ind_long_lat() using indices
New way to use RNetCDF and XML packages which are only suggested
New function convert.ts() to convert POSIXlt or POSIXct date-time from one timezone to an other

phenology 3.70

Correct of bug in toggle_Min_PMin()

phenology 3.69 (2014-06-22)

New function map.scale2() and compassRose2() to change the colors of text and lines

phenology 3.66-3.68

New function clean.knitr() to clean folder after knitr compile
New function local.search() to search a file on local disk
XML package is no more required but suggested
New function logLik() for phenology class

phenology 3.64-3.65

Add compatibility of ind_lat_lon() with RNetCDF package
Change in ind_lat_lon() to make it more general

phenology 3.63 (2014-04-07)

Correct two bugs in function getTide() (when levels are negative and when system cannot use utf-8)
add_phenology() now keeps the name of timeseries added
New parameter silent=TRUE/FALSE for add_phenology()

phenology 3.61-3.62

New function getTide()
Shiny server

phenology 3.60

New parameter in function ind_long_lat() to give the explicit name of longitude and latitude in ncdf file. Defaults are "lon" and "lat". Correction of bug.
New shiny server (experimental)

phenology 3.59

Remove dependency to ncdf4 package and make function ind_long_lat() compatible also with RNetCDF and ncdf packages

phenology 3.57 (2014-02-25)

Parameter folder of function read_folder() accept or a file or a folder
New parameter wildcard for function read_folder()

phenology 3.56

new function ind_long_lat()

phenology 3.55 (2013-11-21)

New function MinBMinE_to_Min()
new parameter growlnotify for fit_phenology and plot.phenology
correcton of a bug to prevent PMinE to become negatif

phenology 3.53-3.54

New functions asc() and chr() to manipulate UTF-8 codes
Function ScalePreviousPlot() returns also the range, the center and the position of labels

phenology 3.52

New function used to toggle between Min and PMin parameters
new parameter legend=TRUE for plot.mcmcComposite()

phenology 3.51 (2013-07-11)

New version of the update check at startup

phenology 3.50 (2013-07-10)

Correct a bug for scale of prior in plot.mcmcComposite()
If prior is uniform, changed the scale to show all prior
Parameters x.plus, x.minus, y.plus, and y.minus in plot_errbar to define absolut position of ends of error bars.
Minor change in print.phenologyout()
Add add=FALSE parameter to plot_errbar()
New function barplot_errbar()

phenology 3.49 (2013-06-24)

Minor change in add_phenology()
New function plot_add()
New function ScalePreviousPlot()
New function plot_errbar()
New function ChangeCoordinate()

phenology 3.47 (2013-06-03)

New format of examples to be compatible with R 3.10

phenology 3.46

New parameter accept for phenology_MHmcmc_p() to run the function in batch mode
Correct the resolution for prior curve in plot()

phenology 3.45

Correction for onAttach() to allow the package to load if internet is present but does not anwser as expected.
compare_AIC() can use list of several object and then the AIC is summed.
New functions as.mcmc.Composite() and as.par.mcmcComposite().
compare_AIC() shows only 3 digits.
compare_AIC() can uses list object summarizing data.

phenology 3.44 (2013-01-29)

add parameter progressbar = TRUE/FALSE for plot and map_phenology() to be used with Sweave
plot_phenology() and plot_map() removed
correct a bug when xlim or ylim were used with plot.phenology()
remove the pdf option for plot.phenology
correction of bug in the .MHalgoGen() function
correct a display bug for maximum likelihood in map_phenology()

phenology 3.42-3.43

first likelihood is stored in mcmcComposite
check for update at load time
compare_AIC() can use any list with elements named AIC or aic
better managment of options for plot
New funtions L_to_LBLE() and LBLE_to_L()
add_format() has been renamed as add_phenology()
add_phenology() and fit_phenology() by default opens a box to choose a file and try to read the file directly
better managment for file reading in phenology_swot()
if fit_phenology() is executed without formated data or parameterfit, it runs add_phenology() or par_init() first.
phenology() stores data in phenology environment.

phenology 3.41 (2012-11-26)

add function phenology_swot() for rapid fit of nesting season
if standard error of parameters is not available, produce NA for SE of nest counts rather than 0

phenology 3.40 (2012-10-07)

add Bayesian analysis

phenology 3.36

change the function compare_AIC() to be used also with package embryogrowth

phenology 3.35

new function adapt_parameters to extract only the useful parameters form a set
the output from a plot can be used with several timeseries analyzed at the same time
add a new class: phenologyout that is created by plot_phenology
add the print.phenologyout and summary.phenologyout function
the moons are now displayed at the top of the graph, not superimposed

phenology 3.34

remove the use of the phenology.env environment

phenology 3.33

internal changes

phenology 3.32

new option for add_format: adjust_ref=TRUE
change on the way that Begin, Peak and End are calculated within par_init

phenology 3.31 (2012-05-15)

internal change to get no warnings during build

phenology 3.30

create two new classes: phenology and phenologymap
create the plot, print, summary methods for these new classes
it is possible to add several datasets at one time with add=list(d1, d2, d3)
for add_format, it is possible to add several format for date with format = c("%d/%m/%Y", "%d/%m/%y"). All formats are tested.
added function read_folder() to open all files from a folder and create a list to be used with add_format function
correct an error for the outputs of plot_phenology with several series
the main calendar dates for each series are shown at the end of the fit
these dates are stored in the result under the name $Dates

phenology 3.29 (2012-04-11)

added function moon_phase()
added moon=FALSE parameter for fit_phenology()
added moon=TRUE for examples of shift_sinusoid()
plot_phenology() return a list of lists with the outputs
added function compare_AIC()