What must be done: * Check Tagloss_cumul() to use hessian or mcmc * simplify generateCF(). * Return Peak, Begin and End confidence interval based on Omeyer et al. (2022) parametrization. THIS IS THE CHANGELOG OF THE "phenology" PACKAGE CHANGES IN VERSION 9.1 (2023-10-16) * New CRAN version - 9.1 (2023-10-16) CHANGES IN VERSION 9.0.14 (2023-10-11) * 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 is 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) CHANGES IN VERSION 8.0.6 (2023-03-22) * 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) CHANGES IN VERSION 7.9 (2022-09-06) * New CRAN version - 7.9 (2022-09-06) CHANGES IN VERSION 7.8-4 (2022-09-06) * 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) CHANGES IN VERSION 7.8 (2022-07-14) * 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) CHANGES IN VERSION 7.5.25 (2020-09-05) * 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) CHANGES IN VERSION 7.2 (2019-01-04) * 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) CHANGES IN VERSION 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) CHANGES IN VERSION 7.0.4 (2018-04-25) * 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 CHANGES IN VERSION 6.0-6.0.3 (2017-10-17) * 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 CHANGES IN VERSION 5.5 (2017-05-14) * Use of SEfromHessian - 5.5 CHANGES IN VERSION 5.4.1 (2017-04-07) * New version for CRAN - 5.4 * phenology() is compatible with shiny 1.0.1 - 5.4.1 CHANGES IN VERSION 5.3.15 (2017-03-03) * 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 CHANGES IN VERSION 5.2.1-5.2.5 (2016-08-15) * 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 CHANGES IN VERSION 5.2 (2016-07-17) * 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 CHANGES IN VERSION 5.1 (2016-05-02) * Minor changes in documentation CHANGES IN VERSION 5.0.3 (2016-04-09) * 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 CHANGES IN VERSION 4.4-4.4.1 (2016-01-13) * 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 CHANGES IN VERSION 4.3.1-4.3.6 (2015-12-09) * 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 CHANGES IN VERSION 4.3 (2015-07-29) * Minor changes in fitRMU() and bugs corrections CHANGES IN VERSION 4.2.3-4.2.4 (2015-06-29) * 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 CHANGES IN VERSION 4.2 (2015-05-09) * New function fitRMU() * Correct add_phenology() description * Correct a bug if no fixed parameter is included CHANGES IN VERSION 4.1 (2015-04-08) * 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 CHANGES IN VERSION 4.0.5 (2015-02-15) * 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. CHANGES IN VERSION 4.0.4 (2015-01-29) * 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 CHANGES IN VERSION 4.0 (2014-10-05) * 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() CHANGES IN VERSION 3.71-3.72 (2014-08-24) * 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 CHANGES IN VERSION 3.70 (2014-07-07) * Correct of bug in toggle_Min_PMin() CHANGES IN VERSION 3.69 (2014-06-21) * New function map.scale2() and compassRose2() to change the colors of text and lines CHANGES IN VERSION 3.66-3.68 (2014-06-04) * 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 CHANGES IN VERSION 3.64-3.65 (2014-04-27) * Add compatibility of ind_lat_lon() with RNetCDF package * Change in ind_lat_lon() to make it more general CHANGES IN VERSION 3.63 (2014-04-06) * 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() CHANGES IN VERSION 3.61-3.62 (2014-03-14) * New function getTide() * Shiny server CHANGES IN VERSION 3.60 (2014-03-08) * 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) CHANGES IN VERSION 3.59 (2014-02-26) * Remove dependency to ncdf4 package and make function ind_long_lat() compatible also with RNetCDF and ncdf packages CHANGES IN VERSION 3.57 (2014-02-23) * Parameter folder of function read_folder() accept or a file or a folder * New parameter wildcard for function read_folder() CHANGES IN VERSION 3.56 (2013-12-09) * new function ind_long_lat() CHANGES IN VERSION 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 CHANGES IN VERSION 3.53-3.54 (2013-10-23) * New functions asc() and chr() to manipulate UTF-8 codes * Function ScalePreviousPlot() returns also the range, the center and the position of labels CHANGES IN VERSION 3.52 (2013-08-05) * New function used to toggle between Min and PMin parameters * new parameter legend=TRUE for plot.mcmcComposite() CHANGES IN VERSION 3.51 (2013-07-10) * New version of the update check at startup CHANGES IN VERSION 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() CHANGES IN VERSION 3.49 (2013-06-23) * Minor change in add_phenology() * New function plot_add() * New function ScalePreviousPlot() * New function plot_errbar() * New function ChangeCoordinate() CHANGES IN VERSION 3.47 (2013-06-03) * New format of examples to be compatible with R 3.10 CHANGES IN VERSION 3.46 (2013-04-08) * New parameter accept for phenology_MHmcmc_p() to run the function in batch mode * Correct the resolution for prior curve in plot() CHANGES IN VERSION 3.45 (2013-02-23) * 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. CHANGES IN VERSION 3.44 (2013-01-28) * 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() CHANGES IN VERSION 3.42-3.43 (2013-01-02) * 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. CHANGES IN VERSION 3.41 (2012-11-25) * 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 CHANGES IN VERSION 3.40 (2012-10-06) * add Bayesian analysis CHANGES IN VERSION 3.36 (2012-07-22) * change the function compare_AIC() to be used also with package embryogrowth CHANGES IN VERSION 3.35 (2012-06-06) * 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 CHANGES IN VERSION 3.34 (2012-05-31) * remove the use of the phenology.env environment CHANGES IN VERSION 3.33 (2012-05-31) * internal changes CHANGES IN VERSION 3.32 (2012-05-23) * new option for add_format: adjust_ref=TRUE * change on the way that Begin, Peak and End are calculated within par_init CHANGES IN VERSION 3.31 (2012-05-14) * internal change to get no warnings during build CHANGES IN VERSION 3.30 (2012-05-13) * 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 CHANGES IN VERSION 3.29 (2012-04-09) * 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()