Tools to Manage a Parametric Function that Describes Phenology

Functions used to fit and test the phenology of species based on counts.


News

THIS IS THE CHANGELOG OF THE "phenology" PACKAGE

        CHANGES IN VERSION 7.3 (2019-01-04)
  • 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)

  • 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

          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()

Reference manual

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