Package: embryogrowth 9.5

embryogrowth: Tools to Analyze the Thermal Reaction Norm of Embryo Growth

Tools to analyze the embryo growth and the sexualisation thermal reaction norms. See <doi:10.7717/peerj.8451> for tsd functions; see <doi:10.1016/j.jtherbio.2014.08.005> for thermal reaction norm of embryo growth.

Authors:Marc Girondot [aut, cre]

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embryogrowth.pdf |embryogrowth.html✨
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NEWS

# Install 'embryogrowth' in R:
install.packages('embryogrowth', repos = c('https://marc-girondot.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.40 score 1 stars 252 scripts 546 downloads 39 exports 37 dependencies

Last updated 3 months agofrom:9f5dac0f82. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-winOKNov 22 2024
R-4.5-linuxOKNov 22 2024
R-4.4-winNOTENov 22 2024
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R-4.3-macNOTENov 22 2024

Exports:calibrate.dataloggerChangeSSMDatabaseTSD.versiondydt.exponentialdydt.Gompertzdydt.linearFormatNestsGenerate_hatchling_metricGenerateAnchorGenerateConstIncGRTRN_MHmcmcHatchingSuccess.fitHatchingSuccess.lnLHatchingSuccess.MHmcmcHatchingSuccess.MHmcmc_pHatchingSuccess.modelinfo.nestsintegral.exponentialintegral.Gompertzintegral.linearlikelihoodRmovementMovingIncubationP_TRTplot_transitionplotRROSIE.versionsearchRSTRNSTRN_MHmcmcswitch.transitiontest.parallelTRN_MHmcmc_ptsdtsd_MHmcmctsd_MHmcmc_puncertainty.dataloggerweb.tsdweightmaxentropy

Dependencies:clicodacolorspacedeSolvefansifarverggplot2gluegtableHelpersMGisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmenloptrnumDerivoptimxpillarpkgconfigpracmaR6rbibutilsRColorBrewerRdpackrlangscalestibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
The package embryogrowthembryogrowth-package
Calibrate data loggers and correct time series of temperaturescalibrate.datalogger
Generate set of parameters for different forms of thermal norm of reactionChangeSSM
Database of RMU for marine turtlesDatabaseNestingArea
Database of TSD information for reptilesDatabaseTSD
Version of database of TSD information for reptilesDatabaseTSD.version
Return the derivative of the exponential functiondydt.exponential
Return the derivative of the Gompertz functiondydt.Gompertz
Return the derivative of the linear functiondydt.linear
Create a dataset of class Nests to be used with searchRFormatNests
Generate a data.frame that can be used as hatchling.metric value for searchR()Generate_hatchling_metric
Generate a set of anchored parametersGenerateAnchor
Generate a data.frame with constant incubation temperature and incubation durationGenerateConstInc
Metropolis-Hastings algorithm for Embryo Growth Rate Thermal Reaction NormGRTRN_MHmcmc
Fit a hatching success model to data using maximum likelihoodHatchingSuccess.fit
Return -log likelihood of the data and the parametersHatchingSuccess.lnL
Metropolis-Hastings algorithm for hatching successHatchingSuccess.MHmcmc
Generates set of parameters to be used with HatchingSuccess.MHmcmc()HatchingSuccess.MHmcmc_p
Return the hatching success according the set of parameters and temperaturesHatchingSuccess.model
Show the histogram of temperatures with set of nestshist.Nests
Show the histogram of temperatures with set of nestshist.NestsResult
Calculte statistics about nestsinfo.nests
Return the derivative of the exponential functionintegral.exponential
Return the result of the Gompertz functionintegral.Gompertz
Return the linear functionintegral.linear
Estimate the likelihood of a set of parameters for nest incubation datalikelihoodR
Return -log L of a fitlogLik.HatchingSuccess
Return Log Likelihood of a fit generated by searchRlogLik.NestsResult
Return Log Likelihood of a fit generated by STRNlogLik.STRN
Return Log Likelihood of a fit generated by tsdlogLik.tsd
Analyze movement recorded within a nest with an accelerometer dataloggermovement
Simulate incubation of a nest with the beginning of incubation varyingMovingIncubation
Timeseries of temperatures for nestsnest
Return number of observations of a fitnobs.HatchingSuccess
Return number of observations of a fitnobs.NestsResult
Estimate the transitional range of temperatures based on a set of parametersP_TRT
Show fonction used for transitionplot_transition
Plot results of HatchingSuccess.fit() that best describe hatching successplot.HatchingSuccess
Plot the embryo growthplot.NestsResult
Plot results of tsd() that best describe temperature-dependent sex determinationplot.tsd
Plot the fitted growth rate dependent on temperature and its densityplotR
Return prediction based on a model fitted with HatchingSuccess.fit()predict.HatchingSuccess
Estimate sex ratio according to constant incubation temperaturepredict.tsd
Fit using the nest databaseresultNest_3p_Dallwitz
Result of the fit using the nest database using Weibull functionresultNest_3p_Weibull
Result of the fit using the nest database using asymmetric normal functionresultNest_4p_normal
Fit using the nest databaseresultNest_4p_SSM
Fit using the nest databaseresultNest_4p_SSM_Linear
Result of the fit using the nest database using transitionresultNest_4p_transition
Result of the fit using the nest database using trigonometric functionresultNest_4p_trigo
Fit using the nest database with weightresultNest_4p_weight
Fit using the nest databaseresultNest_5p_Dallwitz
Fit using the nest databaseresultNest_6p_SSM
Result of the mcmc using the nest databaseresultNest_mcmc_4p_SSM
Result of the mcmc using the nest databaseresultNest_mcmc_4p_SSM_Linear
Result of the mcmc using the nest databaseresultNest_mcmc_6p_SSM
Result of the mcmc using the nest database with anchored parametersresultNest_mcmc_newp
Fit using the nest database with anchored parametersresultNest_newp
Database of TSD information for turtlesROSIE
Version of database of TSD information for reptilesROSIE.version
Fit the parameters that best represent nest incubation data.searchR
Database of of embryonic development and thermosensitive period of development for sex determinationstages
Estimate the parameters that best describe the sexualisation thermal reaction norm within the TSPSTRN
Metropolis-Hastings algorithm for Sexualisation Thermal Reaction NormSTRN_MHmcmc
Summarize the information from a Nests object.summary.Nests
Add a transition parameter on a set of parameters or remove itswitch.transition
Timeseries of constant temperatures for neststempConst
Estimate the likelihood of a set of parameters for nest incubation data with or without parallel computing optiontest.parallel
Generates set of parameters to be used with GRTRN_MHmcmc() or STRN_MHmcmc()TRN_MHmcmc_p
Estimate the parameters that best describe temperature-dependent sex determinationtsd
Metropolis-Hastings algorithm for Sex ratiotsd_MHmcmc
Generates set of parameters to be used with tsd_MHmcmc()tsd_MHmcmc_p
Database of thermosensitive period of development for sex determinationTSP.list
Uncertainty of average temperatures obtained using temperature data loggeruncertainty.datalogger
Run a shiny application for basic functions of tsd functionweb.tsd
Search for the weights of the nests which maximize the entropy of nest temperatures distributionweightmaxentropy