Plot the embryo growth from one or several nests.
The embryo.stages is a list with stage numbers and relative size as compared to final size at the beginning of the stage.
For example for Caretta caretta, embryo.stages=list(number=21:30, size=c(8.4, 9.4, 13.6, 13.8, 18.9, 23.5, 32.2, 35.2, 35.5, 38.5)/39.33) indicates that the stages 21 begins at the relative size of 8.4/39.33.
The default is for the turtle "Caretta caretta".
Series can be indicated as the name of the series, its number or succesion of TRUE or FALSE. "all" indicates that all series must be printed.
show.fioritures parameter does not affect show.test option.
Note: three species have predefined embryo stages. embryo.stages parameter can take the values:
● Data Source:
CranContrib
● Keywords:
● Alias: plot.NestsResult
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GenerateTest
(Package: embryogrowth) :
Generate a data.frame that can be used as test value for searchR()
Generate a data.frame that can be used as test value for searchR()
● Data Source:
CranContrib
● Keywords:
● Alias: GenerateTest
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STRN
(Package: embryogrowth) :
Estimate the parameters that best describe the sexualisation thermal reaction norm within the TSP
Estimate the parameters that best describe the sexualisation thermal reaction norm within the TSP.
The Temperatures parameter is a character string which can be:
● Data Source:
CranContrib
● Keywords:
● Alias: STRN
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plotR
(Package: embryogrowth) :
Show the fitted growth rate dependent on temperature
To show the growth rate, the syntaxe is:
plotR(result=res)
● Data Source:
CranContrib
● Keywords:
● Alias: plotR
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TRN_MHmcmc_p
(Package: embryogrowth) :
Generates set of parameters to be used with GRTRN_MHmcmc() or STRN_MHmcmc()
Interactive script used to generate set of parameters to be used with GRTRN_MHmcmc() or STRN_MHmcmc().
● Data Source:
CranContrib
● Keywords:
● Alias: TRN_MHmcmc_p
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dydt.linear
(Package: embryogrowth) :
Return the derivative of the linear function
Return the derivative of the linear function
dydt.linear(t, size, parms)
● Data Source:
CranContrib
● Keywords:
● Alias: dydt.linear
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Plot the transition function
● Data Source:
CranContrib
● Keywords:
● Alias: plot_transition
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searchR
(Package: embryogrowth) :
Fit the parameters that best represent nest incubation data.
Fit the parameters that best represent data.
test can be a list with two elements Mean and SD and each element is a named vector with the nest name.
● Data Source:
CranContrib
● Keywords:
● Alias: searchR
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FormatNests
(Package: embryogrowth) :
Create a dataset of class Nests to be used with searchR
Will create a dataset of class Nests to be used with searchR
FormatNests(nest, previous=x) with x being a previously formated data.
The raw data must be organized being:
First column is the time in minutes since the beginning of incubation
Each column next is the trace of temperatures, one column for each nest.
For example, for two nests:
Time Nest1 Nest2
0 29.8 27.6
90 30.2 28.8
120 30.4 30.7
180 31.2 32.6
...
65800 30.8 32.6
65890 30.2
65950 30.4
The Nest1 ends incubation at 65800 minutes whereas Nest2 ends incubation at 65950 (last row
with temperature for each).
The parameter Weight is a vector: weight=c(Nest1=1, Nest2=1.2)
It can be used to format database already formated with old format; in this case, just use data=xxx with xxx being the old format database.
● Data Source:
CranContrib
● Keywords:
● Alias: FormatNests
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GRTRN_MHmcmc
(Package: embryogrowth) :
Metropolis-Hastings algorithm for Embryo Growth Rate Thermal Reaction Norm
Run the Metropolis-Hastings algorithm for data.
The number of iterations is n.iter+n.adapt+1 because the initial likelihood is also displayed.
I recommend that thin=1 because the method to estimate SE uses resampling.
If initial point is maximum likelihood, n.adapt = 0 is a good solution.
To get the SE of the point estimates from result_mcmc <- GRTRN_MHmcmc(result=try), use:
result_mcmc$SD
coda package is necessary for this function.
The parameters intermediate and filename are used to save intermediate results every 'intermediate' iterations (for example 1000). Results are saved in a file named filename.
The parameter previous is used to indicate the list that has been save using the parameters intermediate and filename. It permits to continue a mcmc search.
These options are used to prevent the consequences of computer crash or if the run is very very long and processes with user limited time.
● Data Source:
CranContrib
● Keywords:
● Alias: GRTRN_MHmcmc
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providing 
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