MovingIncubation {embryogrowth}

Simulate incubation of a nest with the beginning of incubation varying

Description

Simulate incubation of a nest with the beginning varying day by day
Temperatures must be in a data.frame with one column (Time) being the time and the second the temperatures (Temperature). A third columns can indicate the temperature at the end of incubation (Temperature.end.incubation). Do not use FormatNests() for this dataframe.

Usage

MovingIncubation(
  NestsResult = NULL,
  resultmcmc = NULL,
  GTRN.CI = "Hessian",
  tsd = NULL,
  tsd.CI = NULL,
  tsd.mcmc = NULL,
  SexualisationTRN = NULL,
  SexualisationTRN.CI = "Hessian",
  SexualisationTRN.mcmc = NULL,
  temperatures.df = stop("A data.frame must be provided"),
  temperature.heterogeneity = 0,
  metabolic.heating = 0,
  average.incubation.duration = 60 * 1440,
  max.time = 100 * 24 * 60,
  skip = 1,
  parameters = NULL,
  fixed.parameters = NULL,
  SE = NULL,
  hessian = NULL,
  integral = NULL,
  derivate = NULL,
  hatchling.metric = NULL,
  M0 = NULL,
  embryo.stages = "Caretta caretta.SCL",
  TSP.borders = c(21, 26),
  TSP.begin = 0,
  TSP.end = 0.5,
  replicate.CI = 1,
  parallel = TRUE,
  progressbar = TRUE
)

Arguments

NestsResult

A result file generated by searchR

resultmcmc

A mcmc result. Will be used rather than SE if provided.

GTRN.CI

How to estimate CI for embryo growth thermal reaction norm; can be NULL, "SE", "MCMC", "pseudohessianfrommcmc" or "Hessian".

tsd

A object from tsd() that describe the thermal react norm of sex ratio at constant temperatures

tsd.CI

How to estimate CI for sex ratio thermal reaction norm; Can be NULL, "SE", "MCMC", "pseudohessianfrommcmc" or "Hessian".

tsd.mcmc

A object from tsd_MHmcmc()

SexualisationTRN

A model for sexualisation thermal reaction norm during TSP obtained using STRN()

SexualisationTRN.CI

How to estimate CI of sexualisation thermal reaction norm. Can be NULL, "SE", "MCMC", "pseudohessianfrommcmc" or "Hessian".

SexualisationTRN.mcmc

MCMC object for STRN.

temperatures.df

A data.frame with 2 or 3 columns: Times, Temperatures and Temperatures.end.incubation (facultative)

temperature.heterogeneity

SD of heterogeneity of temperatures. Can be 2 values, sd_low and sd_high and then HelpersMG::r2norm() is used.

metabolic.heating

Degrees Celsius to be added at the end of incubation due to metabolic heating

average.incubation.duration

The average time to complete incubation (not used if metabolic heating is setup)

max.time

Maximum time of incubation

skip

Number of data to skip between two runs

parameters

A set of parameters if result is not provided.

fixed.parameters

Another set of parameters if result is not provided.

SE

Standard error for each parameter if not present in result is not provided

hessian

A hessian matrix

integral

Function used to fit embryo growth: integral.Gompertz, integral.exponential or integral.linear

derivate

Function used to fit embryo growth: dydt.Gompertz, dydt.exponential or dydt.linear. It will replace the one in NestsResult.

hatchling.metric

Mean and SD of size of hatchlings as a vector ie hatchling.metric=c(Mean=xx, SD=yy)

M0

Measure of hatchling size proxi at laying date

embryo.stages

The embryo stages. At least TSP.borders stages must be provided to estimate TSP length

TSP.borders

The limits of TSP

TSP.begin

Where TSP begin during the stage of beginning? In relative proportion of the stage.

TSP.end

Where TSP begin during the stage of ending? In relative proportion of the stage.

replicate.CI

Number of randomizations to estimate CI

parallel

Should parallel computing be used. TRUE or FALSE

progressbar

Should a progress bar be shown ? TRUE or FALSE

Details

MovingIncubation simulate incubation of a nest with the beginning varying day by day

Value

A dataframe with informations about thermosensitive period length and incubation length day by day of incubation

Author(s)

Marc Girondot

Examples

## Not run: 
library(embryogrowth)
data(resultNest_4p_SSM)
ti <- seq(from=0, to=(60*24*100), by=60)
temperatures <- rnorm(length(ti), 29, 5)
temperatures <- temperatures+ti/(60*24*100)/2
layout(mat=1:3)
parpre <- par(mar=c(4, 4, 1, 1)+0.4)
plot(ti/(60*24), temperatures, type="l", xlab="Days", 
     ylab=expression("Nest temperature in "*degree*"C"), bty="n", las=1)
# The sexualisation thermal reaction norm is calculated for South Pacific RMU
out <- MovingIncubation(NestsResult=resultNest_4p_SSM, 
     temperatures.df=data.frame(Time=ti, Temperature=temperatures),
     metabolic.heating = 0, 
     SexualisationTRN = structure(c(71.922411148397, 613.773055147801, 
     318.059753164125, 120.327257089974), 
     .Names = c("DHA", "DHH", "T12H", "Rho25")))
with(out, plot(Time/(60*24), Incubation.length.mean/(60*24), 
     xlab="Days along the season", 
     ylab="Incubation duration", 
     type="l", bty="n", las=1, ylim=c(70, 80)))
with(out, plot(Time/(60*24), TSP.GrowthWeighted.STRNWeighted.temperature.mean, 
     xlab="Days along the season", 
     ylab=expression("CTE for sex ratio in "*degree*"C"), 
      type="l", bty="n", las=1, ylim=c(30, 31)))
par(mar=parpre)
layout(mat=c(1))

## End(Not run)