embryogrowth (version 5.0)

MovingIncubation: 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 (Temperatures). Do not use FormatNests() for this dataframe.

Usage

MovingIncubation(result = stop("A result file from searchR() must be provided"),
  temperatures = stop("A timeseries of temperature must be provided"),
  times = stop("A timeseries of time for each temperature must be provided"),
  temperatures.end.incubation = temperatures,
  average.incubation.duration = 60 * 1440, skip = 1, parameters = NULL,
  fixed.parameters = NULL, SE = NULL, derivate = NULL, test = NULL,
  M0 = NULL, TSP.borders = c(21, 26), embryo.stages = "Caretta caretta",
  replicate.CI = 1, min.length = 40 * 1440, max.length = 150 * 1440,
  progress = TRUE)

Arguments

result

A result file generated by searchR

times

Timeseries of times

temperatures

Timeseries of temperatures

temperatures.end.incubation

Timeseries of temperatures at the end of incubation

average.incubation.duration

The average time to complete incubation

skip

Number of data to skip between two runs

min.length

Minimum length of possible incubation

max.length

Maximum length of possible incubation

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 (not used still)

derivate

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

test

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

M0

Measure of hatchling size proxi at laying date

TSP.borders

The limits of TSP

embryo.stages

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

replicate.CI

Number of randomizations to estimate CI (not used still)

progress

If TRUE, progression bar is shown (desactivate for sweave or knitr)

Value

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

Details

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

Examples

library(embryogrowth)
data(resultNest_4p)
ti <- seq(from=0, to=(60*24*100), by=60)
temp <- rnorm(length(ti), 29, 5)
out <- MovingIncubation(result=resultNest_4p, temperatures=temp,
times=ti)