embryogrowth (version 10.3)

HeterogeneityNests: Model heterogeneity of temperatures.

Description

Generate a model of heterogeneity of temperatures.

Usage

HeterogeneityNests(
  nests = stop("An object of class Nests2, NestsResult, or mcmcComposite."),
  probs = c(0.025, 0.975),
  control.legend.total = list(),
  control.legend.metabolicheating = list(),
  show.full.incubation = TRUE,
  show.first.half.incubation = TRUE,
  col.absolute.difference.full = rgb(blue = 0.1, green = 0.1, red = 1, alpha = 0.01),
  pch.absolute.difference.full = 19,
  col.absolute.difference.first = rgb(blue = 1, green = 0.1, red = 0.1, alpha = 0.01),
  pch.absolute.difference.first = 19,
  show.se = TRUE,
  show.sd = TRUE,
  n.iter = 10000,
  n.adapt = 1000,
  thin = 5,
  adaptive = TRUE,
  return.mcmc = FALSE,
  trace = FALSE,
  rules = rbind(data.frame(Name = "min", Min = 0, Max = 2), data.frame(Name = "max", Min
    = 0, Max = 20), data.frame(Name = "S", Min = 0, Max = 10), data.frame(Name = "P", Min
    = 0, Max = 50), data.frame(Name = "asd", Min = 0, Max = 2), data.frame(Name = "bsd",
    Min = 0, Max = 1)),
  fitted.parameters = c(min = 1, max = 3.94384206319577, S = 0.621279598124434, P =
    5.69863056154757, asd = 0.0139849297499185, bsd = 1.19025174327629),
  fixed.parameters = NULL,
  ...
)

Value

Nothing.

Arguments

nests

An object of class Nests, Nests2, NestsResult, or mcmcComposite.

probs

A vector of two values to set the range of quantiles to define heterogeneity. Use 0 and 1 for min and max.

control.legend.total

A list of options for legend.

control.legend.metabolicheating

A list of options for legend.

show.full.incubation

Show the plot with full incubation?

show.first.half.incubation

Show the plot with first half incubation?

col.absolute.difference.full

The color for absolute difference of temperatures for full incubation.

pch.absolute.difference.full

The pch for absolute difference of temperatures for full incubation.

col.absolute.difference.first

The color for absolute difference of temperatures for first-half incubation.

pch.absolute.difference.first

The pch for absolute difference of temperatures for first-half incubation.

show.se

The standard error of the modelled heterogeneity.

show.sd

The standard deviation of the observed heterogeneity.

n.iter

Number of iteration for MCMC

n.adapt

Number of adaptation for MCMC

thin

Number of thin for MCMC

adaptive

Do adaptive MCMC should be used

return.mcmc

Should the mcmc object be returned?

trace

Show intermediate results.

rules

The rules for max and min for each parameters.

fitted.parameters

The set of fitted parameters with plausible values based on rules.

fixed.parameters

The values of parameters that will not be changed during optimisation.

...

Parameters used for plot.

Author

Marc Girondot

Details

HeterogeneityNests models heterogeneity of temperatures.

Examples

if (FALSE) {
library(embryogrowth)
data(nest)
Laying.Time <- matrix(c("DY.1", "15/05/2010", 
                 "DY.17", "24/05/2010", 
                 "DY.16", "24/05/2010", 
                 "DY.18", "25/05/2010", 
                 "DY.20", "25/05/2010", 
                 "DY.21", "26/05/2010", 
                 "DY.22", "26/05/2010", 
                 "DY.23", "26/05/2010", 
                 "DY.24", "27/05/2010", 
                 "DY.25", "27/05/2010", 
                 "DY.28", "28/05/2010", 
                 "DY.26", "28/05/2010", 
                 "DY.27", "28/05/2010", 
                 "DY.146", "20/06/2010", 
                 "DY.147", "20/06/2010", 
                 "DY.172", "24/06/2010", 
                 "DY.175", "24/06/2010", 
                 "DY.170", "24/06/2010", 
                 "DY.260", "06/07/2010", 
                 "DY.282", "12/07/2010", 
                 "DY.310", "18/07/2010", 
                 "DY.309", "18/07/2010", 
                 "DY.328", "25/07/2010", 
                 "DY.331", "26/07/2010"), byrow=TRUE, ncol=2)
tz <- OlsonNames()[grepl("Asia/Istanbul", OlsonNames())]
Laying.Time_f <- as.POSIXlt.character(Laying.Time[, 2], format = "%d/%m/%Y", tz=tz)
names(Laying.Time_f) <- Laying.Time[, 1]
nests <- FormatNests(data=nest, previous=NULL, col.Time="Time", 
                      LayingTime=Laying.Time_f, simplify=FALSE)
HeterogeneityNests(nests, ylim=c(0, 30))
}