HeterogeneityNests: Model heterogeneity of temperatures.

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

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 = 0.01, Max = 2), data.frame(Name = "max",
    Min = 0.02, Max = 20), data.frame(Name = "S", Min = 0, Max = 10), data.frame(Name =
    "P", Min = 0, Max = 50), data.frame(Name = "asd", Min = 0.01, Max = 2),
    data.frame(Name = "bsd", Min = 0.01, Max = 1)),
  fitted.parameters = c(min = 1, max = 3.95, S = 0.62, P = 5.7, asd = 0.014, bsd = 1.19),
  fixed.parameters = NULL,
  ...
)

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.

Details

HeterogeneityNests models heterogeneity of temperatures.

Value

Nothing.

Author(s)

Marc Girondot [e-mail]

Examples

## Not run: 
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))

## End(Not run)

embryogrowth documentation built on Aug. 24, 2026, 5:07 p.m.