embryogrowth (version 9.5)

plot.HatchingSuccess: Plot results of HatchingSuccess.fit() that best describe hatching success

Description

Plot the estimates that best describe hatching success.
If replicates is 0, it returns only the fitted model.
If replicates is null and resultmcmc is not null, it will use all the mcmc data.
if replicates is lower than the number of iterations in resultmcmc, it will use sequence of data regularly thined.

Usage

# S3 method for HatchingSuccess
plot(
  x,
  xlim = c(20, 40),
  ylim = c(0, 1),
  xlab = "Constant incubation temperatures",
  ylab = "Hatching success",
  bty = "n",
  las = 1,
  col.observations = "red",
  pch.observations = 19,
  cex.observations = 1,
  show.CI.observations = TRUE,
  col.ML = "black",
  lty.ML = 1,
  lwd.ML = 1,
  col.median = "black",
  lty.median = 2,
  lwd.median = 1,
  col.CI = "black",
  lty.CI = 3,
  lwd.CI = 1,
  replicates = NULL,
  resultmcmc = NULL,
  polygon = TRUE,
  color.polygon = rgb(red = 0.8, green = 0, blue = 0, alpha = 0.1),
  what = c("observations", "ML", "CI"),
  ...
)

Value

Nothing

Arguments

x

A result file generated by HatchingSuccess.fit()

xlim

Range of temperatures

ylim

Hatching success range for y-axis

xlab

x label

ylab

y label

bty

bty graphical parameter

las

las graphical parameter

col.observations

Color of observations

pch.observations

Character used for observation (no observations if NULL)

cex.observations

Size of characters for observations

show.CI.observations

Should the confidence interval of the observations be shown?

col.ML

Color of the maximum likelihood model

lty.ML

Line type of the maximum likelihood model (no line if NULL)

lwd.ML

Line width of the maximum likelihood model

col.median

Color of the median model

lty.median

Line type of the median model (no line if NULL)

lwd.median

Line width of the mean model

col.CI

Color of the 95% confidence interval lines

lty.CI

Line type of the 95% confidence interval lines (no line if NULL)

lwd.CI

Line width of the 95% confidence interval lines

replicates

Number of replicates to estimate confidence interval

resultmcmc

Results obtained using HatchingSuccess.MHmcmc()

polygon

If TRUE, confidence interval is shown as a polygon

color.polygon

The color used for polygon

what

Indicate what to plot: "observations", "ML", "CI"

...

Parameters for plot()

Author

Marc Girondot

Details

plot.HatchingSuccess plot result of HatchingSuccess.fit() or HatchingSuccess.MHmcmc() that best describe hatching success

Examples

if (FALSE) {
library(embryogrowth)
totalIncubation_Cc <- subset(DatabaseTSD, 
                             Species=="Caretta caretta" & 
                               Note != "Sinusoidal pattern" & 
                               !is.na(Total) & Total != 0)

par <- c(S.low=0.5, S.high=0.3, 
         P.low=25, deltaP=10, MaxHS=0.8)
         
HatchingSuccess.lnL(par=par, data=totalIncubation_Cc)

g <- HatchingSuccess.fit(par=par, data=totalIncubation_Cc)

HatchingSuccess.lnL(par=g$par, data=totalIncubation_Cc)

plot(g, replicates=0)
plot(g, replicates=10000)

pMCMC <- HatchingSuccess.MHmcmc_p(g, accept=TRUE)
mcmc <- HatchingSuccess.MHmcmc(result=g, parameters = pMCMC, 
                                adaptive=TRUE, n.iter=100000, trace=1000)
plot(g, resultmcmc=mcmc)
plot(g, resultmcmc=mcmc, pch.observations=NULL, lty.mean=NULL)
}