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

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

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 class '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"),
  ...
)

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()

Details

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

Value

Nothing

Author(s)

Marc Girondot

Examples

## Not run: 
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)

## End(Not run)

embryogrowth documentation built on Sept. 11, 2024, 8:16 p.m.