plot.HatchingSuccess {embryogrowth} | R Documentation |
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 graphival 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
See Also
Other Hatching success:
HatchingSuccess.MHmcmc_p()
,
HatchingSuccess.MHmcmc()
,
HatchingSuccess.fit()
,
HatchingSuccess.lnL()
,
HatchingSuccess.model()
,
logLik.HatchingSuccess()
,
nobs.HatchingSuccess()
,
predict.HatchingSuccess()
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)