plot.tsd: Plot results of tsd() that best describe...

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

Plot results of tsd() that best describe temperature-dependent sex determination

Description

Plot the estimates that best describe temperature-dependent sex determination.
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Usage

## S3 method for class 'tsd'
plot(
  x,
  ...,
  show.observations = TRUE,
  show.model = TRUE,
  males.freq = TRUE,
  show.PTRT = TRUE,
  las.x = 1,
  las.y = 1,
  lab.PT = paste("Pivotal ", x$type),
  resultmcmc = NULL,
  chain = 1,
  l = 0.05,
  replicate.CI = 10000,
  range.CI = 0.95,
  mar = c(4, 4, 4, 1) + 0.4,
  temperatures.plot = seq(from = 25, to = 35, by = 0.1),
  durations.plot = seq(from = 40, to = 70, by = 0.1),
  lab.TRT = paste0("Transitional range of ", x$type, "s l=", x$l * 100, "%"),
  col.TRT = "gray",
  col.TRT.CI = rgb(0.8, 0.8, 0.8, 0.8),
  col.PT.CI = rgb(0.8, 0.8, 0.8, 0.8),
  show.CI = TRUE,
  warn = TRUE,
  use.ggplot = TRUE
)

Arguments

x	A result file generated by tsd()
...	Parameters for plot()
show.observations	Should the observations be shown
show.model	Should the model be shown
males.freq	Should the graph uses males relative frequency TRUE or females FALSE
show.PTRT	Should the P and TRT information be shown
las.x	las parameter for x axis
las.y	las parameter for y axis
lab.PT	Label to describe pivotal temperature
resultmcmc	A result of tsd_MHmcmc()
chain	What chain to be used is resultmcmc is provided
l	Sex ratio limits to define TRT are l and 1-l
replicate.CI	replicate.CI replicates from the hessian matrix to estimate CI
range.CI	The range of confidence interval for estimation, default=0.95
mar	The par("mar") parameter
temperatures.plot	Temperatures used for showing curves of sex ratio
durations.plot	Durations used for showing curves of sex ratio
lab.TRT	Label to describe transitional range of temperature
col.TRT	The color of TRT
col.TRT.CI	The color of CI of TRT based on range.CI
col.PT.CI	The color of CI of PT based on range.CI
show.CI	Do the CI for the curve should be shown
warn	Do the warnings must be shown ? TRUE or FALSE
use.ggplot	Use ggplot graphics (experimental). TRUE or FALSE

Details

plot.tsd plot result of tsd() that best describe temperature-dependent sex determination

Value

Nothing

Author(s)

Marc Girondot

See Also

Other Functions for temperature-dependent sex determination: DatabaseTSD, DatabaseTSD.version(), P_TRT(), ROSIE, ROSIE.version(), TSP.list, predict.tsd(), stages, tsd(), tsd_MHmcmc(), tsd_MHmcmc_p()

Examples

## Not run: 
library(embryogrowth)
CC_AtlanticSW <- subset(DatabaseTSD, RMU.2010=="Atlantic, SW" & 
                          Species=="Caretta caretta" & (!is.na(Sexed) & Sexed!=0))
tsdL <- with (CC_AtlanticSW, tsd(males=Males, females=Females, 
                                 temperatures=Incubation.temperature.set, 
                                 equation="logistic"))
# By default, it will return a ggplot object
# Here I show the advantage of using a ggplot object
g <- plot(tsdL)
# You can remove named layers. For example:
names(g$layers)
g$layers["Observations"] <- NULL; plot(g)
# And add some
# Due to a bug in ggplot, it is necessary to remove all names to obtain correct legends
names(g$layers) <- NULL
g + geom_point(data=CC_AtlanticSW, aes(x=Incubation.temperature.set, y=Males/Sexed, 
               size = Sexed), inherit.aes = FALSE, show.legend = TRUE, shape=19)
# Force to use the original plot
plot(tsdL, use.ggplot = FALSE)

## End(Not run)

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