plotR: Plot the fitted growth rate dependent on temperature and its...

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

Plot the fitted growth rate dependent on temperature and its density

Description

Show the fitted growth rate dependent on temperature and its density.
The curve "ML quantiles" is based on delta method.
The curve "ML" just shows the fitted model.
The curve "MCMC quantiles" uses the mcmc replicates to build the quantiles.
The curve "MCMC mean-SD" uses the mcmc replicates to build a symetric credibility interval.
The parameter curve is case insensitive. If only parameters is given, curve must be ML.

Usage

plotR(
  result = NULL,
  resultmcmc = NULL,
  chain = 1,
  parameters = NULL,
  fixed.parameters = NULL,
  temperatures = NULL,
  curve = "ML quantiles",
  set.par = 1,
  ylim = c(0, 5),
  xlim = c(20, 35),
  xlimR = NULL,
  hessian = NULL,
  replicate.CI = 1000,
  cex.lab = par("cex"),
  cex.axis = par("cex"),
  scaleY = "auto",
  lty = 1,
  ltyCI = 3,
  lwd = 1,
  lwdCI = 1,
  col = "black",
  col.polygon = "grey",
  polygon = FALSE,
  probs = 0.95,
  colramp = colorRampPalette(c("white", rgb(red = 0.5, green = 0.5, blue = 0.5))),
  bandwidth = c(0.1, 0.01),
  pch = "",
  main = "",
  xlab = expression("Temperature in " * degree * "C"),
  ylab = NULL,
  yaxt = "s",
  bty = "n",
  las = 1,
  by.temperature = 0.1,
  show.density = FALSE,
  new = TRUE,
  show.hist = FALSE,
  ylimH = NULL,
  atH = NULL,
  ylabH = "Temperature density",
  breaks = "Sturges",
  log.hist = FALSE,
  mar = NULL
)

Arguments

result	A result object or a list of result objects
resultmcmc	A result object from GRTN_MHmcmc() function
chain	The chain to use in resultmcmc
parameters	A set of parameters - Has the priority over result
fixed.parameters	A set of fixed parameters
temperatures	A set of temperatures - Has the priority over result
curve	What curve to show: "MCMC quantiles" or "MCMC mean-SD" based on mcmc or "ML" or "ML quantiles" or "ML mean-SE" for maximum-likelihood. Or "none"
set.par	1 or 2 to designate with set of parameters to show
ylim	Range of values for y-axis
xlim	Range of values for x-axis
xlimR	description to show the curve
hessian	An hessian matrix
replicate.CI	Number of replicates to estimate confidence interval with Hessian if delta method failed
cex.lab	cex value for axis
cex.axis	cex value for axis
scaleY	Scaling factor for y axis or "auto"
lty	The type of lines
ltyCI	The type of lines
lwd	The type of lines
lwdCI	The type of lines
col	The color of the lines
col.polygon	The color of the polygon
polygon	If TRUE, confidence interval is shown as a polygon with color
probs	Confidence or credibility interval to show
colramp	Ramp function accepting an integer as an argument and returning n colors.
bandwidth	numeric vector (length 1 or 2) of smoothing bandwidth(s). If missing, a more or less useful default is used. bandwidth is subsequently passed to function bkde2D.
pch	Character for outlayers
main	Title of the graph
xlab	Label for x axis
ylab	Label for y axis
yaxt	The yaxt parameter of y-axis
bty	Box around the pot
las	Orientation for labels in y axis
by.temperature	Step to built the temperatures
show.density	TRUE or FALSE for use with Hessian or MCMC
new	Should the graphics be a new one (TRUE) or superimposed to a previous one (FALSE)
show.hist	TRUE or FALSE
ylimH	Scale of histogram using ylimH=c(min, max)
atH	Position of ticks for scale of histogram
ylabH	Label for histogram scale
breaks	See ?hist
log.hist	SHould the y scale for hist is log ?
mar	The value of par("mar"). If null, it will use default depending on show.dist. If NA, does not change par("mar").

Details

plotR plots the fitted growth rate dependent on temperature and the density of the mcmc

Value

A list with the value of scaleY to be used with other plotR function and the plot data in xy list element

Author(s)

Marc Girondot [e-mail]

Examples

## Not run: 
library(embryogrowth)
# Note that the confidence interval is not the same for mcmc and ml quantiles
plotR(result = resultNest_4p_SSM, 
             resultmcmc=resultNest_mcmc_4p_SSM, 
             curve = "MCMC quantiles", ylim=c(0, 8))
plotR(resultNest_4p_SSM, curve="ML quantiles", ylim=c(0, 6))
#################
plotR(resultmcmc=resultNest_mcmc_4p_SSM, ylim=c(0, 10), 
             curve = "MCMC quantiles", show.density=TRUE)
#################
plotR(resultmcmc=resultNest_mcmc_4p_SSM, 
             curve = "MCMC quantiles", polygon=TRUE, ylim=c(0, 10))
#################
plotR(resultmcmc=resultNest_mcmc_6p_SSM, ylim=c(0,8), 
      curve = "MCMC quantiles", polygon=TRUE, col.polygon = rgb(0, 1, 0, 1))
plotR(resultmcmc=resultNest_mcmc_4p_SSM, ylim=c(0,8), 
       curve = "MCMC quantiles", polygon=TRUE, col.polygon = rgb(1, 0, 0, 0.5), 
       new=FALSE)
legend("topleft", legend=c("SSM 4 parameters", "SSM 6 parameters"), 
        pch=c(15, 15), col=c(rgb(1, 0, 0, 0.5), rgb(0, 1, 0, 1)))
#################
sy <- plotR(resultmcmc=resultNest_mcmc_4p_SSM, ylim=c(0, 8), 
             curve = "MCMC quantiles", show.density=FALSE)
plotR(resultmcmc=resultNest_mcmc_6p_SSM, col="red", ylim=c(0, 8), 
             curve = "MCMC quantiles", show.density=FALSE, 
             new=FALSE, scaleY=sy$scaleY)
#################
sy <- plotR(result=resultNest_6p_SSM, curve="none", 
             scaleY=1E5, 
             ylim=c(0, 8), 
             show.hist = TRUE, new = TRUE, mar=c(4, 4, 1, 4))
#################
plotR(result=resultNest_6p_SSM, curve="ML", 
             ylim=c(0, 8), 
             show.hist = TRUE, ylimH=c(0,1), atH=c(0, 0.1, 0.2))
################
plotR(result = resultNest_4p_SSM, ylim=c(0, 8), 
             resultmcmc=resultNest_mcmc_4p_SSM, 
             show.density = TRUE, 
             curve = "MCMC quantiles")
#################
plotR(resultmcmc=resultNest_mcmc_4p_SSM, ylim=c(0, 8), 
             curve = "MCMC quantiles", show.density=TRUE, scaleY=1E5)

## End(Not run)

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