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Last data update: 2014.03.03

R: Show the fitted growth rate dependent on temperature

plotR

R Documentation

Show the fitted growth rate dependent on temperature

Description

To show the growth rate, the syntaxe is:
plotR(result=res)

Usage

plotR(result = NULL, parameters = NULL, fixed.parameters = NULL,
  col = "black", legend = NA, SE = NULL, set.par = 1, size = NA,
  xlim = c(20, 35), scaleY = "auto", lty = 1, ltyCI = 3, lwd = 1,
  lwdCI = 1, xlimR = xlim, replicate.CI = 100, show.box = TRUE,
  local.box = "topleft", ...)

Arguments

`result`	A result object or a list of result objects
`parameters`	Indicate some parameters if the result object is not supplied
`fixed.parameters`	Indicate some parameters if the result object is not supplied
`col`	The color to use for a list of colors if several results
`legend`	Text to show in bottom right legend or a list of text if several results
`SE`	The standard error for the parameters or a list of SE if several results. Use NA to force not use SE
`set.par`	1 or 2 or a list of 1 or 2 to designate with set of parameters to show
`size`	If indicated, will show the growth rate for this size
`xlim`	Range of values for x-axis
`scaleY`	Scaling factor for y axis or "auto"
`lty`	The type of line to use if several results as a list
`ltyCI`	The type of line to use for confidence interval as a list
`lwd`	The type of line to use if several results as a list
`lwdCI`	The type of line to use for confidence interval as a list
`xlimR`	Range of values to be displayed for R curve; can be a list if a list of results is used
`replicate.CI`	Number of randomizations to estimate CI
`show.box`	If TRUE show a box with "mean" and "confidence interval"
`local.box`	Position of the box with "mean" and "confidence interval", default="topleft"
`...`	Parameters for plot() such as main= or ylim=

Details

plotR shows the fitted growth rate dependent on temperature

Value

Nothing

Author(s)

Marc Girondot

Examples

## Not run: 
library(embryogrowth)
data(nest)
formated <- FormatNests(nest)
# The initial parameters value can be:
# "T12H", "DHA",  "DHH", "Rho25"
# Or
# "T12L", "DT", "DHA",  "DHH", "DHL", "Rho25"
x <- structure(c(118.768297442004, 475.750095909406, 306.243694918151, 
116.055824800264), .Names = c("DHA", "DHH", "T12H", "Rho25"))
# pfixed <- c(K=82.33) or rK=82.33/39.33
pfixed <- c(rK=2.093313)
resultNest_4p <- searchR(parameters=x, fixed.parameters=pfixed, 
	temperatures=formated, derivate=dydt.Gompertz, M0=1.7, 
	test=c(Mean=39.33, SD=1.92))
data(resultNest_4p)
pMCMC <- TRN_MHmcmc_p(resultNest_4p, accept=TRUE)
# Take care, it can be very long, sometimes several days
result_mcmc_4p_80 <- GRTRN_MHmcmc(result=resultNest_4p,  
	parametersMCMC=pMCMC, n.iter=10000, n.chains = 1, n.adapt = 0,  
	thin=1, trace=TRUE)
data(result_mcmc_4p)
plotR(result=resultNest_4p, SE=result_mcmc_4p$TimeSeriesSE,  
ylim=c(0,0.3))
x <- structure(c(115.758929130522, 428.649022170996, 503.687251738993, 
12.2621455821612, 306.308841227278, 116.35048615105), .Names = c("DHA", 
"DHH", "DHL", "DT", "T12L", "Rho25"))
plotR(parameters=x, xlim=c(20,35))
pfixed <- c(rK=2.093313)
resultNest_6p <- searchR(parameters=x, fixed.parameters=pfixed, 
	temperatures=formated, derivate=dydt.Gompertz, M0=1.7, 
	test=c(Mean=39.33, SD=1.92))
data(resultNest_6p)
plotR(list(resultNest_4p, resultNest_6p),  
col=c("black", "red"), legend=c("4 parameters", "6 parameters"))
##########################################
# new formulation of parameters
data(resultNest_newp)
plotR(resultNest_newp)

## End(Not run)