embryogrowth (version 5.0)

plotR: 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 for plot() such as main= or ylim=

parameters

Indicate some parameters if the result object is not supplied

fixed.parameters

Indicate some parameters if the result object is not supplied

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

legend

Text to show in bottom right legend or a list of text if several results

col

The color to use for a list of colors if several results

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

xlim

Range of values for x-axis

xlimR

Range of values to be displayed for R curve; can be a list if a list of results is used

scaleY

Scaling factor for y axis or "auto"

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"

Value

• Nothing

Details

plotR shows the fitted growth rate dependent on temperature

Examples

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), method = "BFGS", maxiter = 200)
data(resultNest_4p)
pMCMC <- embryogrowth_MHmcmc_p(resultNest_4p, accept=TRUE)
# Take care, it can be very long, sometimes several days
result_mcmc_4p_80 <- embryogrowth_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"))
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), method = "BFGS", maxiter = 200)
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)