embryogrowth (version 5.1)

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

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=

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)