Markov chain Monte Carlo for C4 photosynthesis parameters

Usage

MCMCc4photo(data, niter = 20000, ivmax = 39, ialpha = 0.04, ikparm = 0.7, itheta = 0.83, ibeta = 0.93, iRd = 0.8, Catm = 380, b0 = 0.08, b1 = 3, StomWS = 1, ws = c("gs", "vmax"), scale = 1, sds = c(1, 0.005), prior = c(39, 10, 0.04, 0.02), UPPERTEMP = 37.5, LOWERTEMP = 3)

Arguments

data

observed assimilation data, which should be a data frame or matrix. The first column should be observed net assimilation rate (micro mol per meter squared per secondmicro mol per meter squared per second). The second column should be the observed quantum flux (micro mol per meter squared per secondmicro mol per meter squared per second). The third column should be observed temperature of the leaf (Celsius). The fourth column should be the observed relative humidity in proportion (e.g. 0.7).

niter

number of iterations to run the chain for (default = 20000).

ivmax

initial value for Vcmax (default = 39).

ialpha

initial value for alpha (default = 0.04).

ikparm

initial value for kparm (default = 0.7). Not optimized at the moment.

itheta

initial value for theta (default = 0.83). Not optimized at the moment.

ibeta

initial value for beta (default = 0.93). Not optimized at the moment.

iRd

initial value for dark respiration (default = 0.8).

Catm

see c4photo function.

b0

see c4photo function.

b1

see c4photo function.

StomWS

see c4photo function.

ws

see c4photo function.

scale

This scale parameter controls the size of the standard deviations which generate the moves in the chain.

sds

Finer control for the standard deviations of the prior normals. The first element is for vmax and the second for alpha.

prior

Vector of length 4 with first element prior mean for vmax, second element prior standard deviation for vmax, third element prior mean for alpha and fourth element prior standard deviation for alpha.

Examples

## <strong>Not run</strong>: 
# ## Using Beale, Bint and Long (1996)
# data(obsBea)
# 
# ## Different starting values
# resB1 <- MCMCc4photo(obsBea, 100000, scale=1.5)
# resB2 <- MCMCc4photo(obsBea, 100000, ivmax=25, ialpha=0.1, scale=1.5)
# resB3 <- MCMCc4photo(obsBea, 100000, ivmax=45, ialpha=0.02, scale=1.5)
# 
# ## Use the plot function to examine results
# plot(resB1,resB2,resB3)
# plot(resB1,resB2,resB3,plot.kind='density',burnin=1e4)
# 
# ## <strong>End(Not run)</strong>