search for: photosynthesi

...nderstand what is happening. I explain the steps below in the hope that someone can explain the error and how to correct it. STEP 1: Data set: name: marouane.data. This is a data frame whose first few lines are as follows: > marouane.data[1:13,] species plant leaf irradiance photosynthesis chlorophyll 1 Asclepias.incarnata 1 1 0 -2.091359 0.02619 2 Asclepias.incarnata 1 1 50 1.153241 0.02619 3 Asclepias.incarnata 1 1 100 2.241963 0.02619 4 Asclepias.incarnata 1 1 200 3.541258 0.0261...

...successfully made a self-starting function. getInitial() correctly outputs the initial estimates. I can also use the nlsList with this function to get the separate nonlinear fits by group. However, I get an error message when using the nlme function. Here is the relevent code: fit<-nlsList(photosynthesis~photo(irradiance,Q,Am,LCP)|species/plant/leaf,da ta=marouane.data, + na.action=na.omit) This works, showing that the function "photo" works as a self-starting function. nlme(model=photosynthesis~photo(irradiance,Q,Am,LCP), + data=marouane.data,fixed=Q+Am+LCP~1, + random=Q+Am+LCP~1|spec...

...edly fit a nonlinear regression to a series of data sets using nls and the port algorithm from within a loop. The general structure of the loop is: for(i in 1:n){ … extract relevant vectors of dependent and independent variables … … estimate starting values for Amax and Q.LCP… fit<-nls(photosynthesis~fit.Mitcherlich(irradiance,Amax,LCP,Q.LCP),data=temp , start=list(Amax=Astart,Q.LCP=x,LCP=33),control=list(maxiter=100,tol=5e-4), na.action=na.omit,trace=T,algorithm="port",lower=c(0,0,0)) … } Despite trying to estimate good starting values, the nls function occasio...

...eries of the various explaining variable according to scale (wavelet decomposition). With the coefficients I got from the wavelet decomposition I applied a (multiple) regression, giving some expected results. The net ecosystem exchange (CO2 balance) is mostly determined by the light regime (driving photosynthesis) and the water availability (inducing stress if absent), and this over all the scales. So sadly, pinpointing a certain scale on a certain process wasn't possible. I had hoped to see for example a relation between air temperature and a response of the vegetation/ecosystem, and this for a certa...

...rk in my case. Details: In particular, I can obtain convergence for each group (plant) separately using either nls or nlsList, but cannot get convergence using nlme. My function is a non-rectangular hyperbola with 4 parameters (theta, Am, alpha, Rd): #Nonrectangular hyperbola for photosynthesis # myfunct (1/(2*theta))*( alpha*Irr + Am -sqrt((alpha*Irr+Am)^2-4*alpha*theta*Am*Irr))-Rd I have written a self-starting function (NRhyperbola) to provide starting values. This self-starting function works. When I use this self-starting function with nlsList using a data set with the group...

...been recording these data at 12 stations along the savannah river for two years now. The longest set of readings that are continuous without interuption is 53 days. I would like to look at the power spectral density at each of these sites (most likely one day will be the overridding trend due to photosynthesis and respiration). I would also like to look at the cross spectrums between to contiguous site to look for advective transport from the upstream sections.I have used spectrum to get a periodogram. This I don't believe is the power spectral density. If it is I am unsure how to determine the #...