search for: irradiance

Dear R users, I want to do a fitted.contour plot of selected columns of a dataframe M with M$AM and M$Irradiance as x and y axes respectively. The level of the contour shall be determined by M$PR. Some words on my data first. Dataframe M looks like: head(M$Irradiance) [1] 293 350 412 419 477 509 head(M$AM) [1] 2.407 2.161 1.964 1.805 1.673 1.563 head(M$PR) [1] 70.102 72.600 75.097 80.167 79.644 82.633 To...

hi, i am having trouble getting a particular time series to plot. this is what i have: > class(irradiance) [1] "ts" > irradiance[1:30] 197811 197812 197901 197902 197903 197904 197905 197906 1366.679 1366.729 1367.476 1367.739 1368.339 1367.883 1367.916 1367.055 197907 197908 197909 197910 197911 197912 198001 198002 1367.484 1366.887 1366.935 1367.034 1366....

...n get plain text to wrap. However, when I try these methods on my label, the exact string is returned, rather than evaluating the math symbols. My starting point: x<-c(1:10) y<-seq(5,50,5) par(mar=c(6,6,6,1),cex.lab=1.3,cex.axis=1.2) plot(x,y, xlab=NA, ylab=expression(paste("Saturating Irradiance, ",E[k],", ",mu,"mol photons ", m^-1," ", s^-1))) An unsuccessful example: plot(x,y, xlab=NA, ylab=strwrap(expression(paste("Saturating Irradiance, ",E[k],", ",mu,"mol photons ", m^-1," ", s^-1)), width=26)) I've trie...

...nd cannot understand 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 3.541...

Hi: I am using the following command: xyplot(dat6$CO3*1e6 ~ dat6$irradiance, data=dat6, group=ref, xlab=list(label=expression(paste("Irradiance (", mu, "mol photons", m^"-2", " ", s^"-1", ")")), cex=1.3), ylab=list(label=expression(paste("Carbonate concentration (x ", 10^"6", " ",...

...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|species,na.action=na.o...

...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 occasionally experiences problems w...

...itial quantum yeild # (1/(2*theta))* (alpha*Irr + Am - sqrt((alpha*Irr + Am)^2 -4*alpha*theta*Am*Irr))- Rd } attr(,"initial") function (mCall, LHS, data) { xy <- sortedXyData(mCall[["Irr"]], LHS, data) if (nrow(xy) < 3) stop("Too few unique irradiance values") fit <- smooth.spline(xy[, "x"], xy[, "y"]) alpha <- predict(fit, x = 0, deriv = 1)$y if(min(xy[,"x"],na.rm=T)>0)delta.for.zero<-alpha*(min(xy[,"x"],na.rm=T)- 0) if(min(xy[,"x"],na.rm=T)<=0)delta.for.zer...

...39;t figure out where or how. Would someone who has successfully done this be willing to look at my code and see where the problem arises? > NRhyperbolaInit function(mCall,LHS,data) { xy<-sortedXyData(mCall[["x"]],LHS,data) if(nrow(xy)<3){ stop("Too few unique irradiance values") } theta<-0.75 Rd<-min(xy[,"y"]) Am<-max(xy[,"y"]) + abs(Rd) if(sum(xy[,"x"]<50)>3)alpha<-coef(lm(y~x,data=xy,subset=x<50))[2] if(sum(xy[,"x"]<50)<=3)alpha<-0.07 value<-c(theta,Am,alpha,Rd) names(value)&lt...

...blem > To: r-help@r-project.org > Message-ID: > <c642e63c0811260824l7adc65e4tf9177ad2fad01132@mail.gmail.com> > Content-Type: text/plain > > hi, > > i am having trouble getting a particular time series to plot. this is what > i > have: > > > class(irradiance) > [1] "ts" > > irradiance[1:30] > 197811 197812 197901 197902 197903 197904 197905 197906 > 1366.679 1366.729 1367.476 1367.739 1368.339 1367.883 1367.916 1367.055 > 197907 197908 197909 197910 197911 197912 198001 198002 > 1367.484 1366...