search for: chla

Hello all, I am trying to use lme to examine how a response variable (Chla) changes over time in different treatments (2 Temp & 2 Light levels). Within each treatment combination, there are two replicate tanks (each with unique TankID) with coral fragments in them. All tanks are subject to the same environment until Time=0, when treatments are imposed, and Chla...

Hi, I wonder if anybody could help me in converting this easy SAS program into R. (I'm still trying to do that!) PROC IMPORT OUT= WORK.CHLA_italian DATAFILE= "C:\Documents and Settings\carleal\My Documents\REBECCA\stat\sas\All&nutrients.xls" DBMS=EXCEL2000 REPLACE; GETNAMES=YES; RUN; data chla_italian; set chla_italian; year=year(datepart(date)); month=month(datepart(date)); run;...

R helpers, I am working with the R program performing multivariate regression trees (MRT). I have a matrix with species and environmental variables saved as a CSV file (sprot_matrix.csv), I have 42 species and 8 environmental variables (SECCHI+PH+TA+PTOT+NTOT+CHLA+AREA+ MEANDEP) for 104 samples Title SpA SpB SpC SpD Varible1 Variable2 Variable3 Sample1 Sample 2 Sample 3 Sample 4 Sample 5...

...obs. of  13 variables:  $ mnO2: num  9.8 8 11.4 4.8 9 13.1 10.3 10.6 3.4 9.9 ...  $ Cl  : num  60.8 57.8 40 77.4 55.4 ...  $ NO3 : num  6.24 1.29 5.33 2.3 10.42 ...  $ NH4 : num  578 370 346.7 98.2 233.7 ...  $ oPO4: num  105 428.8 125.7 61.2 58.2 ...  $ PO4 : num  170 558.8 187.1 138.7 97.6 ...  $ Chla: num  50 1.3 15.6 1.4 10.5 ...  $ a1  : num  0 1.4 3.3 3.1 9.2 15.1 2.4 18.2 25.4 17 ...  $ a2  : num  0 7.6 53.6 41 2.9 14.6 1.2 1.6 5.4 0 ...  $ a3  : num  0 4.8 1.9 18.9 7.5 1.4 3.2 0 2.5 0 ...  $ a4  : num  0 1.9 0 0 0 0 3.9 0 0 2.9 ...  $ a5  : num  34.2 6.7 0 1.4 7.5 22.5 5.8 5.5 0 0 ...  $ a...

...s, I have tried an lme model with “time” and “basin” as random factors. I have put hydrological cycle as a fixed factor, since I’m interested in quantifying their effect. But I’m not sure if there are other possibilities to do this. This is my model structure: Model1<-lme(shannon<-log(chla+1)*hyd_cycle+toc*hyd_cycle, random=~time|basin) Note that I have not put “replicate” within the random structure (random=~time|basin/replicate), and this is my major concern. I’m not sure if I have to include “replicate” in the random structure, since replicates are randomly taken each time, an...

...uis, and I have a problem with a dataset. Its name is algae and count the collection of data in a lake and respective proliferation of algae. The parameters that it has are: "mxPH", "mnO2", "Cl", "NO3" "NH4", "oPO4", "PO4", "Chla" and "a1" all numerics. a1 - algae1 If I try to do SVM with him, it doesn't generate a square matrix, why? If I try to do same thing in another dataset as Glass of the package "mlbench" with the data(Glass) that has the parameters: "RI", "Na", &quo...

...s the partial correlation between two variables given a set of other variables) but I do not know how to change to a Spearman Rank Correlation method [pcor(c("BCDNA","ImProd","A365"),var(PCor))] Here''s a glimpse of my data (data is raw data). A436 A365 Chla ImProd BCDNA 0.001 0.003 0.624889 11.73023 0.776919 0.138 0.126 0.624889 27.29432 0.357468 0.075 0.056 0.624889 105.3115 0.429785 0.009 0.008 0.312444 55.2929 0.547752 0.005 0.002 0.624889 26.9638 0.738775 0.018 0.006 0.312444 31.14836 0.705814 0.02 0.018 2...

Hello, I installed the newest version of R (3.0.2) as well as the newest version of nlme (3.1-113) in order to use summary.lmList and other nlme functions. Once loading the new library, lmList and summary.lm can be found, but a number of additional functions cannot be found via command. Versions installed and loaded are correct. Any suggestions on how to allow for these functions of the new

...m+FishIBIUsed +QHEI+QHEIsub+QHEImwh_h+QHEIcov+QHEIchan+QHEIrip+QHEIpool+QHEIrif+QHEIgrads+ QHEIgradv+QHEImwh+QHEIcovtype+QHEIwwh+QHab+QHabBuff+QHabEros+QhabPool+ QHabWDRatio+QHabRif+QHabFines+QHabCov+QHabRating+QHabSize+TP+TKN+NH3+NH3Min +NO3NO2N+BOD+TSS+TSSMax+TDS+SSC+SSCMax+Chloride+Sulfate+Ecoli+ChlA+DOper+ DOperMin+DOperMin1_5+DOmgL+DOmgLMean+DOmgLMax+Cond+pH+pHMax+Trans+Temp+ TempMin+Temp4+Crop100+Crop500+CropSub+Dev100+Dev500+DevSub+For100+For500+ ForSub+Pas100+Pas500+PasSub+Wat100+Wat500+WatSub+Wet100+Wet500+WetSub+ Undev100+Undev500+UndevTotal+Undev100NoPas+Undev500NoPas+UndevTotNoPas, dat...

...after the colon.] Remove these, or change them, using, e.g.: class(obj$DateTime) <- NULL class(obj$AnyVariable) <- 'numeric' ## leaves the actual labels/units intact so that you can later restore them. 2) Execute your lme() statement &c on the object, e.g.: test.1 <- lme(Chla ~ PO4, random=~1|Site, data=obj) ## or simply: lme(obj) augPred(test.1) plot(augPred(test.1)) (Note that if you are using a data.frame() as your data object you will need to supply a 'primary' statement to augPred(), e.g. augPred(test.1, primary=~PO4). Regards, Mark Difford. --------...

...re zooplankton biomass (bm) is the dependent variable and the continuous explanatory variables are: -time in Julian days (t), to creat a long-term linear trend -Julian days of the year (t_year) to create an annual cycle - Mean temperature of Winter (temp_W), Temperature of September (temp_sept) or Chla. Questions: 1) To introduce a tensor product modifying the annual cycle in my model, I tried 2 different approaches: - a) gam ( bm ~ t + te (t_year, temp_W, temp_sept, k = c( 5,30), d= ( 1,2), bs = c( ?cc?,?cr?)), data = data) -b) gam ( bm ~ t + te (t_year, temp_W, temp_sept, k = 5, bs = c( ?cc?,?c...

Dear friends. I use nls() and encounter the following puzzling problem: I have a function f(a,b,c,x), I have a data vector of x and a vectory y of realized value of f. Case1 I tried to estimate c with (a=0.3, b=0.5) fixed: nls(y~f(a,b,c,x), control=list(maxiter = 100000, minFactor=0.5 ^2048),start=list(c=0.5)). The error message is: "number of iterations exceeded maximum of

Hi all- I fit a zero-inflated Poisson model to model bycatch rates using an offset term for effort. I need to apply the fitted model to a datasets of varying levels of effort to predict the associated levels of bycatch. I am seeking assistance as to the correct way to code this. Thanks in advance! Laura [[alternative HTML version deleted]]