search for: chlorophyll

Sorry for disturbing you with another newbie question! I have a data frame about coastal waters quality parameters: for some parameters (e.g. NH3) I have only 1 observation for each sampling station and each sampling date, while in other cases (chlorophyll) I have 1 obs for each meter-depth for each station and date. How can I select only the max chlorophyll value for each station/date? example row station date depth chlorophyll 1 Castagneto 21/06/01 -0.5 2.0 2 Castagneto 21/06/01 -1.5 2...

...strptime, etc. All examples seem to use some version of day month year as date format. However I have Weekly composite data so ONLY want to input the dates as Week.Year (eg 35.2011). strptime seems to show this is possible using %W for week (UK convention) and %Y for year. My data is in a df called chlorophyll and has a date column. I tried to use the following (after I converted to characters using as.character); chlorophyll$date <- strptime("chlorophyll$date", "%W.%Y") It recognised the year but replaced the week part with todays date (16TH August). Any advice? Thanks Natalie...

Hello all, I can't seem to figure how to use a greek character in expression() in plot() labels without adding a space. So for example below when plotting this out x<-1:10 plot(x,x^2, xlab=expression(Chlorophyll~italic(a)~mu~g~cm^-2)) the axis label read as μ g cm^-2 because I have space there with a tilda. But if I remove the tilda then my units are mug cm^-2. Can anyone recommend a way that I can modify the axis label to look for like this: μg cm^-2 Thanks in advance! Sam [[alternative HTML versi...

I am having difficulty understanding the syntax of the nlme() function for nonlinear mixed models. The data frame is called Marouane.chlorophyll. The model involves a dependent variable (Absorb) and an independent variable (Ch.surf), which are both numeric variables in the data frame. The data are hierarchically grouped as Espece, Plante nested within Espece, and Feuille nested within Plante (i.e. leaves within plants within species). Es...

Hello, I would like to evaluate the relationship between flows and phytoplankton abundance (or Chlorophyll a concentrations) using a changepoint analysis.? Specifically, I have two study questions: Study Question 1: Are there certain flow thresholds that result in spikes in phytoplankton abundance? Study Question 2: Are the duration of certain flows important for phytoplankton abundance (e.g., would a...

Dear users I am fitting a Generalized Additive Mixed Models (gamm) model to establish possible relationship between explanatory variables (water temperature, dissolved oxygen and chlorophyll) and zooplankton data collected in the inner and outer estuarine waters. I am using monthly time-series which are auto-correlated. In the case of the inner waters, I have applied satisfactoryly (by ACF and PACF) an corAR1() as follows: gamm.zoo <- gamm(zoo~s(water.temperature) + s(dissolv...

Hello, I am a new user to R and have a(proabably very basic) question relating to a boxplot with eleven sites in a river system where i measured Chlorophyll a concentrations. The eleven sites are made up of three sites above a point source pollution site; three sites below this pollution source and five sites in a different unaffected river. The following code is for a simple plot of the data boxplot(Chl~Site,data=p,col="slategrey", boxwe...

DateTime,Temp,SpCond,DOConc,Depth,pH,ORP,Turbidity+,Chlorophyll,Battery,Cond,DO%,Salinity,TDS 01/13/2006 17:01,10.87,84,9.36,0.664,7.3,132,28.8,3.1,11.5,0.062,84.6,0.04,0.055 01/13/2006 17:16,10.9,84,9.36,0.66,7.31,133,28.7,2.9,11.5,0.062,84.7,0.04,0.055 01/13/2006 17:31,10.92,84,9.36,0.655,7.3,132,28.4,2.6,11.4,0.062,84.8,0.04,0.055 01/13/2006 17:46,10.96,85,9...

...d(Pico, Nano, Micro), list(Depth),FUN=mean))* *rownames(coral) <- coral[,1] * *coral <- t(coral[,-1]) # Remove Station col and transpose* *barplot(coral, main="Size fractionated Chl a for Coral", * * ylab = "Coral", xlim = c(0,8), horiz = TRUE,* * xlab = expression ("Chlorophyll a " ~~ (mu*g ~ l^{-1})), * * col =c("light green", "green", "dark green"),* * legend = rownames(coral))* Here is the *head(Coral) *before station col removal and t() Seamount Station Depth Pico Nano Micro Total_Ch 185 Coral 1401 Surface 0.216 3.270...

Hi, I am looking at the effects of two explanatory variables on chlorophyll. The data are an annual time-series (so are autocorrelated) and the relationships are non-linear. I want to account for autocorrelation in my model. The model I am trying to use is this: Library(mgcv) gam1 <-gam(Chl~s(wintersecchi)+s(SST),family=gaussian, na.action=na.omit, correlat...

...); %sort_event(2.0); %sort_event(2.0); %sort_event(2.0); %sort_event(2.0); %sort_event(2.0); %sort_event(2.0); %sort_event(2.0); %sort_event(2.0); %sort_event(2.0); %sort_event(2.0); %sort_event(2.0); %sort_event(2.0); %sort_event(2.0); %sort_event(2.0,last=1); /* Combine bloom information with all chlorophyll values */ data chla_sep; merge sort_dataset(keep=station date bloom pred ucl lcl) chla_italian (rename=(chl_a=chla)); by station date; * lcl=exp(lcl); * ucl=exp(ucl); * pred=exp(pred); if bloom=. then bloom=1; if bloom=0 then chla1=chla; else chla1=.; if bloom=1 then chla2=chla...

...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 0.02619 5 Asclepia...