search for: nutrient

...values of model parameters, or could we use anova() with likelihood ratios, AIC and BIC, with (or without) method="ML" (with didn't seem right to me)? I also received an error using adaptive Gaussian quadrature (but not Laplacian approximations): > mod2 <- lmer(yb ~ reg*nutrient*amd + + (1|rack) + (1|status) + + (1|popu) + (1|popu:amd) + + (1|gen) + (1|gen:nutrient) + (1|gen:amd) + + (1|gen:nutrient:amd), + data=datnm, family=binomial, method="AGQ") Error in lmer(yb ~ reg * nutrient * amd + (1 | rack) +...

...ction updater(input, item) { 2. var item_data = item.getElementsByTagName(''span'')[0]; 3. var pars = ''item-data='' + item_data.innerHTML + ''&input-text='' + input.value; 4. new Ajax.Updater(''nutrients'',''fooddb/browser/nutrients'', {method : ''get'', parameters : pars, onFailure: reportError, onComplete: reportComplete, onSuccess: reportSuccess}); 5. } 6. function reportError(request) 7....

...ndom" effects, and then relying on Helmert contrasts and AIC, BIC, and LRT to simplify fixed effects. Maybe this was wrong? > load("tf.RdataBin") > library(lme4) > options(contrasts=c("contr.helmert", "contr.poly")) > mod <- lmer(tfb ~ reg+nutrient+amd +reg:nutrient+ + (1|rack) + (1|popu) + (1|gen), data=dat.tb2, family=binomial, method="Laplace") > summary(mod) Generalized linear mixed model fit using Laplace Formula: tfb ~ reg + nutrient + amd + reg:nutrient + (1 | rack) + (1 | popu) + (1 | gen) Data: dat.tb2...

...var item_data = > item.getElementsByTagName(''span'')[0]; > 3. > var pars = ''item-data='' + > item_data.innerHTML + ''&input-text='' > + input.value; > 4. > new > Ajax.Updater(''nutrients'',''fooddb/browser/nutrients'', > {method : ''get'', parameters : pars, onFailure: > reportError, > onComplete: reportComplete, onSuccess: > reportSuccess}); > 5. > } > 6. > functi...

Hi everyone, I am trying to construct a glm and am running into a couple of questions. The data set I am using consists of 6 categories for the response and 6 independent predictors representing nutrient concentrations at sample point locations. Ultimately I'd like to use the probabilities for each response category in a simulation model such that these probabilities are used to define a realized ecological niche. When I try the following it works for a single response. Typha.glm <- glm(...

...generalized linear model and am interested in using the random effects that are output for further analysis. My random effect is interacting with two different fixed effects (which which are factors with two levels each). When I retrieve the random effects I get something like this: (Intercept) nutrient (Intercept) light (Intercept) Aa-0 0.59679192 0.34824858 2.241424479 -2.335037842 0.775359364 Ag-0 -2.73719135 2.10428715 -0.980046942 -1.832587350 -1.938942967 Ak-1 -0.13221525 1.03282635 -0.624239559 1.594044342 0.313188938 Alc-0 1.16506640 -0.05914007 1....

...and I've been unable to find the answers to my questions by trawling through the R help archives. I'm hoping someone here can help me. I'm running an analysis on Seedling survival (count data=Poisson distribution) on restoration sites, and my main interest is in determining whether the Nutrients (N) and water absorbing polymer Gel (G) additions to the soil substrate contribute positively to the survival of the seedlings, over a 3 year time period (for simplicity I'm just using 3 time periods, each in the same season for the 3 successive years). Fixed factors: Nutrients (0 and 1), Gel...

Dear All, I am a researcher doing research in plant growth and I have a statistical problem that seems to not be able to handle. Recently, I conducted an experiment about plant growing in three different nutrient-level sediments. I harvested these every three week (three harvests in all). Some growth traits of these plants were recorded (e.g. total biomass, leaf biomass and stem biomass). In addition, I found that the total plant biomass may also influence these traits. So, I am going to use total bioma...

...ut) nut1<-data.frame(Nitrate, Total_Nitrogen, Phosphate, Total_Phosphorus) nut1<-as.matrix(nut1) rownames(nut1)<-group ylimlist=list(c(0,10), c(0,10), c(0,0.25), c(0,0.25)) dotplot(nut1, groups=FALSE, horizontal=FALSE, scales = list(relation='free' ), ylim=ylimlist, ylab="Nutrient Concentration (mg/L)") I have two issues currently: eliminating y and x tick labels between panels, and creating error bars. 1st issue: Figure 4.1 in Deepayan Sarkar's book creates a simple 2x2 dotplot that only has x and y axis tick labels on the bottom and left margins of the whole fig...

Dear All, I have some time series data where X=month and Y=nutrient concentration (I can have several concentration data for one month). Is there a way to fit for it an Harmonic Function. Is there a package, script,etc which I can use? Thx -- View this message in context: http://r.789695.n4.nabble.com/Fitting-a-Harmonic-Function-to-Time-Series-Data-tp3901266p3...

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...and I've been unable to find the answers to my questions by trawling through the R help archives. I'm hoping someone here can help me. I'm running an analysis on Seedling survival (count data=Poisson distribution) on restoration sites, and my main interest is in determining whether the Nutrients (N) and water absorbing polymer Gel (G) additions to the soil substrate contribute positively to the survival of the seedlings, over a 3 year time period (for simplicity I'm just using 3 time periods, each in the same season for the 3 successive years). Fixed factors: Nutrients (0 and 1), Gel...

Dear R-Experts. I collected different datas about Nitrogen content (mg/ml) in Dung. The dung was eighter fresh (day=0) or had different ages (15,29,47) to observe nutrient changes over time. Now I like to draw a boxplot. boxplot(nmgml~day) abline((nmgml~day) The Problem is, that the boxplot considers the day values as groups and not as time series (neighter when the days are numeric or factors). The result is, that the regression line looks different as when I dr...

...ere is not, but I would like to make a plea for this feature. It would be nice to be able to plot Total Inorganic Nitrogen Total Phosphorus and the ratio of the two- the numbers on the axis are not related, but the previous two are surely related to the last (this ratio has been suggested to show nutrient limitation, but there is the possibility that the concentrations of the two constituents are high enough where the ratio is not that meaningful). Or maybe when particulate organic carbon is related to macroinvertebrate density with scales as divergent as 1mg/L to 1000insects/m^2 . The good parts...

...m also very interested to know just what the breakpoint in the data is. Essentially if x<psi y = a + bx + error, where b is negative else y=0+error and I want to know the value of psi, as well as a and b. The error is also most likely gamma distributed, as values<0 are not possible (nutrient concentrations). I have attempted to use the segmented package, specifying something close to the visually estimated breakpoint as the value of psi, but it continues to return fits with a breakpoint that occurs somewhere in the middle of the linear portion of the line, and the slope and in...

...gt; Predatory.Fish.Abundance, bottom.up.herb.fish, NA Prev.Year.Herbivorous.Invert.Abundance -> Predatory.Invert.Abundance, bottom.up.herb.invert, NA Prev.Year.Herbivorous.Invert.Abundance -> Predatory.Fish.Abundance, bottom.up.herb.invert.fish, NA Mean.Temp.C -> Kelp.Abundance, mean.nutrients.from.temp, NA Prev.Year.Predatory.Invert.Abundance -> Predatory.Invert.Abundance, prev.year.pred.invert, NA Prev.Year.Predatory.Fish.Abundance -> Predatory.Fish.Abundance, prev.year.pred.fish, NA Prev.Year.Herbivorous.Fish.Abundance -> Herbivorous.Fish.Abundance, prev.year.herb.fish...

Hello guys I am new to this list and for R too. I am wondering if there is a patch for the SPSS reading code on the foreign package, in order to be able to read long variable names. Right now read.spss() just trunc the names to 8 characters. Or if someone could help me on other way: I have to process everyday a lot of SPSS Syntax Files and Dat files that come from one system that can only export

Hi, I am trying to run a 1D nutrient-phytoplankton-zooplankton model in R using the package 'deSolve'. The code is shown below: DEPTH = seq(2.5, 147.5, 5) NPZ = function(t, state, params){ with(as.list(params), { P <- state[1:NB] Z <- state[(NB + 1): (2*NB)] N <- state[(2*NB + 1): (3*NB)] F.I =...

I am running 1.3.1 on a Windows (NT 4.0) machine. I've fit a nonlinear model intended to predict crop yield from nutrient information, and want to use the profile function. If I type say, profile(simparj.fm) I get the following error message: "Error in prof$getProfile(): number of iterations exceeded maximum of 5.25515e-308" I used the profiler function to profile simparj,fm step by step, profiling one para...

Dear All, I am working with linear mixed-effects models using the lme4 package in R. I created a model with the lmer function including some main effects, a two-way interaction and a random effect. Now I am searching how I could incorporate an interaction between the random effect and one of the fixed effects. I tried to express the interaction in: