search for: abund

...r version of the below model, and keep getting the same error. What does this error mean? Below is the full code, but I've tried this with all sorts of subsets of the model, making sure to keep all of the proper error terms. --- fish.invert.data<-data.frame(Prev.Year.Predatory.Invert.Abundance, Prev.Year.Predatory.Fish.Abundance, Predatory.Invert.Abundance, Predatory.Fish.Abundance, Prev.Year.Herbivorous.Invert.Abundance, Prev.Year.Herbivorous.Fish.Abundance, Herbivorous.Invert.Abundance, Herbivorous.Fish.Abundance, Kelp.Abundance,...

Greetings, I am new to R and am hoping to get some tips from experienced R-programmers. I have a dataset that I've read into R as a dataframe. There are 5 columns: Plot location,species name, a species number code (unique to each species name), abundance, and treatment. There are 272 plots in each treatment, but only the plots in which the species was recorded have an abundance value. For all species in the dataset, I would like to add zeros to the abundance column for any plots in which the species was not recorded, so that each species has 2...

I'm looking over good-code a post-doc in my lab wrote and trying to learn how it works. I came across the following: rel.abundance <- as.matrix(read.delim("rel.abundance.csv",row.names=1,as.is =TRUE)) rel.abundance <- log2(rel.abundance-min(rel.abundance)+1) I'm not sure what the second line is doing. I ran each line in R and couldn't see a noticeable difference in the output. I assume log2() tak...

Hello, please excuse the simplicity of this question as I am not very good with stats. I am taking a class, using R which I am learning at the same time, and the questions asks us to "Estimate the average abundance using Poisson regression with a log link". I can estimate the abundance from "x", but I can seem to figure out how to get the average abundance in this method. Any suggestions would be welcome as I have spent about 4 hours trying to figure this one out. Thanks. -- View this mes...

Hi all, I am fairly new to R and I am trying to run mvpart and create a MRT using explanatory variables and covariables. I've been following the procedures in Numerical Ecoogy with R. The command (no covariables) which works fine - ABUNDTMRT <- mvpart(abundance ~ .,factors,margin=0.08,cp=0,xv="1se",xval=nrow(abundance),xvmult=100,which=4) where abundance is 4th root transformed fish abundance (103 species x 168 samples), and factors is the relief (high, medium, low profile, sand inundated reef, flat), benthos (coral,...

Dear R users, I am having problems trying to fit quasipoisson and negative binomials glm. My data set contains abundance (counts) of a species under different management regimens. First, I tried to fit a poisson glm: > summary(model.p<-glm(abund~mgmtcat,poisson)) Call: glm(formula = abund ~ mgmtcat, family = poisson) . . . (Dispersion parameter for poisson family...

Hi fellow R users, I have a dataset that looks something like this. species class abundance K 1 592 K 2 288 G 1 254 G 2 239 C 2 173 D 2 123 E 3 89 F 2 87 B 2 86 H 2 82 I 1 79 J 2 76 B 1 73 D 3 72 A 2 62 L 2 58 I want to plot a stacked barchart. species is the x-axis, abundance is y-axis, and class will appear as the stacks in different colours. I need the species to be displayed in d...

Buenas tardes, tengo 2 dfs: Dieta de (108x11) y Abund de (591x108). Necesito multiplicar cada columna de la 1ª (108 elementos) por cada fila de la 2ª (108 elementos) y crear una nueva df con las sumas de esas multiplicaciones. He hecho esto, pero no sale y creo que está lejos de estar bien: Res <- matrix(nrow=nrow(Abund),ncol=ncol(Dieta))...

Hi there, I'm using the lattice package to create an xy plot of abundance vs. depth for 5 stages of barnacle larvae from 5 species. Each panel of the plot represents a different stage, while different loess smoothers within each panel should represent different species. However, I would like depth to be on the y-axis and abundance to be on the x-axis, because this i...

...icable examples. Thanks in advance, and, if you need any further information, please let me know. # My experiment:# I have 1 site on 3 different rivers (independent)(sites 1,2 and 3). # I visit each site 2 times (time 1 and 2). # On each visit, I take 5x replicate insect samples and calculate total abundance for each replicate.# Site 1 is in an area called "yellow" and sites 2 and 3 are in an area called "blue". # My data frame: data=data.frame(site=c(rep(1,10),rep(2,10),rep(3,10)),replicate=c(rep(1:5,6)),time=c(rep(1,5),rep(2,5),rep(1,5),rep(2,5),rep(1,5),rep(2,5)),abundance=c...

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Hello, How can I randomly sample individuals within a sites from a site (row) X species abundance (column) data frame or matrix? As an example, the matrix "abund2" made below. ##### (sorry, Im a newbie and this is the only way I know to get an example on here) abund1 <- c(150, 300, 0, 360, 150, 300, 0, 240, 150, 0, 60, 0, 150, 0, 540, 0, 0, 300, 0, 240, 300,...

Dear all, I have run the confint() function according to below and I get the following error message: > confint(stepAIC.glm.spe.var.konn2.abund, level=0.95) Waiting for profiling to be done... Error: missing value where logical needed In addition: Warning message: NaNs produced in: sqrt((fm$deviance - OriginalDeviance)/DispersionParameter) or > confint(stepAIC.glm.spe.var.konn2.abund, parm="DIA", level=0.95) Waiting for pro...

..."Cannot compute exact p-values with ties" error. I have read that this function now uses an asymptotic formula that allows for ties, so do not understand why I am getting this error. (I am running version 2.4.0.) I read the following data in from a CSV file: species,ecoldom,ecolrank,abundance,persistence,behavdom,behavrank,aggrlevel Fv,0.108333333,6,2.5,0,0.351351351,5,0.12195122 Mq,0.114583333,5,2,0,0.167539267,5,0.287878788 N,0.125,3,0.5,0,0.285714286,5,0.333333333 S,0.116792929,4,11,0.125,0.684027778,2,0.723214286 Th,0.164737654,1,22.5,0.875,0.717948718,2,1.614285714 Ts,0.1319444...

I am using two mixed effect models. Firstly, what I am trying to do is to compare green roofs abundance with brownfield, green roof with green space abundance, and finally green space with brownfield abundance. I am unsure if I have done the correct model. I have to use a mixed effect model because my data is nested. This is the code and output > model1<-lmer(Total.abundance~Habitat+(1|Si...

...4" for (i in names(water)[3:10]){ fname<-paste("Henni/GFX/fem",i,".png",sep="") mname<-paste("Henni/GFX/mal",i,".png",sep="") png(fname,1000,1000) xyplot(N_female~eval(parse(text=i)) |group,xlab=i,ylab="Abundance") graphics.off() png(mname,1000,1000) xyplot(N_male~eval(parse(text=i)) |group,xlab=i,ylab="Abundance") graphics.off() } well, to anyone's surprise, there are no plots in the folder. the loop finishes (i, fname and mname have values assigned) and executi...

I am trying to understand my population abundance data and am looking into analyses of change point to try and determine, at approximately what point do populations begin to change (either decline or increasing). Can anyone offer suggestions on ways to go about this? I have looked into bcp and strucchange packages but am not completely convi...

Hey, I am trying to create barplot of abundances over time (in days). The period is over 171 days, so I don't want to have all labels there but only the first day of the month. I couldn't find anything like this on the forum yet. Mostrly it's about year to year data. This is the relevant part of my table: datum month abundance...

Hi, I would like to calculate the RELATIVE euclidean distance. Is there a function in R which does it ? (I calculated the abundance of 94 chemical compounds in secretion of several individuals, and I would like to have the chemical distance between 2 individuals as expressed by the relative euclidean distance. Some compounds are in very low abundance whereas others are in high abundance, that's why I would like to c...

...hers: the name of species and the locality where they were collected. So, the samples are defined as 'each species on each locality'. For every sample I'd like to do multiple imputation (when applicable), test for the presence of outliers, standardize the variables, correct some species abundances, save individual samples to tab delimited text file, and assemble each individual sample (now, without NAs and outliers, corrected abundances, and with the new standardized variables) into a single data set. That task is pretty complex to me, since my programming knowledge is poor (and my free...