search for: abun

Hi, I am trying to combine a long list but I can't work out how to do it, for example: abun<-list(rep(0,5),rep(0,7),rep(0,4),rep(0,10)) nb<-c(5,5,1,8) fill.abun <- function(x, y) { set <- sample(1:length(x), size = y) x[set] <- rlnorm(length(set)) return(x) } abun <- mapply(fill.abun, abun, nb) abun ## I want all the data in one...

...plified code is below. Any suggestions would be greatly appreciated. Thanks for your time, Dan plotdf=data.frame( tag=1:100, pspp=c(rep("Sp1",40),rep("Sp2",30),rep("Sp3",20),rep("Sp4",5),rep("Sp5",5)), dim=runif(100)*100) plotdf[1,] abun.table=as.data.frame(table(plotdf$pspp)) #2.1 calculate Smax (count of species) Smax=length(abun.table$Freq[abun.table$Freq>0]) Smax traitdf=data.frame( tspp=c("Sp1","Sp2","Sp3","Sp4","Sp5"), width=runif(5), abun=abun.table$Freq) tra...

...I came across the HSD.test in the agricolae-package, but... unfortunately I do not get an output (like here in the answer http://stats.stackexchange.com/questions/31547/how-to-obtain-the-results-of-a-tukey-hsd-post-hoc-test-in-a-table-showing-groupe ) I did it like this: ###### ANOVA anova.typabunmit<-aov(ds.typabunmit$abun ~ ds.typabunmit$typ) summary(anova.typabunmit) summary.lm(anova.typabunmit) ###### post HOC tukey.typabunmit<-TukeyHSD(anova.typabunmit) tukey.typabunmit ###### HSD HSD.test(anova.typabunmit, "abun", group=TRUE) and the ONLY output is this: Name: abu...

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...

Hello, Im working on a 50933 point count bird abundance dataset. I've succeeded in calculating a distance matrix for this entire set, but I don't have sufficient memory to convert this to a matrix, as below... abun.dist <- dist(abun.mat[1:50993,1:235) test <- rowMeans(as.matrix(abun.dist)) Error in matrix(0, size, size) : too many ele...

Dear members of the list, I'm fitting ordinal regressions using polr, and in some models I get the error copied below. Dependent variable is an ordered factor of bird abundance categories, and predictors are continuous habitat variables. > ro6 <- polr(formula = abun ~ InOmbrot + Oliva.OC + ToCultAr + DivCulArb + AltitMax + COORXY) > summary(ro6) Re-fitting to get Hessian Error in La.svd(x, nu, nv, method) : error code 8 from Lapack routine dgesdd In ad...

...the right direction of figuring out what downweight() is doing? I am using vegan to perform CCA on diatom assemblage data. I have a lot of rare species, so I want to reduce the influence of rare species in my CCA. I have read that some authors reduce rare species by only including species with an abundance of at least 1% in at least one sample (other authors use 5% as a rule, but this removes at least half my species). If I code it as follows: cca(downweight(diatoms, fraction=5) ~ ., env) It is clearly not removing these species entirely from analysis, as some authors suggest. So I am wonderin...

...", "site3", "site4") colnames (comm) <- c("spA", "spB", "spC", "spD") comm # note that site 1 has only spA and spB, so I'd expect it to # have sing.sp = 0 (no singular species) require (FD) ex1 <- dbFD (fd, comm, w.abun = FALSE, corr="cailliez", clust.type="ward") ex1 # site 1 comes out with sing.sp = 2. Why is that? Any insight / advice would be greatly appreciated! Many thanks, Sarah University of Chicago [[alternative HTML version deleted]]

Hello I'm currently using the dbFD function of the FD package and i'm having some things that I can't do. Is there any way to check the relations between dbFD indexes? Function cor for example? I can't manage to put the informations correctly dbFD function gives a lot of output (indexes - nbsp, sing.sp, FRic, FEve, FDiv, FDis and RaoQ). I want to see the relationships between

...gives the Feve, Fdis, RaoQ and CWM values for my data. When I run the function with ?calc.Frich=T?, I see the warning that I wrote below and no one of the values are calculated. Could you please tell me how can I fix this problem and have the FRic value for my data? Func.div?dbFD ( trait_data, abundance_data, calc.FRic = T, corr="cailliez", w.abun = T, CWM.type = "all" ) FRic: Dimensionality reduction was required. The last PCoA axis (out of 6 in total) was removed. FRic: Quality of the reduced-space representation = 0.9402678 QH6114 qhull precision error: initial simp...