search for: rarefaction

Hi everybody, i'm trying to draw rarefaction curves to estimate a population size from genotyped faeces. I used the Gimlet software which gave me a script and a "rarefaction.txt" file. I've copied both files in the work directory of R. I changed library(nls) by library(stats) in the script. But now, i'm still unable to run i...

Hi List, I’m using the vegan function specaccum to produce a rarefaction curve. In the function’s help it says: “Function ‘specaccum’ finds species accumulation curves or the number of species for a certain number of sampled sites or individuals”. Well, I would like to finds this curve for individuals, but when I compute it the function (using the ‘rarefaction’ method)...

Hi all, I used R (vegan package) to make rarefaction curves and I calculated the Chao index for each curve. However, the plateau is far from reached. What I want to do now is the following: Based on the Chao index, I want to extrapolate the curve so I get an x-value which gives me an estimation of the total number of clones I'd have to pick up an...

...ts in particular because they're most likely to be familiar with the equation in question but I'll be happy to discuss the problem with anyone who's willing to take a whack at it. I'm trying to write a function to calculate the large sample variance of species richness estimates by rarefaction using the Heck et al (1975) equation. I won't try to reproduce the equation here because it's complex and I don't know how to render it readibly in ASCII characters, but if anyone wishes a faxed copy I'll gladly provide one. If you have Krebs _Ecological_Methodology_ it's on p...

Hello! I am eager to learn if I only have a data about the relationship between otu and sample, could I use the function capscale, and final make a point plot that x-axis is CAP1 and y-axis is CAP2? Besides, what function could I use to make the different rarefaction curve with different color in the a plot in R? Appreciate very much. Sincerely!...

Hi everybody, I'm not very experienced with R software. I have used it several times for some of the population genetics analyses. I have problem with executing one of the script. The script is created by another software called Gimlet and it is aimed to calculate rarefaction curve in R software. However, when I try to execute the script, it says: *Error in library(nls) : there is no package called 'nls'.* I used the script previously on another PC about 2 or 3 years ago without problems. I tried to reinstall R but no help. I'm using the version 2.13.0. A...

.... 0 .. .. . . . . 3504 876 219 8 12 0 1 0 . 1 where sector are nested within quadrants, quadrants within plot and plots within SIC. For each sector time spent to collect plant assemblage is available. What I'm trying to perform is an analysis of rarefaction of species richness considering area and time. I'm practical with the vegan package but here I need some different analyses. My first step should be the analysis of species rarefaction with area and my question is: how many species, on average, would be collected in an area of one sector? and c...

...;, "F07", "F09", "F11", "F13", "F14", "F17", "F18", "F19", "P20", "Main") for(obs in Frags) { A.*obs* <- accumresult(Species, y=Environment, factor='Fragment', level=*obs*, method='rarefaction', conditioned =T, gamma = 'boot' , permutations=100, scale='abundance') P.*obs* <- accumplot(z,addit=FALSE, ci=2,ci.type='bar', col='1', cex=1, xlab='abundance', pch=1, labels=*obs*) } The idea is to create variables such as A.F05 and P.F09, but...

.... And if I am not mistaken, the list Usenet groups sci.stat.consult is not currently active. Let me explain briefly: Through different microbiota datasets, I have plotted PCoA, db-RDA and sPLS-DA using 3 different types of normalization methods (Total sum of squares, cumulative sum of squares and rarefaction). For each dataset and multivariate analysis (PCoA, db-RDA or sPLS-DA) in order to easily interpret if the different normalization strategies creates me different or equivalent PCoA for example, I have calculated the Procrustes sum of squares and the RV coefficient of co-inertia. However, for the R...

Quisiera intercambiar ideas con aquellos que lo hayan utilizado. Muchas gracias y bonito día! ---- *Angela Andrea Camargo Sanabria* Estudiante Doctorado en Ciencias Biológicas Laboratorio de Ecología de poblaciones y comunidades tropicales Centro de Investigaciones en Ecosistemas (CIEco) UNAM, campus Morelia Antigua Carretera a Pátzcuaro # 8701 Col. Ex-Hacienda de San José de la Huerta, CP 58190