Displaying 15 results from an estimated 15 matches similar to: "rarefaction curves: unable to run the R script from Gimlet"
2011 Jun 28
3
Error in library (nls)
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
2001 Nov 13
1
rarefaction variance
Here's a question for ecologists on the r-help list-- I'm addressing this
to ecologists 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
2009 Nov 13
0
Rarefaction Curve by Individuals not Sites - vegan (specaccum)
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) gives me Sites, Richness
2014 Jul 08
0
Extrapolation of rarefaction curve
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 and sequence in order to have a full coverage of
2013 Apr 03
2
Ask help
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.
2012 Jan 25
1
loops
I've been struggling to get a loop to work. I want to create a new
variable in each loop with data from some function.
for example:
# part of the names for the variables to be created
Frags <- c("F04", "F05", "F07", "F09", "F11", "F13", "F14", "F17", "F18",
"F19", "P20",
2007 Oct 05
0
use of specaccum in routine procedure
Dear list members, I have a data.frame so shaped:
Sector Quadrants Plot Sic Time Species1 Species2 Species3
.. Species-n
1 1 1 1 5 0 0 1
. 0
2 1 1 1 12 1 1 1
. 0
3 1 1 1 34 0 1 0
. 0
4 1 1 1 23 1 1 0
. 0
5 2 1 1 22 1 1 1
. 1
6 2 1 1 10 1 1 1
. 1
7 2 1 1 2 1 0 0
. 0
8 2 1 1 2 0 0 1
. 0
9 3 1 1 12 0 0 0
. 1
.
.
.
.
.
.
.
.
.
.
2013 Feb 11
2
Alguien ha usado R para calcular curvas de rarefacción de especies en análisis de diversidad?
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
2009 Oct 20
1
how to draw stacked ellipses to illustrate the shared and specific of multiple objects using R
Dear R-help listers,
I am now asking for helps on how to draw stacked ellipses to
illustrate the shared and specific of multiple objects using R.
My problem comes from my population genetics study. Now, I genotyped
three species, and I get known about the amount of shared and specific
haplotypes in each of the species and their combinations. I want to
illustrate this result in three stack
2009 Aug 31
1
permutation test - query
Hi,
My query is regarding permutation test and reshuffling of genotype/phenotype
data
I have been using the haplo.stats package of R. for haplotype analysis and I
would like to perform an analysis which I'm requesting your advice.
I have a data set of individuals genotyped for 12 SNP and a dichotomous
phenotype.
At first, I have tested each of those SNP independently in order to bypass
2010 Mar 29
1
xyplot second y-xis and legend
Dear list,
I try to set a secondary y-axis in a lattice xyplot. This works. However, I
am unable to set a proper legend/key together with the 2nd y-axis under
general xyplot procedures. See example below.
The combination of the par.settings with simpleTheme and other settings
seems to go wrong.
I couldn't find a solution from previous topics. Any suggestions? thanks in
advance!
Robbert
2006 Apr 03
0
R/qtl
Dear all,
I am running qtl mapping. I have 75 RI lines with some residual
heterogeneous loci. The loci are code A, B or H(heterogeneous).
Questions:
1) R/qtl determine the data is F2 intercross.
2) Warning message about strange genotype pattern
> library(qtl)
> dat=read.cross("csv", file="rqtl_trt.csv")
--Read the following data:
75 individuals
2012 Mar 19
0
simple matching with R
Hello,
I would like to use the simple matching coefficient in R to compare
genotypic data from two years (there are some inconsistencies in the
genotype notations in the 2 years and I want to find out the error).
Is there a R code I could use? How does my matrix needs to look like?
I have 50 genotypes and each genotype is genotyped with 780 markers for
two different years. So I need to compare
2010 Jul 18
6
CRAN (and crantastic) updates this week
CRAN (and crantastic) updates this week
New packages
------------
* allan (1.0)
Alan Lee
http://crantastic.org/packages/allan
Automates Large Linear Analysis Model Fitting
* andrews (1.0)
Jaroslav Myslivec
http://crantastic.org/packages/andrews
Andrews curves for visualization of multidimensional data
* anesrake (0.3)
Josh Pasek
http://crantastic.org/packages/anesrake
This
2009 Sep 01
1
Logistic Politomic Regression in R
Hi everyone,
I'm trying to do an Logistic Politomic Regression in R. Because I have my resposes variables and the aswer is 0 and 1 in 3 bacterial genes. Somebody know how to do this in R in a easy way?
Thank so much,
José Bustos
Facultad de Ciencias
Universidad Catolica Ssma.
Concepcion
Chile
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