Displaying 20 results from an estimated 700 matches similar to: "cca constraining variables table"
2010 Apr 27
1
cca standard error species
Dear all,
I realised a correspondence analysis with function cca() of vegan library.
Just like in Okansen (2010) in the example of R help:
library(vegan)
data(varespec)
data(varechem)
vare.cca<-cca(varespec~ Al + P + K, varechem)
With plot.cca() function I represented the species matrix in the next way:
plot(vare.cca,display="species")
Being similar to:
plot((c(-2,2)),(c(-2,2)),
2012 Nov 27
1
CCA plot
Hi, I have a couple questions about fitting environmental (land use
factors, plant species presence-absence, and soil variables) constraints to
my CCA biplot. 1. After successfully plotting species and site scores in my
CCA, I have been trying to insert the biplot arrows of the environmental
constraints in my data set using the text() function. When I do that, the
plot changes completely. Is there
2016 Sep 05
3
Tests of all canonical RDA axes
Estimados,
Buenas Tardes,
Estoy teniendo problema para testar la significancia de los ejes del RDA. NO se cual seria el error.
Alguien me podría ayudar? Desde ya muchas gracias.
Saludos, Luis
# Tests of all canonical axes
anova.cca(ssp.rda.hel, by="axis", step=1000)#Para saber la significancia de cada eje
Error in anova.cca(ssp.rda.hel, by = "axis", step = 1000) :
2010 Jul 20
1
Exporting NMDS distance matris to csv
If you submit these lines, you end up with variable "vare.dis". I want
to export vare.dis to csv. Stuck I am.
library(vegan,logical.return = TRUE) #return=true verifies package is
available
library(MASS,logical.return=TRUE) #return=true verifies package is
available
data(varespec) #varespec is an example data file in the vegan package
vare.dis <- vegdist(varespec)
2012 May 23
1
procrustes (vegan) plot of residual differences
Hello
This is a simple question but I couldn't google an answer.
In the procrustes function of the vegan package, one uses
plot(procrustes_object, kind=2) to obtain a plot of the residual
differences. For instance:
data(varespec)
vare.dist <- vegdist(wisconsin(varespec))
library(MASS)
mds.null <- isoMDS(vare.dist, tol=1e-7)
mds.alt <- isoMDS(vare.dist,
2006 Nov 16
2
question about capscale (vegan)
Hello,
I am interested in using the capscale function of vegan package of R. I
already have a dissimilarity matrix and I am intended to use it as
'distance' argument. But then, I don't know what kind of data must be in
'comm' argument. I don't understand what type of data must be referred
as 'species scores' and 'community data frame' since my data refer to
2010 Apr 13
1
vegan (ordisurf): R² for smoothed surfaces
Dear r-helpers,
I just read in an article by Virtanen et al. (2006) where vegetation-environment relationships are studied by fitting smoothed surfaces on an NMDS ordination using GAMs (Wood 2000). The authors describe, that they used R? as goodness-of-fit statistic, which they compare to the R? of fitted vectors. Calculations were carried out using the package vegan (Oksanen).
I know that I can
2008 Aug 07
2
panel.arrows problem in custom panel function
Dear List,
I am writing a custom panel function and xyplot method to plot the
results of a procrustes analysis from the vegan package.
I am having trouble getting the call to panel.arrows to work as I wish
when conditioning. The attached file contains the function definitions
for the xyplot method and the custom panel and prepanel functions I am
using. This example, using data and functions from
2013 Jul 12
2
vegan capscale 'subscript out of bounds' error
Hi list,
I am using the capscale function in vegan_2.0-7 to do a constrained
principal coordinates analysis, and I kept getting the following error
message:
Error in Y.r[, oo, drop = FALSE] : subscript out of bounds
I googled but I couldn't find an answer. Could anyone tell me why this
error msg and what to do?
Here is the command I used:
2023 Dec 08
2
regarding CCA plot
Hii rstudio members
I am learning rstudio, For my manuscript I am trying to plot CCA using
species and environmental data. But I am getting error like
Error in cca.default(sptrans, envtrans) :
all row sums must be >0 in the community data matrix
*My code is like *
library(vegan)
library(ggplot2)
library(dplyr)
rassspec<-read.csv("C:/Users/hp/Desktop/R_data/rassspec.csv",
2010 Jun 14
3
remove last char of a text string
Dear R experts,
is there a simple way to remove the last char of a text string?
substr() function use as parameter start end only... but my strings are of
different length...
01asap05a -> 01asap05
02ee04b -> 02ee04
Thank you all,
Gianandrea
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2008 Aug 07
6
multiple tapply
Hi folk,
I tried this and it works just perfectly
tapply(iris[,1],iris[5],mean)
but, how to obtain a single table from multiple variables?
In tapply x is an atomic object so this code doesn't work
tapply(iris[,1:4],iris[5],mean)
Thanx and great summer holidays
Gianandrea
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2011 Mar 28
1
ordination in vegan
Hi all,
I have site data with plant species cover and am looking for trends. I'm
kind of new to this, but have done lots of reading and can't find an answer.
I tried decorana (I know it's been replaced by ca.) and see a trend, but I'm
not sure what it means. Is there a way to get the loadings/eigenvectors of
the axes (like in PCA)? Is there a way to do this with rda() too? How
2008 Aug 28
3
drop unused levels in sqldf
Hi,
sqldf is a fantastic package, but when the SELECT procedure runs unused
levels remain in the output. I tried with the drop function, but without
success. Do you have any suggestions?
Thanx, Gianandrea
data(iris)
require(sqldf)
base<-sqldf("select * from iris where Species <> 'setosa'")
str(base) # Species with 3 levels!
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2009 Feb 19
2
dotplot points color
Dear list,
is it possible to change the background color of dotplot's points? I tried
in many ways but unsuccessfully
Thanks in advance
Gianandrea
require(lattice)
dotplot(variety ~ yield | site, data = barley, groups = year, pch=21)
dotplot(variety ~ yield | site, data = barley, groups = year, pch=21,
bg=c("2","3")) ??!!!
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2013 Mar 27
1
Conditional CCA and Monte Carlo - Help!
Hi All,
I am using canonical correspondence analysis to compare a community
composition matrix to a matrix of sample spatial relationships and
environmental variables. In order to parse out how much variance is
explained purely by space (S/E) or the environment (E/S) I am using a
conditional (partial) CCA. I want to test significance via Monte Carlo but
I can not find a way to do this with a
2011 May 10
3
metaMDS and envfit: Help reading output
Hello R experts,
I've used metaMDS to run NMDS on some fish abundance data, and am also working on correlating environmental data to the NMDS coordinates. I'm fairly new to metaMDS and NMDS in general, so I have what are probably some very basic questions. My fish abundance data consists of 66 sites for which up to 20 species of fish were identified and counted. I ran metaMDS on this data
2009 Mar 03
1
Self-Organizing Map analysis
Dear list,
I read the SOM package manual but I don't understand how to perform (for
example) 1) the SOM analysis on Iris data 2) with a visualization similar to
that of figure 7 in
http://www.cis.hut.fi/projects/somtoolbox/package/papers/techrep.pdf
Any suggestion? Thanks in advance,
Gianandrea
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2008 Sep 23
1
plot error
HI there,
why these lines of code are correct
plot(count~spray, data = InsectSprays)
plot(InsectSprays$count)
but this return an error:
plot(count, data = InsectSprays);
"data" method is not implemented in plot?!
Thanx, Gianandrea
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2004 May 13
2
BIO-ENV procedure
I've been unable to find a R package that provides the means of
performing Clarke & Ainsworth's BIO-ENV procedure or something
comparable. Briefly, they describe a method for comparing two separate
sample ordinations, one from species data and the second from
environmental data. The analysis includes selection of the 'best'
subset of environmental variables for explaining