similar to: rda variance partioning in vegan problems

Displaying 20 results from an estimated 1000 matches similar to: "rda variance partioning in vegan problems"

2010 Nov 17
1
Total inertia in package Vegan?
Dear all at the R-project help list. I have run into a problem when it comes to getting values for "total inertia" and "R-squared" for my DCA using "decorana" in the package "vegan". I have tried the "goodness" function, but the reply indicates that it does not work with "decorana" class objects. In Canoco one gets the Total inertia in
2012 Jan 11
2
Vegan(ordistep) error: Error in if (aod[1, 5] <= Pin) { : missing value where TRUE/FALSE needed
I am getting the following erro rmessage in ordistep. I have a number of similarly structured datasets using ordistep in a loop, and the message only occurs for some of the datasets. I cannot include a reproducible sample - the specific datasets where this is occur ing are fairly large and there are several pcnm's in the rhs of the formula. thanks for any pointers that may allow me to
2017 Jul 18
3
Redundancy canonical analysis plot problem in 3D using VEGAN, RGL, SCATTERPLOT3D and SFSMISC
Hello Sir I am getting problem in plotting in CCA . Could you please help me? I wrote the below command but I don't know why it is taking only first 5 env data rather than all 9. > strain.data <- read.xlsx("Dee rhiz.xlsx", sheetName="strain", header = T, row.names = 1) > env.data <- read.xlsx("Dee rhiz.xlsx", sheetName="env", header = T,
2012 Jan 10
0
Error message in vegan ordistep
I am getting the following erro rmessage in ordistep. I have a number of similarly structured datasets using ordistep in a loop, and the message only occurs for some of the datasets. I cannot include a reproducible sample - the specific datasets where this is occur ing are fairly large and there are several pcnm's in the rhs of the formula. thanks for any pointers that may allow me to
2017 Jul 19
0
Redundancy canonical analysis plot problem in 3D using VEGAN, RGL, SCATTERPLOT3D and SFSMISC
We need to keep the discussion on the list. When I run your code, there are several problems. strain.data <- read.xlsx("Dee rhiz.xlsx", sheetName ="strain", header = T, row.names = 1) str(strain.data) # lists 9 columns at the end with all NAs strain.data1 <- (strain.data, sqrt.dist = TRUE) # this is not a valid R line. I get Error: unexpected ',' in
2011 Mar 10
1
vegan CCA I am Completely new to ordination analyses
Dear list, I am trying to predict species volume from bioclimatic data, I have various sites and I have a data frame with species volume and the corresponding bioclimatic data for each site. I read on a discussion forum that you can use ordination to predict species abundance (in my case volume) from 'new' climate data for sites where you do not know the abundance. Unfortunately I
2013 Aug 27
2
Encontrar las variables más importantes en componentes principales
Hola compañeros de la lista. Qué tal. Tengo un análisis de componentes principales, en el que se evalúan aproximadamente 1000 variables. Usando la función dudi.pca e inertia.dudi obtengo una cantidad de información sobre la influencia de las variables sobre los dos componentes principales. Me gustaría saber si existe alguna función que sobre esta información me arrojara la lista de
2011 Sep 23
0
vegan rda na adaptation
Dear R users, I know, the topic is more related to the r-sig-ecology. I decided to post it to the r-help as some specific topics of my question deals with NA-values and RDA (R vegan) and an adaptated RDA code due to a specific study design (including a second matrix). I am calculating a RDA for a dependent matrix (different variables for tree performance) and different explanatory
2017 Sep 17
0
Help with RDA analysis, function ''varpart'' in vegan
The varpart function does not have na.action argument, and all undefined arguments are regarded as explanatory data sets X (they come after ?). Best wishes, Jari Oksnaen
2017 Sep 17
0
Help with RDA analysis, function ''varpart'' in vegan
I am not familiar with the vegan package, so I am just making a guess here. If 'na.action=na.omit' is part of the call to varpart, try removing it from the function call and moving it above as follows: options(na.action="na.omit") RDA_Ger <- varpart(comm, x1, x2, x3, transfo="hellinger", scale = FALSE) Maybe that will help. Regards, Eric On Sat, Sep 16, 2017 at
2017 Sep 16
2
Help with RDA analysis, function ''varpart'' in vegan
I'm trying to perform a RDA analysis in the vegan package using the "varpart" function. I have a matrix of community structure data in different sites (rows), which I want to explain using 3 matrices of environmental data. The 3 matrices are: water quality parameters; local land use variables; total land use variables. In each matrix, the number of the rows is the same (the
2013 Aug 29
1
Resumen de R-help-es, Vol 54, Envío 22
Hola! No he podido consultar la doc. del paquete ade4, algo debe estar caído en CRAN ahora mismo. Dos cosas sobre la metodología -aun desconociendo los detalles de cómo lo hace ade4: El output de un PCA, los "pesos" de cada variable en las dimensiones de los componentes se interpretan como correlaciones, a mayor valor absoluto mayor asociación variable-componente. Ahora, como tales
2010 Nov 17
0
How do I get "total inertia"+"R-squared" in R?
Dear people at the R-help-list. I have run into a problem in the package "vegan", while using the function "vegan", and would greatly appreciate any advice how to solve the problem. I have put in my data R, using the "decorana" function in the package "vegan" and received nice coordinates for the DCA of sites and species, as well as the Eigenvalues for the
2004 Jun 22
1
Need for advise for Correspondence Analysis
Dear R users, I m quite a novice in using R for factor analysis and I would need some help to choose the right function. I have a contingency table and I would like to perform a Correspondence analysis on this table, followed by a hirarchical clustering of my variables projected in on the first principal components. Here are my question : - what is the more appropriate function to do so ...
2015 Jan 20
2
Kickstarting several *different* setups
On 01/20/2015 08:41 AM, Tom Grace wrote: > I would suggest that the "right way" would be to kickstart all your > machines the same way, and then use a configuration management tool > (like Puppet or Chef) to customize them Seconded. Personally, I recommend either ansible or bcfg2 over other tools. Puppet has a larger user base, but when I talk to users at conferences (such
2009 Dec 20
2
plot de un cca realizado con Ade4
Un saludo a todos. Estoy haciendo un ACC y utilizo el paquete Ade4. Cuando quiero realizar un plot del resultado utilizo plot(). el resultado son 6 gráficos: loadings, correlation, inertia axes, scores and predictions, eigenvalues y species. Lo que quería saber es cómo representar en una sola ventana (los 6 gráficos a parecen en la misma) el gráfico correspondiente a Species. Gracias por vuestra
2013 Aug 22
1
varpart
Dear R-users I applied vegan's varpart function to partition the effects of explanatory matrices. Adj. R square for the unique fraction [a] is 0.25. Does anyone know why the decomposition by hand using rda gives me a different result for [a] (constrained proportion is 0.32)? I used cbind() for the conditional fractions, but it should be similar to condition()? Thanks very much
2009 Feb 04
2
lua assist
Hello, For Lua inclusion in Syslinux an idea to ship with an com32/lua/assist directory and an com32/lua/patches directory. In the patches directory patches against a pristine lua tarball and the assist dir contains scripts for further tayloring. This is what I have in mind: | milleune at inertia:~ | $ git clone http://www.stappers.it/tracking/syslinux/.git syslinux-lua-stappers | milleune at
2015 Feb 21
9
Winbind backend : rid is too much underappreciated
I just came to the conclusion that the rid backend has been very much underappreciated. Too much mental inertia about how things used to be made? After strugling for two days to configure a member server against a Samba Active Directory with the ad/RFC2307 backend, I turned to the rid backend and voil?! all my problems are gone. Having to manually edit uids/gids in UNIX Attributes under RSAT
2006 Apr 20
2
PCA biplot question
Hi everyone, I'd like to project two pcas onto one device window. I plot my first PCA: biplot(prcomp(t(cerebdevmat)), var.axes=FALSE, cex=c(1,.1), pc.biplot=TRUE) Now I'd like to project the features of another PCA onto this graph. Any suggestions? I know this is easily done in MatLab but haven't figured it out in R. Thanks, Tanya [[alternative HTML version deleted]]