Displaying 20 results from an estimated 1300 matches similar to: "data type problem for vegan package"
2008 Jun 01
2
optim error - repost
Here is a clean version. I did this with nls and it works (see below), but
I need to do it with optim. Keun-Hyung
# optim
vol<-rep(c(0.03, 0.5, 2, 4, 8, 16, 32), 3)
time<-rep(c(2,4,8),each=7)
p.mated<-c(0.47, 0.48, 0.43, 0.43, 0.26, 0.23, NA, 0.68, 0.62, 0.64, 0.58,
0.53, 0.47,
0.24, 0.8, 0.79, 0.71, 0.56, 0.74, 0.8, 0.47)
eury<-data.frame(vol=vol, time=time, p.mated=p.mated)
2008 Nov 12
1
read.table with many blanks (reposting)
Thanks Jim for pointing out how to properly ask.
Here is is my question and a small subset of the data and output.
I have a data set with many blanks. The blanks should be replaced with zero
once imported.
I tried read.table, read.csv (R 2.8 version),or scan, but none was
successful.
Any suggestion, please..
thanks.
Keun-Hyung
>garoben=read.table("c:\\Rdata\\garoben.txt",header=T,
2008 Dec 22
3
row sum question
Dear helpers,
I'm using R version 2.8.0.
Suppose that I have a small data set like below.
[,1] [,2] [,3] [,4]
a 1 1 0 0
b 0 1 1 0
c 1 1 1 0
d 0 1 1 1
First, I'd like to find row sum of values uniquely present in each row, but
only sequentially from the top row, meaning that if the value is shown in
the above row(s) already, the
2010 Aug 13
1
subsetting data points within confidence limit
Dear R-list
Suppose I have a data set stored in hmet, for which I did get confidence
limit on a linear regression as shown below.
My question is how I can subset only data points which are within the
confidence limit.
Thank you.
Keun-Hyung
---------------------------------------------------------------
Al=rnorm(100, 3)
Cd=rnorm(100, 0.2)
hmet=data.frame(Al=Al, Cd=Cd)
plot(Al,
2008 Jun 01
2
optim error
I saw a similar question but I still don't fully understand how to implement
optim.
Can someone help me out with this?
Thanks. Keun-Hyung
> vol<-rep(c(0.03, 0.5, 2, 4, 8, 16, 32), 3)
> time<-rep(c(2,4,8),each=7)
> p.mated<-c(0.47, 0.48, 0.43, 0.43, 0.26, 0.23, "null", 0.68, 0.62, 0.64,
0.58, 0.53, 0.47,
+ 0.24, 0.8, 0.79, 0.71, 0.56, 0.74, 0.8, 0.47)
>
2008 Jun 23
2
Writing Vector to a File
Dear experts,
I try not to trouble the list again after this question.
I want to print this vector into a file
> myvec
[1] --Control --Control --Control --Control --Control HBA2 HBA1
[8] HBA1 --Control HBB --Control HBB HBA1 MBP
[15] --Control HBA1 HBA2 HBB PTGDS GAPDH UBC
[22] --Control GAPDH TPT1 HUWE1 PRM1 CKM
2007 Jun 05
2
generating many matrices
I'd like to generate many matrices (let's say 100 matrices of 4x4), of which
diagonal elements are being drawn from each set of sample of known
distribution.
What would be the best way? I've been trying to find any previous threads
for this topic, but haven't been able to find one.
Thanks. Kevin
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2017 Jun 13
1
How to remove dead peer, osrry urgent again :(
On Tue, 13 Jun 2017 at 06:39, Lindsay Mathieson <lindsay.mathieson at gmail.com>
wrote:
>
> On 13 June 2017 at 02:56, Pranith Kumar Karampuri <pkarampu at redhat.com>
> wrote:
>
>> We can also do "gluster peer detach <hostname> force right?
>
>
>
> Just to be sure I setup a test 3 node vm gluster cluster :) then shut down
> one of the nodes
2017 Jun 13
0
How to remove dead peer, osrry urgent again :(
On 13 June 2017 at 02:56, Pranith Kumar Karampuri <pkarampu at redhat.com>
wrote:
> We can also do "gluster peer detach <hostname> force right?
Just to be sure I setup a test 3 node vm gluster cluster :) then shut down
one of the nodes and tried to remove it.
root at gh1:~# gluster peer status
Number of Peers: 2
Hostname: gh2.brian.softlog
Uuid:
2012 Jul 27
1
labeling loading vectors in vegan
Hello,
I am using vegan to do an NMDS plot and I would like to suppress the labels
for the loading vectors. Is this possible? Alternatively, how can I avoid
overlap?
Many thanks for the help.
Example code:
#perform NMDS using metaMDS() function
spe.nmds<-metaMDS(data, distance='bray',k=2 , engine = "isoMDS",
autotransform=F, trymax=1000)
#calculate the loading (i.e.,
2013 Sep 06
1
Fwd: calculating dissimilarity index of islands (vegan and betapart)
Dear List,
This is Elaine, a postgraduate studying in bird distributions in East Asia.
I want to calculate Simpson dissimilarity index,
based on a presence/absence matrix of bird species in islands in East Asia.
(matrix row: 36 islands/matrix column: species ID)
(R package vegan to make NMDS and R package betapart)
In most papers using vegan for NMDS and betapart for dissimilarity
2013 Apr 26
1
NMDS in Vegan: problems in stressplot, best solution
Hello,
I can draw a basic stress plot for NMDS with the following code in package
Vegan.
> stressplot(parth.mds, parth.dis)
When I try to specify the line and point types, it gives me error message.
> stressplot(parth.mds, parth.dis, pch=1, p.col="gray", lwd=2, l.col="red")
Error in plot.xy(xy, type, ...) : invalid plot type
In the above code, if I removed line type,
2008 Apr 14
1
Vegan R^2 and tau values for metaMDS
I am using the function metaMDS with jaccard distances to ordinate a
set of constituent by site matrix. I can post this data if it would
be helpful, but it is large to include in an email. I can also
provide reproducable code if necessary. I would like to get an R^2
value for the axes of the ordination configuration that I get with
metaMDS in the vegan package is there a way to do this- is it
2007 Aug 24
1
Adding new points to a metaMDS ordination ("vegan" pkg)
Hi, I've been using R for a while now but I've got a problem with
metaMDS (in the vegan package) that I can't quite figure out.
I have a set of proportion data (from 0-1, rows sum to 1) that I apply
metaMDS to using the command:
nMDS.set=metaMDS(sqrt(test.set),distance="euclidean",k=3,zerodist="add",autotransform=FALSE)
I am using a squared-chord distance
2012 May 09
1
reception of (Vegan) envfit analysis by manuscript reviewers
I'm getting lots of grief from reviewers about figures generated with
the envfit function in the Vegan package. Has anyone else struggled to
effectively explain this analysis? If so, can you share any helpful
tips?
The most recent comment I've gotten back: "What this shows is which
NMDS axis separates the communities, not the relationship between the
edaphic factor and the
2009 Sep 09
2
"predict"-fuction for metaMDS (vegan)
Dear r-Community,
Step1: I would like to calculate a NMDS (package vegan, function metaMDS) with species data.
Step2: Then I want to plot environmental variables over it, using function envfit.
The Problem: One of these environmental variables is cos(EXPOSURE). But for flat releves there is no exposure. The value is missing and I can't call it 0 as 0 stands for east and west. Therefore I
2009 Jan 21
1
vegan metaMDS
Hi,
I'm trying to use metaMDS with a dissimilarity matrix of angles, not
Bray-Curtis, and I wanted to know if there is an in-built function to
produce a plot of stress values against dimensions, that could be used to
determine the 'true' dimension of the solution. The number of objects is
only a lowly 8 so any solution higher than 2-dimensional is not likely to be
interpretable,
2001 Nov 13
0
VEGAN: R functions for vegetation ecologists
A colleague has just passed me this interesting
address:
http://cc.oulu.fi/~jarioksa/softhelp/vegan.html
"Vegan: R functions for vegetation ecologists"
"Vegan package is intended to help vegetation ecologists and
other community ecologists to use R. It is not a completely
self-contained package, but it complements other R functions.
.../...
At this first stage, vegan implements
2008 Nov 13
1
R not responding
Dear R help team,
I am sorry to put urgent in the subject but to be honest I am in big
troubles if I cannot make R to work in my computer.
I am a PhD student in statistics and most of my homeworks and projects are
in R.
I have been using R in my mac book pro, mac os X 10.5.5 without problems
until yesterday. I don't know what happened. Now every time I try to access
R it takes a long time
2008 Nov 13
1
Urgent: R not responding
Dear R help team,
I am sorry to put urgent in the subject but to be honest I am in big
troubles if I cannot make R to work in my computer.
I am a PhD student in statistics and most of my homeworks and projects are
in R.
I have been using R in my mac book pro, mac os X 10.5.5 without problems
until yesterday. I don't know what happened. Now every time I try to access
R it takes a long time