similar to: nMDS with R: missing values

I'm not sure how you are incorporating time period into your data structure. Typically we are looking at plots or assemblages as the rows and taxa as the columns. Time period adds a third dimension that could be added as blocks of rows. For example, depending on the resolution of your data, one approach would be to have up to 8 rows for each locality: Loc1.1000, Loc1.2000, . . . Loc1.8000. If

Hello, For many years we have modified the '/etc/named.conf' file to include local settings. The disadvantage with this is of course that when bind is updated, it creates an '/etc/named.conf.rpmnew' file. We then have to determine what is new, and apply the relevant changes to our modified named.conf file. There is, however, an '/etc/named' directory which I assumed was

Dear All, I was wondering whether anyone might be able to provide some advice with an nMDS / R problem. I'm trying to run nMDS on a dataset that contains many missing values and was wondering how I can account for the missing values when running nMDS? It seems as though the data are being grouped depending on where the zero values appear. Any suggestions greatly appreciated. Thank you very

On Tue, 2018-12-04 at 08:19 +0000, J Martin Rushton via CentOS wrote: > The '/etc/named.conf.rpmnew' file supplied is a bare minimum to > "configure the ... server as a caching only nameserver (as a localhost > DNS resolver only)". As soon as you start adding any structure to it > things change, not just are added to. See >

Hello, In trying to resolve a problem with a cron job, we can see when the job starts by looking in the /var/log/cron log file. However, I was asked if when the job ends could also be logged. (It seems to be something that crops up every so often over the years.) I found on the 'net this article https://serverfault.com/questions/248915/crontab-is-there-any-log-with-begin-and-end-time which

Hello, I was looking at a process through the '/proc' file system, and came across a process name which seemed to contain a hex value: lrwxrwxrwx. 1 xymon xymon 0 Aug 2 14:07 /proc/58032/exe -> /usr/sbin/xymond;5d44410e (deleted) I am aware of what the 'deleted' part means, but have no idea what the ';5d44410e' part means. Is this some sort of thread reference? The

Hi! Thanks for providing great help in R-related statistics. Now, however I'm stuck. I'm not a statistics person but I was recommended to use R to perform a nmds plot and PerMANOVA of my dataset. Sample(treatment) in the columns and species (OTU) in the rows. I have 4 treatments (Ambient Temperature, Ambient temperature+Low pH, High temperature, High temperature+low pH), and I have 16

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,

I have some scripts using certwatch from the crypto-utils package. This rpm seems to be unshipped with EL8. Any ideas whats the "new" tool to check pem cert files? -- Leon

I set this computer up with Centos 8 a few days ago. "systemctl status mlocate-updatedb.timer" says "Active (waiting)". But the mlocate database hasn't been updated since the last time I ran updatedb manually. # ls -l /var/lib/mlocate/* -rw-r-----. 1 root slocate 22944208 Feb 29 10:30 /var/lib/mlocate/mlocate.db What have I missed? -- MELVILLE THEATRE ~ Real D 3D

Hi, I'm using nmds command (library vegan) to analyze some fishing data. I'd like to plot not only points, but also the names of species and stations in a specified position. I used the command text(nmds$points[,1], nmds $points[,2],labels=row.names(nmds $points),pos=3,cex=0.5) But the labels are sometimes overlapped. Is there any way to use identify, or a similar command, to plot the

Can't remember if I posted this before... We're getting warnings from rkhunterWarning: Checking for prerequisites [ Warning ] All file hash checks will be skipped because: This system uses prelinking, but the hash function command does not look like SHA1 or MD5. Now, googling, I find people saying to rm /etc/prelink.cache, then run rkhunter --propupd. Works. And then,

Hi I am new to Cygwin and Linux. I installed R under Cygwin as part of the setup I chose "All" during installation, for all packages. So I have the FULL installlation of cygwin up and running, including gfortran. *Under Cygwin, how do I check and configure the path to the various libraries?* I am trying below command and it says, cannot find "lgfortran" But I have installed

Hi, forgive me if someone has already posted about this but I have had a look and cannot find the answer, also I am very new to R and been getting the grips with this. I have been trying to use Adonis to find out if there are significant difference between groups on data that I have analyses with NMDS, and have been struggling with getting this to work and understanding what is going on. I am

Dear r-helpers! How can I integrate other distances (in the form of a dist object) into function metaMDS? The problem: metaMDS needs the original data.frame for the calculation and only the default distances of function vegdist are allowed. Any suggestions are greatly appreciated! Thank you, Kim -- Jetzt kostenlos herunterladen: Internet Explorer 8 und Mozilla Firefox 3.5 - sicherer, schneller

Hi Im currently trying to plot my NMDS data together with fitted variables (envfit funct) on an ordination plot. The plot function shows two displays="sites" and "sp". I was wondering how to plot it so that the sites come up as different points for different sites but the species come up as actual names? It looks a little busy at the moment with everything in. Sya -- View

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)

Hi I have just (finally) started to poke around in R and wanted to analyse a stream fish dataset with 28 sites and 18 species. When trying to follow the Vegan manual to run nmds from distance measures calculated by the vegdist function it turns out that I have two sites (streams) with the exactly the same four species (I have used pres-abs data in this case). When I try to run isoMDS I get an

Hi, I am currently working on some data and feel that NMDS would return an excellent result. With my current data set however I have been experiencing some problems and cannot carry out metaMDS. I have tried with a few smaller data sets which I created for practice sake and this has worked fine. I think it is the set up of my data set that is causing me trouble. I have 18 columns and 18 rows,

I have a data matrix that contains site data for paired infested and control plots. For example: ab ac ad af ag ah 1 .024 x x x x x 2 .9 x x x x x 3 1.5 x x x x x 4 2.3 x x x x x 5 1.0 x x x x x 1c .75 x x x x x 2c 2.1 x x x x x 3c 1.7 x x x x x 4c 10.2 x x x x