similar to: ordisurf (pkg vegan) gives implausible result

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

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

I have a general question about using thin plate splines in the surf and ordisurf routines. My rudimentary knowledge of a gam is that with each predictive variable there is a different smooth for each one and then they are added together with no real interaction term (because they don't handle this well?). Now, If I have two variables that have a high D^2 score and a low GCV score (I am

I am beginning to work with the 'ape' package in R, and have run into some trouble. I generated a UPGMA tree based on DNA sequence distance in Paup* and read it into R, where it became an object of class "phylo". However, I need it to be classified as a "dendrogram" for my purposes (to use it to order the layout of a heatmap). I get an error using as.hclust.phylo

What does Generalized Cross Validation score mean. I preform and ordisurf on an ordination (nmds) with an environmental variable. I am trying to figure out "how well" the environmental varibles predict/explain the sites placements in species space. Any help would be greatly appreciated. Any pointers to literature... would be welcome. thanks in advance, -- Stephen Sefick Research

Hello, I want to fit a Gompertz model for tree diameter growth that depends on a 4 levels edaphic factor (?Drain?) and I don?t manage to introduce the factor variable in the formula. Dinc is the annual diameter increment and D is the Diameter. >treestab > Dinc D Drain [1,] 0.03 26.10 2 [2,] 0.04 13.05 1 [3,] 0.00 24.83 1 [4,] 0.00 15.92 4

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

Dear r users I have a question in coding continuous variables in logistic regression. When "rcs" is used in transforming variables, sometime it gives implausible associations with the outcome although the model x2 is high. So what's your tips and tricks in coding continuous variables. P.S. How to code variables as linear+square in the formula such as lrm. lrm(y~x+sqrt(x))

For those of you wanting to salvage your Cisco ATA-186 after inadvertent locking, or after recovering your devices from a vendor who has locked them, here is a rainy-day project for you: http://www.sst.com/downloads/datasheet/S71077.pdf The above document gives exact specifications on the 4mb flash EEPROM that stores all program and configuration data on the ATA-186 (aka Komodo.) If you

I'm pretty new to R and would appreciate some help interpreting the output of a function that was recommended to me. I've used the *envfit *function in the vegan package to plot vectors of four climate variables onto a species matrix ordination. The output indicates that only a single variable (mean_temp) is significant: ***VECTORS NMDS1 NMDS2 r2

Hi everybody, How can I get text from RScript (e.g. syntax, reminder) into the result text. Sink() does not do that - I only read the results and therefore I have to 'guess' which syntax was used where - reminders I wrote are lost. Bw and thank you in advance, Roberto [[alternative HTML version deleted]]

https://bugs.freedesktop.org/show_bug.cgi?id=59069 Priority: medium Bug ID: 59069 Assignee: nouveau at lists.freedesktop.org Summary: nouveau E[ DRM] fail ttm_validate QA Contact: xorg-team at lists.x.org Severity: major Classification: Unclassified OS: Linux (All) Reporter: kees.bakker at xs4all.nl

Hi, I''m currently building a small rails application that needs to store web traffic information. Similar to google analytics and clicky. (but simpler) It needs to store refer domains and visitors. Integration goes through a small javascript snippet. My question is: What database server is the fastest and should I use for this app? I was thinking about SQLlite. Thanks for your time,

Dear Sir/Madam, I converted the .dta into .Rdata with the foreign library read.dta. However, when I use fix() I get the message that the dates are discarded. Before fix(), class(dateX) gives 'dates' as class; after fix() class(dateX) gives 'character' Why is that? Best regards, Rob Bakker [[alternative HTML version deleted]]

Hi, I've a directory of large log files (> 100M) that I want to rsync to another server in short intervals (say every minute). With the --append option I can avoid resending whole files at every sync. But rsync still calculates the checksum over the complete files every time, which claims a significant share of CPU and IO resources. Since the log files are always written in append-only

Hello List, ? I have a dataset consisting of strings that I want to split while saving the delimiter. ? Some example data: ?leucocyten + gramnegatieve staven +++ grampositieve staven ++? ?leucocyten ? grampositieve coccen +? ? I want to split the strings such that I get the following result: c(?leucocyten +?, ??gramnegatieve staven +++?, ??grampositieve staven ++?) c(?leucocyten ??, ?grampositieve

Hi everybody, Question: why are my dataframe and numeric variables a character? I read an excel file via readxl but my dataframe is a character, and numeric variables, eg "yi", are also a character. My excelfile is in English numeric Sometimes the dataframe was indeed a dataframe, but I do not know why it did sometimes. Thank you in advance, Roberto PS I used "guess". The

I thought replacing the spaces following instances of +++,++,+,- with "\n" and then reading with scan should succeed. Like Ivan Krylov I was fairly sure that you meant the minus sign to be "-" rather than "?", but perhaps your were using MS Word as an editor which is inconsistent with effective use of R. If so, learn to use a proper programming editor, and in any case

Hello, I have the following situation: Samba with ldap passdb backend. In my setup I have a group called exact: ------------ dn: cn=exact,ou=Groups,dc=ahm,dc=nl objectClass: posixGroup,sambaGroupMapping cn: exact gidNumber: 1000 sambaSID: S-1-5-21-4269728302-1655870493-3894479995-3001 sambaGroupType: 4 memberUid: gerrit,piet,hornie ------------ maps to the unix group exact: exact

My setup is as follows: I am running Vmware Server on Ubuntu Feisty. This is the puppetmaster. I am running a guest of Ubuntu Gutsy. This is the puppet. When I try to run puppetd on the guest I get the expected message "notice: Did not recieve certificate" Going back to the server and running "puppetca --list" does not list any requests. As a hunch I telneted the hosts