Re: [R-sig-eco] How do I convert a matrix from abundant into presence/absence data?

2013-02-12 Thread Farrar . David
Seems for that approch M should me a matrix (which I bet it actually is in this case) not a data frame. I wonder about the following, if you will forgive a slight digression: It seems for really large matrices there could be a speedup as well as savings of memory with something like. M - (M0)

Re: [R-sig-eco] Using rq() for least absolute deviation regression

2011-04-26 Thread Farrar . David
The short answer is that what you seem to want is the rq() default with tau not specified. (Default is tau=.5). In general rq() minimizes a sum of weighted absolute residuals. The weights depend on tau (the conditional quantile of interest), and turn out to be equal with tau = 0.5, i.e.,

Re: [R-sig-eco] Transforming logits to probabilities

2010-07-08 Thread Farrar . David
One can always use the delta method (statistical differentials) for problem of that sort, but in case the idea is to compute a confidence interval, intervals based on asymptotic normality should be computed in the scale where normality is most plausible, likely logit in this case, and the

Re: [R-sig-eco] Log transforming zero value data (+ quantile regression)

2009-06-25 Thread Farrar . David
Nate, I sent you some material off the list, before I saw your more detailed discussion of quantile regression issue here on the list. Here are a couple points for benefit of other participants. 1. Since the R quantile regression package supports nonlinear quantile regression, so you

Re: [R-sig-eco] missing data in PCA

2009-04-06 Thread Farrar . David
For combining imputation with PCA, transcan{Design} could be interest. For imputation, I have been hearing about the mice program. The documentation for princomp() suggests that a covariance matrix can be entered via the covmat argument. David F r-sig-ecology-boun...@r-project.org wrote

Re: [R-sig-eco] nls function

2008-10-30 Thread Farrar . David
In addition to the other comments, you may find it helpful to look at using function derivative information in the nonlinear regression section of Venables and Ripley. David [EMAIL PROTECTED] wrote on 10/29/2008 07:56:01 AM: Dear R-ecology subscribers, Here is a small contamination

Re: [R-sig-eco] Clustering large data

2008-10-10 Thread Farrar . David
This may be a long shot. You might try shutting down R and running your script from a command (DOS) window using the RTERM.EXE utility. Things do seem to run a little better that way as a rule. David ONKELINX, Thierry [EMAIL PROTECTED] Sent by: [EMAIL PROTECTED] 10/10/2008 10:12 AM To

Re: [R-sig-eco] Improving efficiency in a simulation model

2008-10-09 Thread Farrar . David
Dulce, Chapters dealing with R OOP and R/C interfacing can be found in Chambers, J.M. 2008. Software for Data Analysis. Springer. David Dulce M. Bustamante [EMAIL PROTECTED] Sent by: [EMAIL PROTECTED] 10/09/2008 04:47 PM To r-sig-ecology@r-project.org cc Subject [R-sig-eco] Improving

Re: [R-sig-eco] Clustering large data

2008-10-07 Thread Farrar . David
Thanks for the illustration of xtabs. A quibble: Doesn't the following work, substituting as.matrix() for matrix()? (Does seem to conserve the dimensions and dimension names.) matrify-function(datatable, formula = units~site+spp, relativize=F){ tbl-xtabs(formula,data=datatable) mx