Re: [R] Specify order of groups negative binomial (glm.nb)

2016-02-25 Thread Katharine Miller - NOAA Federal
onal preference. > >> > >> See ?C or ?contrasts, which I understand to be alternative ways of > >> doing the same thing (and would appreciate correction is this is > >> wrong). Or this can be done through the "contrasts" argument of > >> glm.nb. &

[R] Specify order of groups negative binomial (glm.nb)

2016-02-25 Thread Katharine Miller - NOAA Federal
Hi, I am using the glm.nb function to evaluate differences in the catch of individual species of fish across three river tributaries. The dependent variable is catch per unit effort (CPUE), and the independent variable is the the tributary (Trib_cat). CPUE is derived from the fish counts divided

[R] R Kohonen counts plot from unit classification?

2015-02-06 Thread Katharine Miller - NOAA Federal
I am new to the R Kohonen package. I plotted the counts per cell and then compared it to the unit.classif. from the som output - but I can't seem to get it to match up. Cells that show no counts in the counts plot have 3 or more data objects assigned to them in the unit. classif. I can provide t

Re: [R] Problem with R colors

2013-12-09 Thread Katharine Miller
- > David L Carlson > Department of Anthropology > Texas A&M University > College Station, TX 77840-4352 > > -Original Message- > From: r-help-boun...@r-project.org > [mailto:r-help-boun...@r-project.org] On Behalf Of Katharine > Miller > Sen

[R] Chart colors

2013-12-09 Thread Katharine Miller - NOAA Federal
Hello, I am having difficulty obtaining the correct colors in my R charts. > colors()[c(552, 254, 26)] [1] "red" "green" "blue" But, if I specify col=552 in my barplot, I get gray bars. Likewise, col=254 gives bright pink, and col=26 is a red-orange. I get accurate results when I spell out

[R] Problem with R colors

2013-12-09 Thread Katharine Miller
Hello, I am having difficulty obtaining the correct colors in my R charts. > colors()[c(552, 254, 26)] [1] "red" "green" "blue" But, if I specify col=552 in my barplot, I get gray bars. Likewise, col=254 gives bright pink, and col=26 is a red-orange. I get accurate results when I spell out

[R] Species names in distance matrix

2012-07-13 Thread Katharine Miller
I have a function that requires a distance matrix of class dist with species names as row names. For the life of me, I cannot figure out how to get dist() to include species names. I am sure this must be easy, because a lot of packages and functions out there require dist objects to have row name

Re: [R] Question with R CMD SHLIB in 64 bit R

2012-04-15 Thread Katharine Miller
Yes. I have version 2.15.0 of Rtools as well. I went ahead and re-installed both R and Rtools just to make sure everything was OK. But that did not fix the problem. - Katharine 2012/4/15 Uwe Ligges > > > On 14.04.2012 21:53, Katharine Miller wrote: > >> OK. So, I have 64

Re: [R] Question with R CMD SHLIB in 64 bit R

2012-04-14 Thread Katharine Miller
OK. So, I have 64 bit Windows 7 and I have installed R 2.15.0 Thanks 2012/4/14 Uwe Ligges > > > On 14.04.2012 19:01, Katharine Miller wrote: > >> Hi, >> >> Sorry - I should have said that I was using Windows 7 on a 64 bit computer >> in my earlier post.

Re: [R] Question with R CMD SHLIB in 64 bit R

2012-04-14 Thread Katharine Miller
.04.2012 00:24, Katharine Miller wrote: > >> Hi, >> >> I have some C++ code that I compiled into a dll for use in 32 bit R and >> would like to recompile for use in 64bit R. I thought it would be as easy >> as going to R-2.15.0\bib\x64 and running R CMD SHLIB mfregRF.c >

[R] Question with R CMD SHLIB in 64 bit R

2012-04-13 Thread Katharine Miller
Hi, I have some C++ code that I compiled into a dll for use in 32 bit R and would like to recompile for use in 64bit R. I thought it would be as easy as going to R-2.15.0\bib\x64 and running R CMD SHLIB mfregRF.c but that doesn't do anything. It doesn't give me any error messages, but it also

[R] Help predicting random forest-like data

2012-04-10 Thread Katharine Miller
Hi, I have been using some code for multivariate random forests. The output from this code is a list object with all the same values as from randomForest, but the model object is, of course, not of the class randomForest. So, I was hoping to modify the code for predict.randomForest to work for p

[R] randomForest - NaN in %IncMSE

2011-09-20 Thread Katharine Miller
Hi I am having a problem using varImpPlot in randomForest. I get the error message "Error in plot.window(xlim = xlim, ylim = ylim, log = "") : need finite 'xlim' values" When print $importance, several variables have NaN under %IncMSE. There are no NaNs in the original data. Can someone hel

[R] randomForest partial dependence plot variable names

2011-08-04 Thread Katharine Miller
Hello, I am running randomForest models on a number of species. I would like to be able to automate the printing of dependence plots for the most important variables in each model, but I am unable to figure out how to enter the variable names into my code. I had originally thought to extract the