Re: [R-sig-eco] horizontal lines in stacked bargraph ggplot

h Columbia From: Philippi, Tom [tom_phili...@nps.gov] Sent: Wednesday, August 20, 2014 11:42 AM To: Mitchell, Kendra Subject: Re: [R-sig-eco] horizontal lines in stacked bargraph ggplot Not a definitive answer, but 3 suggestions. 1) try ggsave() for your .svg 2) try col

[R-sig-eco] horizontal lines in stacked bargraph ggplot

Hi All I posted this question in the ggplot user group but realized that it's not super active and I'm on a deadline for presenting this graph, so sorry about the cross-posting. I'm making stacked bargraphs to show distribution of major taxonomic groups across a treatment regime (using ggplot

Re: [R-sig-eco] BiodiversityR CAPdiscrim error

Sent: Thursday, February 20, 2014 5:19 AM To: Mitchell, Kendra Cc: r-sig-ecology Subject: Re: [R-sig-eco] BiodiversityR CAPdiscrim error Hi Kendra, (sorry I got your name wrong, missed the comma.) [cc'ing the list: better to keep stuff there, so others could comment.] Ah, that's the troub

[R-sig-eco] BiodiversityR CAPdiscrim error

I'm trying to run CAPdiscrim on a dissimilarity matrix with a catagorical variable attached on the right with cbind str(MD2.tyc.om) num [1:34, 1:35] 0 0.53 0.857 0.962 0.763 ... - attr(*, "dimnames")=List of 2 ..$ : NULL ..$ : chr [1:35] "" "" "" "" ... CAPdiscrim(MD.2.tyc.om~MD.2.tyc.om[,

Re: [R-sig-eco] NA error in envfit

From: Gavin Simpson [ucfa...@gmail.com] Sent: Friday, December 06, 2013 11:09 AM To: Dixon, Philip M [STAT] Cc: Mitchell, Kendra; r-sig-ecology@r-project.org Subject: Re: [R-sig-eco] NA error in envfit Phillip, You approach to using factors misses an important consideration; the

Re: [R-sig-eco] NA error in envfit

Thanks, makes sense to remove a variable that has no variation and it fixed the issue. And that is much easier than building and installing from source. -- Kendra Maas Mitchell, Ph.D. Post Doctoral Research Fellow University of British Columbia 604-822-5646

Re: [R-sig-eco] NA error in envfit

ip M [STAT] [pdi...@iastate.edu] Sent: Thursday, December 05, 2013 8:42 AM To: Mitchell, Kendra Cc: r-sig-ecology@r-project.org Subject: NA error in envfit Kendra, I wonder if the problem is a factor level with no observations. One of the frustrating things about factors (class variables) in R is tha

[R-sig-eco] NA error in envfit

I'm running a bunch of NMS with vectors fitted (slicing and dicing a large dataset in different ways). I'm suddenly getting an error from envfit f.bSBS.org.fit<-envfit(f.bSBS.org.nms, f.bSBS.org.env, permutations=999, na.rm=TRUE) Error in vectorfit(X, P, permutations, strata, choices, w = w,

[R-sig-eco] manipulating species matrices

I have a large species matrix with counts that I want to express as ratio to the reference plots. I want to use a heatmap to display change in species as a ratio to the reference the layout is samples by rows and species by columns, it's currently a data.frame with row.name=sample name, header

Re: [R-sig-eco] subsetting lower triangle distance matrix based on variable in another object

: Mitchell, Kendra Subject: Re: [R-sig-eco] subsetting lower triangle distance matrix based on variable in another object Hi Kendra I had a similar problem a while back. As Jari says, you have to do the subsetting while the object is an ordinary matrix, and then convert it back to a "dist"

[R-sig-eco] subsetting lower triangle distance matrix based on variable in another object

I have a number of dissimilarity matrices built in another program that I'd like to subset then run NMS. #read in distance matrix b_bc03 <-data.matrix(read.table("bac_final.an.thetayc.0.03.lt.ave.dist", row.names=1, header=T, fill=TRUE)) # creates a 736x736 double matrix #read in environmental

[R-sig-eco] betapart and nms

I'm working on a large bacterial dataset, 700 samples with ~5600 species (rare species <100 observations have been removed). The samples are from experimental plots from 6 ecozones. I've done nms, betadisp, and permanova using several dissimilarity measures (jaccard, sorenson, Yuen's theta).

Re: [R-sig-eco] extract distance from betadisp {vegan}

that's my current hypothesis. -- Kendra Maas Mitchell, Ph.D. Post Doctoral Research Fellow University of British Columbia From: Gavin Simpson [gavin.simp...@ucl.ac.uk] Sent: Monday, April 22, 2013 3:41 PM To: Mitchell, Kendra Cc: r-sig-ecology@r-project.

[R-sig-eco] extract distance from betadisp {vegan}

I've run betadisp on a set of communities and would now like to compare the distance for each sample from it's centroid to other measures such as alpha diversity. Basically I want to check that increased dispersion isn't simply a reflection of overall diversity. It seems like I should be able