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....thick.bh+ht.any, random=~1|site, family=Gamma(link=log), data=rws30.BL) Error in hglm.default(X = X, y = Y, Z = z, family = family, rand.family = rand.family, : Length of X and Z differ. > * Dennis Murphy <djmuser at gmail.com> Tue, May 17, 2011 at 6:18 PM To: Benjamin Caldwell <btcaldwell at berkeley.edu> Hi: Someone else (Wayne Zhang, CNA) asked a similar question re hierarchical Gamma models on R-help today and responded to suggestions as follows: "Hglm does the work! Thanks! Also, I find that the developing version of lme4, called lme4a, has the capability to fit Gam...

Dear r helpers; I'm interested in reading from and writing to large .xlsx files fairly regularly. (Why, the naysayers may ask - and the answer is basically colleagues and clients who prefer that format). I've tried out the XLConnect and xlsx libraries, but the java implementation they use just takes too much RAM for the files I'm working with. gdata leverages perl and works really

Dear R users, I'm starting to use 'apply' functions rather than for loops in R, and sometimes the output is a bit different than what I want. In this case, the command was tapply(myvector,myindex,cumsum) And the output was something like this: $`SNRL1 Core 120` [1] 2.8546 4.0778 5.2983 6.3863 7.5141 8.5498 9.5839 10.6933 $`SNRL1 Core 230` [1] 7.6810 8.7648 9.8382

Hello, I'm just trying to wrap my head around the syntax for creating loops, functions in R. I have an array of values from a .csv. Looks something like header<-c(species,coefficient1, exponent1, coefficient2, exponent2, constant) with a species name for the first column, and values for coefficient1, exponent1, coefficient2, exponent2, constant for each species. The values are

Hello, I'm trying to create a vector of r^2 values for using a function which I will run in a "for" loop. Example: per<-rnorm(100,.5,.2)^2 x<-rnorm(100,10,5) y<-rnorm(100,20,5) fr<-data.frame(x,y,per) test<-rep(0,9) plotter<-function(i){ temp.i<-fr[fr$per <=(i*.10),] with(temp.i, plot(x, y, main=(i*.10),)) mod<-lm(y~x-1,data=temp.i)

Evening folks, I'm trying to print a series of graphs to .jpeg using a variable as the title, but run into the difficultly that I can't find a way to append the file extension to the .jpeg (in this case extensionless!) files. Example: ---- species.name="CussoniaHolstii" dia<-10:100 biomass = -21.4863 + 0.5797 * (dia ^ 2) biomass jpeg(species.name) plot (biomass,

Addendum: I tried a gamma fit in glmmPQL and got the same errors. *Ben Caldwell* PhD Candidate University of California, Berkeley On Tue, May 17, 2011 at 3:51 PM, Benjamin Caldwell <btcaldwell@berkeley.edu>wrote: > Hello > After seeing this ( > https://stat.ethz.ch/pipermail/r-sig-mixed-models/2011q1/005213.html) email > I thought I would check the issue with a gamma family in lme4 hadn't been > fixed; can I fit a hierarchical gamma model in lme4 at this time? The...

Hi, I'm trying to run a basic simulation and sensitivity test by running an equation with two variables and then plotting the results against each of the vectors. R is running the vectors like this : 0 with 0, 1 with 1, etc. I would like it to run them like 0 for 1:100, 1 for 1:100, and then the reverse (so 100^2*100@ iterations. How do I get it to do that? Here's what I have so far:

I have some elements in a vector with extraneous information (e.g. file name and sample IDs) that I'd like to strip from every element. For example, I would like "SPI1.S1.str1.P3.sample.tif" "SPI1.S1.STR2.P1.sample.tif" to read "SPI1.S1.str1.P3" "SPI1.S1.STR2.P1". Will someone help me with the syntax in gsub? It needs to be something like

So I needed to merge 17 .csv files, and did so by brute force, but I might need to do so again. Anyone have suggestions for a for loop that might do the below for me (where a:r are separate .csv files) ab<-merge(a,b,all=TRUE) cd<-merge(c,d,all=TRUE) ef<-merge(e,f,all=TRUE) gh<-merge(g,h,all=TRUE) ij<-merge(i,j,all=TRUE) kl<-merge(k,l,all=TRUE) no<-merge(m,n,all=TRUE)

Hi, I'm trying to plot an equation in two variables to get a feel for sensitivity to its parameters. I've run expand.grid to get made-up vectors of the combinations of the two independent variables, and am trying to plot the output of the dependent, M, against both the dependent in a 3d space. t <- 0:100 DBH <- 10:100 TxDBH<-expand.grid(t,DBH) time<-TxDBH[,1]

Sub: using glmer to fit a mixed-effects model with gamma-distributed response variable Hello, I'm currently trying to fit a mixed effects model , i.e.: > burnedmodel1.2<-glmer(gpost.f.crwn.length~lg.shigo.av+dbh+leaf.area+ bark.thick.bh+ht.any+ht.alive+(1|site/transect/plot), family=gaussian, na.action=na.omit, data=rws30.BL) If I run this code, I get the error below: Error:

Hello all, * * I'm having some difficulty, and I think the problem is with how I'm using append() nested inside a for loop. The data are: y,x 237537.61,873 5007.148438,227 17705.77306,400 12396.64369,427 228703.4021,1173 350181.9752,1538 59967.79376,630 140322.7774,710 42650.07251,630 5382.858702,264 34405.82429,637 92261.34614,980 144927.1713,1094 362998.7355,1420 203313.6442,1070

Another question on functions - I have something that looks like plotter<-function(i){ temp.i<-rwb[rwb$vector1 <=(i*.10),] with(temp.i, plot(vector2, vector3, main=(i*.10),)) mod<-lm(vector3~vector3-1,data=temp.i) r2<-summary(mod)$adj.r.squared rsqrd[i]<-r2 legend("bottomright", legend=signif(r2), col="black") abline(mod) rsqrd<<-rsqrd } I'd

Dear R help; I'm currently trying to combine a large number (about 30 x 30) of large .csvs together (each at least 10000 records). They are organized by plots, hence 30 X 30, with each group of csvs in a folder which corresponds to the plot. The unmerged csvs all have the same number of columns (5). The fifth column has a different name for each csv. The number of rows is different. The

Hello, I have a vector, "dates", as a series of 3 digit elements, i.e. > date [1] 528 528 528 528 528 528 528 528 528 528 528 528 708 708 708 708 708 708 [19] 708 708 708 708 529 529 529 529 529 529 529 529 529 529 529 529 529 529 [37] 529 624 I need to convert them into julian, but have to insert a "/" or "-" after the first number within each element of the

Dear R helpers Reproducible example: #warning - this causes a hard freeze on the machines I've tried it on matrix.holder<- matrix(rnorm(150), nrow=30, ncol=5) Out= expand.grid(matrix.holder[,1],matrix.holder[,2],matrix.holder[,3],matrix.holder[,4], matrix.holder[,5]) Problem: I'm running an analysis that I would like to do using a matrix containing all the possible combinations of

Hello, I've written a small function that's supposed to save me some time, and it's ending up killing it- the intention is to iteratively subset a dataset fram on framevec, fit a model (either lm or nls depending on type) and return the r2 or AIC from the model, respectively. Although as far as I can tell in my code the plots are dependent on the fit of the model to the data and the

Dear R help; I'll preface this by saying that the example I've provided below is pretty long, turgid, and otherwise a deep dive into a series of functions I wrote for a simulation study. It is, however, reproducible and self-contained. I'm trying to do my first simulation study that's quite big, and so I'll say that the output of this simulation as I'd like it to be is

Dear R help, I have some readings in three dimensions (x, y, z) and an amplitude for each. I'd like to visualize the data using ggplot, using tile plots, as I have some additional point data I would like to eventually overlay on the tile plots. I would like to subset the data by sections, slices if you will, in the z dimension, and plot the data for that slice. I can do all of this, but am