search for: jpoulsen

Hello R-Users, I am trying to label points on an xYplot. I can label the points, but then I lose the error bars. I suspect that I should be using panel.xYplot rather than panel.xyplot, but that didn't work either... Can anybody help me out? Example code is below. First xYplot has error bars, second tries to label the points and the bars disappear. Thanks, John a=c(1:4)

Hello, I am trying to run a logistic regression with random effects on proportional data in glmmBUGS. I am a newcomer to this package, and wondered if anyone could help me specify the model correctly. I am trying to specify the response variable, /yseed/, as # of successes out of total observations... but I suspect that given the error below, that is not correct. Also, Newsect should be a

Hello, I apologize in advance as this example seems really elementary. Below I have created a simple scatterplot with lines. I would like to label each line with the name of the village, instead of using a legend. Can someone please let me know how to do it. Thanks in advance -- John Pop=c(1406,1862,2333,2664,2685,2521,2726,0,0,0,0,214,289,365,900,952,1002,1205,1041,942,1004,

Hello, I am trying to graph a violin plot like the example in panel.violin(lattice) with the singer data - see below Does anyone know how to change the color of the boxplot on the graph from blue to green? I tried a number of changes, but to no avail. Thanks for your help, John bwplot(voice.part ~ height, singer, panel = function(..., box.ratio) {

Hello, I am trying to plot a curve over points plotted with se's in xYplot (see example below). I can get Figure 1 below to plot the data with error. However, I keep getting a the error message "Error using packet 1 object "y" not found" Can anyone see what I am doing wrong? Thanks! John ------------------------------- a=0.002; b=31.7; c=0.51

Hello, I am trying to make a xyplot plot with points that are different symbols. I want to call the symbol type (pch) from a column in my dataframe. Here is a simplified example. In my real example I also have groups, which I have not included here. This example doesn't change the symbols or colors. Any help you can provide would be appreciated. Thanks, John x<-c(1:12)

Hello, I am having a problem specifying the correlation structure in lme which leads to the error: Error in getCovariate.corSpatial(object, data = data) : Cannot have zero distances in "corSpatial". I have specified a grouping variable which is the only fix I could find by searching this error on R-help. ISee the below example. When my samples (tran) - which are transects

Hello R-users, I have code that gives me the important variables from an analysis. I need to input these variables into a different analysis. To do this, I need to modify them slightly... 1) remove all numbers at the end of the variables, 2) remove all periods. I tried to do it with the awkward code below. It works to remove all the numbers, but when I try to remove the period everything

...st or most elegant way to do it. How would you do it? What functions/packages should I look into, in order to improve these plots? Thanks in advance for your comments and suggestions, Peter ------------------------------ Message: 29 Date: Sun, 21 Sep 2008 18:41:22 -0400 From: John Poulsen <jpoulsen@zoo.ufl.edu> Subject: [R] glmer -- extracting standard errors and other statistics To: r-help@r-project.org Message-ID: <48D6CD92.10305@zoo.ufl.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hello, I am using glmer() from lmer(lme4) to run generalized linear mixed mode...

Hello, I have been using mgcv to run GAM hurdle models, analyzing presence/absence data with GAM logistic regressions, and then analyzing the data conditional on presence (e.g. without samples with no zeros) with GAMs with a negative binomial distribution. It occurs to me that using the negative binomial distribution on data with no zeros is not right, as the negative binomial allows zeros.

Hello R-Users, I have recently run into several problems using vgam() in the VGAM package. I am hoping someone might have some solutions... Briefly, I have been trying to fit GAM models for zero-altered negative binomial models. 1. When fitting smoothed parameters (e.g. s(X, df=2)) changing the degrees-of-freedom has no effect on the level of smoothing (e.g. number of knots for the

Hello, The simple example below plots three species by year and site. However, I would like the points to occur in groups horizontally, rather than on top of each other. I thought jitter might work, but haven't been successful in getting it to do what I want. Any ideas? Thanks in advance. John wt=rnorm(27,5,0.6) yr=rep(c(2000,2001,2002),each=3)

Hello, I am using glmer() from lmer(lme4) to run generalized linear mixed models. However, I am having a problem extracting the standard errors for the fixed effects. I have used: summary(model)$coef fixed.effects(model) coef(model) to get out the parameter estimates, but do not seem able to extract the se's. Anybody have a solution? Thanks, John

Hello, I have a dataset that has counts, but I need to expand the dataset so that each of the counts has its own line in the dataset (row) and is given and id. It looks something like: Site Type Cnt 1 "A" 3 1 "B" 0 2 "C" 2 I want the dataset to look like: Site Type ID 1 "A" 1 1 "A" 2 1 "A" 3 1 "B" 0 2 "C" 1 2

Hello, I am looking for some general advice on which graphics package to use to make a figure demonstrating my experimental design. I want to design a circle with 7 sectors inside. Then I will want to shade the sectors depending on densities of observations in the sectors. I will also want to draw horizontal lines at increments along the sectors to demonstrate different distances out to

Hello R-Users, I am plotting several histograms to demonstrate zero-inflated data using lattice. Because there are so many zeros, it is difficult to see the observations of non-zeros on the graph (i.e. the y-axis scale is too large). I would like to break the y-scale so that the non-zeros at least show up on the graph. Below is an example of the code for the histogram (e.g. I have several

Hello, I want to build a function to call up a column of a data.frame by the names of the columns. I have column names that are sequentially named (col1, col2, etc.). How do I change a character expression into something that will be understood as a data.frame column. For example: example<-data.frame(cbind(col1=1:10, col2=21:30, col3=41:50)) call.fun<-function(t){

Hello, I am running a GLMM using R2Bugs, but am getting the below error message. I am including the entire output, although the 2nd and 3rd lines seem to indicate the problem. Note that I do define N (it is an integer) and send it to a datalist (see the R commands and model below). Interestingly, when I put all of this into OpenBugs directly, the model runs. I do have reasons, however, that I

Hello, I am using xyplot and am happy with my graph, *except* that I cannot get the symbols to be filled. I tried using bg=c("red3","red","black","lightgrey")) in both the key and the xyplot function, that that was obviously not the answer. I would like the sybols to be filled with the same colors as the lines. Does anybody have an answer? In case