similar to: Exclude 0 values from plot

Hello, I plot the abundance of a species in relation to the date. To have the date as a continous variable I put it in the format "standard" in excel (f.ex. 39939 means 06.05.2009). R uses 39939 on the x axis, but I would like to have "06.05". I tried to use as.Date as suggested in some discussion but I don't manage to use it, the returned date is not correct. Do you have

Hello! I am trying to model data on species abundance (count data) with a poisson error distribution. I have a fixed and a random variables and thus needs a mixed model. I strongly doubt that my model is overdispersed but I don't know how to get the overdispersion parameter in a mixed model. Maybe someone can help me on this point. Secondly, it seems that quasi models cannot be implemented

Hello! I would like to make a scatterplot of my data, but the problem is that several points have the same x and y values and are represented as only one point. I wonder if there is a way to represent the data points, but with point size representing the frequency of the depicted x-y value? Thank you! -- View this message in context:

Hello! It is not really linked to R, but can somebody explain me why we sometimes make a mantel test directly for to distance matrices and sometimes we first make a gradient analysis and then a mantel test between the axis? Thank you -- View this message in context: http://www.nabble.com/Mantel-test-tp25439984p25439984.html Sent from the R help mailing list archive at Nabble.com.

Hello, I performed a Mantel test and plotted communitiy similarities. I would like to add a least square line. I thought about using abline taking as slope the r-statistic of the Mantel test and calculating the y-intercept analytically. Is this method correct? Is there any function for this calculation? Thank you -- View this message in context:

Hello, I would like to plot a large number of graphs (43) in a same window. I tried wit par(mfrow=c(8,5)), but when I give the code for the plots I receive a error message saying that the margins are to wide. Can someone help me? Is it possible to put so many graphs in a single window? Thank you -- View this message in context:

Hello, I am trying to do contrasts after applying a binomial mixed effect model with the function lmer. I have to extract the fix effect values, but as I write fixef(model), I get this error message: Error in UseMethod("fixef") : no method for 'fixef' with objects of class "mer" Has anybody some ideas why? And how can I then post-hoc testing my data if I cannot do

Hello! I have a dataset with monthly temperatures for 4 different years and I would like to test if they are significantly different between the years. As I collected the data for different sites I wondered if there were some possibility to perform the calculation at once or if I have to repeat it for each site. I tried like this: Model_Temp <- lmer(Temp ~Year +

Hello! When I am analyzing proportion data, I usually apply logistic regression using a glm model with binomial family. For example: m <- glm( cbind("not realized", "realized") ~ v1 + v2 , family="binomial") However, sometimes I don't have the number of cases (realized, not realized), but only the proportion and thus cannot compute the binomial model. I just

I'm having the most curious error while using the sem package. For the model I'm working with, I keep getting the following error: Error in J[cbind(1:n, observed)] <- 1 : subscript out of bounds I''ve used debug=TRUE with sem, and there don't appear to be any problems with model - there are no latent variables in this model. The variables in the covariance matrix

I'm looking over good-code a post-doc in my lab wrote and trying to learn how it works. I came across the following: rel.abundance <- as.matrix(read.delim("rel.abundance.csv",row.names=1,as.is =TRUE)) rel.abundance <- log2(rel.abundance-min(rel.abundance)+1) I'm not sure what the second line is doing. I ran each line in R and couldn't see a noticeable difference in

Hi all, I am fairly new to R and I am trying to run mvpart and create a MRT using explanatory variables and covariables. I've been following the procedures in Numerical Ecoogy with R. The command (no covariables) which works fine - ABUNDTMRT <- mvpart(abundance ~ .,factors,margin=0.08,cp=0,xv="1se",xval=nrow(abundance),xvmult=100,which=4) where abundance is 4th root

Hi fellow R users, I have a dataset that looks something like this. species class abundance K 1 592 K 2 288 G 1 254 G 2 239 C 2 173 D 2 123 E 3 89 F 2 87 B 2 86 H 2 82 I 1 79 J 2 76 B 1 73 D 3 72 A 2 62 L 2 58 I want to plot a stacked barchart. species is the x-axis, abundance is y-axis, and class will appear as the stacks in different colours. I need the species to be displayed in descending

Greetings, I am new to R and am hoping to get some tips from experienced R-programmers. I have a dataset that I've read into R as a dataframe. There are 5 columns: Plot location,species name, a species number code (unique to each species name), abundance, and treatment. There are 272 plots in each treatment, but only the plots in which the species was recorded have an abundance value. For

Hi guys, I'm very new to R and have been teaching myself over the past few months - it's a great tool and I'm hoping to use it to analyse my PhD data.As I'm a bit of a newb, I'd really appreciate any feedback and/or guidance with regards to the following questions that relate to generalized linearmixed modelling (or, at least, I think they do!)(if there is a 'better',

Hi. I am currently trying to run some Spearman correlations, and have encountered two issues. 1) When using cor.test() with a variable that includes ties, I get the "Cannot compute exact p-values with ties" error. I have read that this function now uses an asymptotic formula that allows for ties, so do not understand why I am getting this error. (I am running version 2.4.0.) I

Hi there, I'm using the lattice package to create an xy plot of abundance vs. depth for 5 stages of barnacle larvae from 5 species. Each panel of the plot represents a different stage, while different loess smoothers within each panel should represent different species. However, I would like depth to be on the y-axis and abundance to be on the x-axis, because this is more intuitive as an

I am using two mixed effect models. Firstly, what I am trying to do is to compare green roofs abundance with brownfield, green roof with green space abundance, and finally green space with brownfield abundance. I am unsure if I have done the correct model. I have to use a mixed effect model because my data is nested. This is the code and output >

Hello, please excuse the simplicity of this question as I am not very good with stats. I am taking a class, using R which I am learning at the same time, and the questions asks us to "Estimate the average abundance using Poisson regression with a log link". I can estimate the abundance from "x", but I can seem to figure out how to get the average abundance in this method. Any

Hi, I would like to calculate the RELATIVE euclidean distance. Is there a function in R which does it ? (I calculated the abundance of 94 chemical compounds in secretion of several individuals, and I would like to have the chemical distance between 2 individuals as expressed by the relative euclidean distance. Some compounds are in very low abundance whereas others are in high abundance,