similar to: calculating means

My objective is to look at differences in two species of fish from morphometric measurements. My morphometric measurements are head length, eye diameter, snout length, and measurements from tail to each fin. I want to use discrimanant function analyis to determine if there are differences between the two species. I am familiar with R but new to discrimannt function analysis. I want to learn

Hi, I am using aggregate to compute means for later plotting. There are two factors involved and the problem is that the values of the second factor ( Age ) in the means are not in the right order because "10" comes inbetween "1" and "2" What I really want is the numeric value of Age but as.numeric and as.integer returns the level value instead. Is there a way to

Hello All, I have a data frame (dput information below) with food item weight for fish species. I need to calculate the Mean proportion by weight of each food item for each specie, as show in solution data frame (dput information below). I use the ddply function (plyr package) in two steps. First calculate the proportion of weight for each individual: step1 = ddply (example, .(ID), transform,

I am creating an application to run a fishing tournament (see http:// www.ruby-forum.com/topic/51209 for a little background) Now I am running into an issue trying to calculate a leader board. each participate can enter multiple fish but only the largest fish per a given species counts towards the overall score. My entries table looks like this:

Hi Listers, I am trying to reflect a PCA biplot in the x-axis (i.e. PC1) but am not having much success. In theory I believe all I need to do is multiply the site and species scores for the PC1 by -1, which would effectively flip the biplot. I am creating a blank plot using the plot command and accessing the results from a call to rda. I then use the calls to scores to obtain separate site and

Hello! I'm a PhD student working with coral reef fish diversity in Mexico. I want to do species accumulation curves but I have differential sampling effort for each "sample". Do you know or have developed an R script that consider the differential effort of each sample? PRIMER and other programs use each pack of species as a replica without the possibility of telling the program that

I am designing an application to run a fishing tournament I am hosting. Each fish entered will be given a point total based on the length of the fish and the species of fish. Each species has a point multiplier. For Example Trout have a multiplier of 10 so a 20 inch Trout would have a score of 200. My conundrum is in where and when do I calculate the points. The options I have come up

Hi I have just (finally) started to poke around in R and wanted to analyse a stream fish dataset with 28 sites and 18 species. When trying to follow the Vegan manual to run nmds from distance measures calculated by the vegdist function it turns out that I have two sites (streams) with the exactly the same four species (I have used pres-abs data in this case). When I try to run isoMDS I get an

Hello, I'm sorry if this seems similar to my last post but I thought it was significantly different to warrent a new thread. Using the dataset below, is there a way to generate a bar/line plot for the TACC/Catch of every lvl of stock? i.e. OR1,OR3,OR5. The picture at the bottom of this post is an example of the bar/line plot for OR1 which was generated when OR1 was the only stock in the

I am modeling the effects of an environmental variable (X) on fish recruitment (Y) for several, ecologically related species (i) using a mixed-effects model. The linear relationship between X and Y includes a fixed effect that is common across all species and random effects that vary by species. In the lmer() notation from the package lme4: Model<- lmer(Y ~ X +(X|i)) Because the residuals of

Hi Listers, This has a simple answer but it has been eluding me nonetheless. I have been building a PCA plot from scratch with the ability to plot predefined groups in different colors. This has worked fine but when I try to get a polygon drawn around each of the groups it is not recognising my colour file correctly and is only printing the first colour in the file....code is below

Hi, I have a dataset called 'fish'. fish$Species returns extract 1. When I use fish$Species != c("CRA","PHC"), i.e. I want all species except "CRA" and "PHC", I get extract 2 which is blatantly wrong. Can anyone see what I'm doing wrong? Regards, James EXTRACT 1 > fish$Species [1] ALB ALB ALB ALB ALB ALB ALB ALB ALB ALB ALB ALB ALB

Hello R experts, I have having a difficult time figuring out how to perform and interpret an ANCOVA of my nested experimental data and would love any suggestions that you might have. Here is the deal: 1) I have twelve tanks of fish (1-12), each with a bunch of fish in them 2) I have three treatments (1-3); 4 tanks per treatment. (each tank only has one treatment applied to it) 3) I sampled

Hi there, I have been having trouble running negative binomial regression (glm.nb) using library MASS in R v2.15.0 on Mac OSX. I am running multiple models on the variables influencing the group size of damselfish in coral reefs (count data). For total group size and two of my species, glm.nb is working great to deal with overdispersion in my count data. For two of my species, I am getting a

Hi, I''m new to Ruby and Rails, and I''m running Ruby 1.8.4 with Rails 1.0 on Ubuntu 5.10 (breezy). I wanted to have a model Software, with the table as software (since ''software'' is the plural too). I appreciate one can simply use something like use_table or whatever (can''t remember the exact command) in the Model file, but I''d much rather

Dear R-list, I have a statistical problem with the comparison of two short time-series of density data in an ecological framework. I have to compare two short time series (5 years, one value for each year) of species density data (it is the density of fish in two different streams) to test if the two means of the five densities are significantly different, so basically if the two mean

Hello R experts, I've used metaMDS to run NMDS on some fish abundance data, and am also working on correlating environmental data to the NMDS coordinates. I'm fairly new to metaMDS and NMDS in general, so I have what are probably some very basic questions. My fish abundance data consists of 66 sites for which up to 20 species of fish were identified and counted. I ran metaMDS on this data

Colleagues ---------------------------------- System info: Version 1.3.0 (2001-06-22) on NT ESS v. 5.1.18 using emacs ver. 20.4 ---------------------------------- I have generated an object (class = by) with NA values and want to plot the output as a bargraph: x2 <- by(scl.nos, species, sum) These data are summed counts of fish by species > x2 INDICES: AGI [1] 0.729927

Hi, I'm trying to use the function "error.bars", but the program don't find it, and I dont't found any package with this function. Is there some another functin to draw barplots with error bars? Sueli Rodrigues Eng. Agr?noma - UNESP Mestranda - USP/ESALQ PPG-Solos e Nutri??o de Plantas Fones (19)93442981 (19)33719762

Hi, [I sent this to the plyr mailing list (late) last night, but it seems to be lost in the moderation queue, so here's a shot to the broadeR community] Apologies in advance for being more verbose than necessary, but I'm not even sure how to ask this question in the context of plyr, so ... here goes. As meaningless as this might be to do with the `iris` data, the spirit of it is what