similar to: Barchart reorder

Given the following data frame ("freq.sp"), > str(freq.sp) `data.frame': 42 obs. of 4 variables: $ behav : Factor w/ 6 levels "approach","bowride",..: 1 1 1 1 1 1 1 2 2 2 ... $ species: Factor w/ 7 levels "COAST_SPOT","EAST_SPINR",..: 1 2 3 4 5 6 7 1 2 3 ... $ n : int 193 194 563 357 570 369 74 194 208 633 ... $ pct :

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

I am having trouble displaying a dendrogram of evolutionary relationships (a phylogram imported from the ape package) as the vertical component of a heatmap, but keeping the hierarchical clustering of the horizontal component. The relationships of the vertical component in the generated heatmap are not that of the dendrogram, although the ordering is. In more detail, I am attempting to generate

Hello everybody! I??m trying to create figures summarizing the abundance of a given species (y), by its length classes (x), year (conditional factor) and a grouping named as "fraction". I am using the lattice??s barchart but some problems arises: When I run the function, the sizes become characters, and this is the starting problem for me when trying to adjust the

Can anyone point me in the right direction of figuring out what downweight() is doing? I am using vegan to perform CCA on diatom assemblage data. I have a lot of rare species, so I want to reduce the influence of rare species in my CCA. I have read that some authors reduce rare species by only including species with an abundance of at least 1% in at least one sample (other authors use 5% as a

Hi, I have a dataset that looks like the one below. data plot plantno. species H 31 ABC D 2 DEF Y 54 GFE E 12 ERF Y 98 FVD H 4 JKU J 7 JFG A 55 EGD . . . . . . .

R experts, Is there anyway to reorder inside each group? In the following example, the bar of year 1932 is always plotted before the bar of year 1931, may I change the order inside each groups of bars? library(lattice) barchart(yield ~ variety | site,data=barley, groups = year, layout = c(1,6),auto.key = list(points = FALSE, rectangles = TRUE, space = "right"),ylab = "Barley Yield

Hi R community, I am trying to obtain a sample from a matrix but sample(my.matrix) doesn't do what I need. I have a matrix of 1287 interactions between the species in columns and the species in rows and I want to obtain a smaller matrix with say, 800 interactions, that may or may not have the same number of columns and/or rows (i.e., some interactions may not be retrieved in a smaller sample).

Hi, I have a small problem when using barchart. I have the following data: letters a 6 f 18 1 a 15 10 j 12 9 i 12 4 d 9 5 e 6 The data is from a survey and summaries the alternatives selected in one question. The idea is to have a bar chart illustrating the count of each selection in descending order. The data frame is already ordered in

Hi,Can I use "reorder" function with barchart as in dotchart? Here are some codes which do not work for me. Thanks Chetty ___________________________ a1c.cast$bmi.cat.reordered[a1c.cast$eth!="Other"] <-with(a1c.cast[a1c.cast$eth!="Other",],reorder(bmi.cat.ordered[a1c.cast$eth!="Other"], BP.FN.RATE,median )) barchart(BP.FN.RATE~

Hi, I am a new R user and am trying to construct a palaeoenvironmental transfer function (weighted averaging method) using the package rioja. I've managed to insert the two matrices (the species abundance and the environmental data) and have assigned them to the y and x values respectively. When I try and enter the 'WA' function though, I get an 'Error in FUN' message (see

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

Apologies for the empty email earlier! I have species abundance data sampled at a weekly frequency or sometimes monthly depending on the year. The goal is to identify the dates in an annual cycle in which the cumulative abundance of a species reaches some threshold. Here's an example of the data for 1 species over an annual period: "mc_pheno" is the object created from this data:

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

Dear List, I have a 47 species * 83 samples matrix containing percentage abundance data. I have two cluster analyses one of the samples and one of the species, and have ordered the rows and columns of the species by samples matrix according to these two cluster analyses. So far so good! Now what I want to do is create a plot with the species dendrogram at the top of the plot, the samples

Dear, I would like to post the following question to the r-help on Nabble (thanks in advance for the attention, Gustavo Vieira): Hi there. I have a data set on hands with 5,220 cases and I'd like to automate some procedures (but I have almost no programming knowledge). The data has some continuous variables that are grouped by 2 others: the name of species and the locality where they were

Hi all I have been trying to use the randomForest package to model insect species abundance in different habitats and identify the key variables (landscape/climate etc) in determining abundance, which has all worked fine and I get nice variable importance plots etc. Many thanks to everyone on this help forum who has given tips/advice along the way. But the percentage variance explained /pseudo r

Hi, I have an error with fisher.alpha from the vegan package. > fisher.alpha(data[[1]]) Error in nlm(Dev.logseries, n.r = n.r, p = p, N = N, hessian = TRUE, ...) : missing value in parameter I am trying to find fisher alpha for a list of 100 data frames, and I tried it on individual data frames in the list, which gave me the error above. I have every data frame in the same format as the

Dear List, I have a data set stored in the following format: > head(dat, n = 10) id sppcode abundance 1 10307 10000000 1 2 10307 16220602 2 3 10307 20000000 5 4 10307 20110000 2 5 10307 24000000 1 6 10307 40210000 83 7 10307 40210102 45 8 10307 45140000 1 9 10307 45630000 1 10 10307 45630600 41 >

I hope you can help with this one. I have two matricies: 1. A species abundance matrix: <http://r.789695.n4.nabble.com/file/n4643979/2species_matrix.jpg> 2. A species trait score matrix: <http://r.789695.n4.nabble.com/file/n4643979/2trait_matrix.jpg> The trait matrix lists trait scores for each species as listed in the species abundance matrix. I would like to create a script