search for: speci

The following command produces red axis line in a pairs plot: pairs(iris[1:4], main = "Anderson's Iris Data -- 3 species", pch = "+", col = c("red", "green3", "blue")[unclass(iris$Species)]) Trying to fool pairs in the following way produces the same plot as above: pairs(iris[1:4], main = "Anderson's Iris Data -- 3 species",pch = "+", col =...

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: +-------------+--------------+------+-----+--------------------- +----------------+ | Field | Type | Null | Key | Default | Extra | +-------------+--------------+------+-----+-------------...

Hello, I have tried to find this out some other way, but unsuccessful I have to try this list. I assume this should be quite simple. I have a dataset with 4 columns, "Sample_no", "Species", "Nitrogen", "Carbon" in csv format. In the species column I have many different species with varying number of obs per species Eg "Sample_no" "Species" "Nitrogen" "Carbon" 1 Cod 15.2 -19.0 2 Haddock 14.8 -20.2 3 Cod 15.6...

Dear List, I have a data frame called trait with roughly 800 species in, each species have 15 columns of information: Species 1 2 3 etc.. a t y h b f j u c r y u etc.. I then have another data frame called com with the composition of species in each region, there are 506 different communities: community species NA1102 a NA1102 c NA0402 b NA0402 c A...

Hi, First I should note I am relatively new to R so I would appreciate answers that take this into account. I am trying to perform an MDS ordination using the function ?metaMDS? of the ?vegan? package. I want to ordinate species according to a set of functional traits. ?Species? here refers to ?sites? in traditional vegetation analyses while ?traits? here correspond to ?species? in such analyses. My data looks like this: Trait1 Trait2 Trait3 Trait4 Trait5 Trait? Species1 228.44 16.56 1.66 13.2...

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 all species in the dataset, I would like to add zeros to the abundance column for any plot...

I have a data frame with two factors (sampling 'unit', 'species'). I want to calculate the number of unique 'species' per 'unit.' I can calculate the number of unique values for each variable separately, but can't get a count for each ?unit?. > data=read.csv("C:/Desktop/sr_sort_practice.csv") > attach(data) > data[...

Dear R Gurus, Let's get the technical details out of the way first: Computer: 1.83 GHz MacBook R version 2.5.1 I have a data set that contains the following variables: site, species, total.vines. I need to partition the main data set by site, the further select only those species that occurred at each site. When I select by site (site.name<-subset(data frame,Site=="Site name"), the resulting data frame is normal, containing all the records for that par...

Hi, sorry by this off. I'm still try to understand nested design. I have the follow example (fiction): I have 12 plots in 4 sizes in 3 replicates (4*3 = 12) In each plot I put 2 species (A and B) to reproduce. After a period I make samples in each board and count the number of individuals total (tot) and individuals A and B (nsp). Others individuals excepts A and B are in total of individuals. This make a dataset with the 24 lines and not 12. Its smell pseudoreplication in a...

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 rule, but this removes at least half my species). If I code it as follows:...

...rting out with R and having some trouble with combining plots. I am playing with the famous iris dataset (checking out example dataset in R while reading through Introduction to datamining) What I would like to do is create three graphs (combined boxplots) besides each other for each of the three species (Setosa, Versicolour and Virginica) with each graph showing showing four boxplots Sepal.Length, Sepal.Width, Petal.Length and Petal.Width. I can create the boxplot for the total dataset by doing the following: data(iris); boxplot(iris[1:4]); However I would like to have this repeated for each...

In a number of different situations I'm trying to remove factor levels that are represented by less than a certain number of rows, e.g. if I had the dataset aa below and wanted to remove the species that are represented in less than 2 rows: data(iris) aa <- iris[1:101,] In this case, since I can see that the species virginica only has one row, I can write: table(aa$Species) setosa versicolor virginica 50 50 1 aa[aa$Species != "virginica", ] but:...

I would be incredibly grateful to anyone who'll help me translate some SAS code into R code. Say for example that I have a dataset named "dat1" that includes five variables: wshed, site, species, bda, and sla. I can calculate with the following SAS code the mean, CV, se, and number of observations of "bda" and "sla" for each combination of "wshed," "species," and "site," restricting the species considered to only three of several spec...

Hei, i am trying to plot the means of two variables (d13C and d15N), by 2 grouping factors (Species and Year) that i obtained by the function tapply. I would like to plot with different colours according to the Year and show the "Species" as data labels. My data looks like this: Species d13C d13N Year "Species1" 14,4 11.5 2009 "Species2&quot...

Dear R users, I have a problem with something called "NaNs" in a nested mixed model. The background is that I have studied the number of insect nymphs emerging from replicated Willow genotypes in the field. I have 15 replicates each of 4 Willow genotypes belonging two 2 Willow species. Now I want to elucidate the effect of Willow genotype on the number of emerging nymphs. Previously I performed a simple one-way anova with "genotype" as explanatory factor and "number of nymphs emerging" as dependent variable, but the editor of the journal I've submitted...

Hola, tengo una matriz de especies donde cada celda tiene datos con caracteres (son parentesis). Cómo la puedo reordenar considerando tanto filas como columnas? Ejemplo: ,Specie 1, Specie2, Specie3 Specie1, NA, 3(1-4), 8(6-9) Specie2, 5(2-6),NA, 5(4-6) Specie3, 2(1-3), 10(5-15), NA Quiero: ,Specie 2, Spe...

I want to analyze the co-occurrence of some species. In some papers, the authors said that the index"the number of species combinations (COMBO)" is a good index. I try to calculate the index by R language. But I can not get the right value. I think that I do not understand the concept of the index because my english is not good. The con...

Dear all, In a greenhouse experiment we tested performance of 4 different species (B,H,P,R) under 3 different water levels in 10 replications. As response variable e.g. the number of emerging sprouts were measured on three dates. A simple Anova considering every measurement date separately shows a higly significant effect of species and moisture (and partly the interaction of...

..." doesn't work because there is no instance that has class "c". Is there any way to solve this problem? library("randomForest") # load the iris plant data set dataset <- iris numberarray <- array(1:nrow(dataset), nrow(dataset), 1) # include only instances with Species = setosa or virginica indices <- t(numberarray[(dataset$Species == "setosa" | dataset$Species == "virginica") == TRUE]) finaldataset <- dataset[indices,] # just to let you see the 3 classes levels(finaldataset$Species) # create the random forest randomForest(formula...

Hi I have a data.frame with dim = 18638 (rows) 6 (cols) names(dat) [1] "id" "long" "lat" "species" "type" "size" Variable "species" and "type" are factors. Species has 5 levels "BOV" "CAP" "CER" "OVI" "POR" Variable "type" has 11 levels "BRD" "CL" ... "OTHER&...