similar to: randomForest Species Distribution Modelling

Any suggestions on the following would be grateful. I'm trying to impute data, where a fictitional dataset is defined as... set.seed(110) n <- 500 test <- data.frame(smoke_status = rbinom(n, 2, 0.6), smoke_amount = rbinom(n, 2, 0.5), rf1 = rnorm(n), rf2 = rnorm(n), outcome = rbinom(n, 1, 0.3)) # smoke_status (0, 1, 2) is c("non-smoker, "ex-smoker",

Dear List members, I would like to test whether an observed occupancy of lakes in a landscape has occurred randomly (by chance) or not. How can I do that? The problem is that it concerns only a single species and I would like to use binary data only. At first I thought of generating null models and test the observed occupancy against the randomly generated one. However, this needs more than one

Hi everyone, I am working with the dbFD function of the FD package, and there's something funny happening with the value of sing.sp in the output. Basically, I have a species-function matrix and a community matrix. One site in particular has 6 species, 4 of which have identical functional coding. I thus expect nbsp = 6 and sing.sp = 2 for this site. However, nbsp = sing.sp = 6. This

Dear all, I am new to R and even newer to mapping with R. I have installed PBSMapping, maptools and maps, and I am struggling to produce a map of fish abundance in the Grand Banks. I have tried several approaches to plot the bathymetry in my study area: 1) download the data from http://topex.ucsd.edu/cgi-bin/get_data.cgi (42N46N313W307W) To start with, the map I get is blank between

Dear List, I am running constrained correspondence analysis for abundance data of 7 birds. However, I would like to check which bird prefers which environment gradient by showing the species with different colors of the dots in cca plot (package vegan). Please kindly help and thank you Elaine [[alternative HTML version deleted]]

Dear all, I'm performing a detrended correspondence analysis on vascular plant community data (296 species), and I have a question on the species scores projected in the ordination diagram. When I run a ordiplot all species are projected in the output graph, but I'd like to restrict the number of species plotted in the final graph. Some species are so rare in the data, that no relevant

I have a question about the function "duleg" in the package "labdsv". How the p-value is calculated ? Dufrene and Legendre (1997) have shown two calculation way ; one is the difference between the observed value and the mean of those obtained from random permutations and another is the rank of the observed value in the randomly generated distribution ordered in decreasing

I am at my wit's end. I am not sure what is wrong with this data matrix. It is sparse because it is a matrix of species, but I have looked at the row totals and column totals and they are positive. metaMDS(x.d) Error in if (autotransform && xam > 50) { : missing value where TRUE/FALSE needed What is wrong? And in the future how in God's name do I easily diagnose whatever

I am refering to a function call like this: >data(iris) >x <- svmlight(Species ~ ., data = iris) I tried to see the content of it by typing: > Species ~ . but it gives nothing. How can I see it's content ? - P.Dubois

I have 4 very large species lists and I would like to compare them. I have the following results from running Sorenson’s dissimilarity tests: Norfolk Fens compared to Suffolk Coastal Fens: QS=0.583961142689298 Norfolk Fens compared to Breckland Edge Fens: QS=0.714896020281379 Norfolk Fens compared to Other Fens:

Dear, I wanna make cross-validation for the species data of species distribution models. Please kindly suggest any package containing cross validation suiting the purpose. Thank you. Elaine [[alternative HTML version deleted]]

Hi, I have three years of species presence/absence data for a set of ~100 ponds, with a list of associated habitat characteristics (park, vegetation, hydroperiod, etc.). The datasets differ slightly by year because some ponds were dry in some years and not in others. My goal is to look at habitat associations for a couple focal species. For each year, I have a data table that looks like

Does anyone know of example r-code/packages for carrying out analysis? Preferably this would have examples from real experimental data of two or more competing species... Thanks Chris Buddenhagen [[alternative HTML version deleted]]

row <- c("a","b","c","d","e","f","g") #rows from larger data frame row.1 <- c("a","b","c","g") #rows of smaller data frame because d, e, and f don't contain any of the species, but the zeros are important x <- data.frame(sp1=rnorm(4), sp2=rnorm(4), sp3=rnorm(4),

Dear all I'm trying to calculate the number of shared species between sites. I have a dataframe with in the first column the names of the sites; the names of the other columns are the species names. To use the shared function from the package RICH one needs to input different matrices. So actually, I want to split the dataframe per row so that each row becomes a separate matrix and then

Dear everyone, I am doing some work about species richness estimation. Nonparametric estimation (such as Chao1, Jacknife1) can be done just using function "specpool()" and "estimateR()" in package "vegan". The problem is that I can not found any functions for parametric estimation (such as MMMeans, MMruns, Michaelis-Menten). Do you know any function for doing this?

Hello, Is it possible to include information about phylogenetic relatedness among species (when species are replicates for each study within a meta-analysis) in a meta-anlaysis in the metafor package? Alternatively, I wonder if the method f Lajeunesse 2009 American Naturalist has been adopted in R in any fashion? Thanks, Scott Chamberlain [[alternative HTML version deleted]]

Dear All, The Decision and Policy Analysis (DAPA) program of the International Center for Tropical Agriculture (CIAT), a not-for-profit agriculture, biodiversity and ecosystems research center, supported by the Consultative Group of International Agricultural Research (CGIAR), with headquarters in Cali, Colombia is looking for a visiting researcher to work on various modeling projects, primarily

Hi, I am working with a species-by-trait .csv file (columns=traits, rows=species) and get the following warning message when trying to plot results of both metaMDS and pcoa:  "Warning message: In ordiplot(x, choices = choices, type = type, display = display,  :   Species scores not available" I am using a Gower's transformation in both procedures within the metaMDS or pcoa

Hi Ansley It looks good to me but I did not run the analysis as I am too lazy to install "indicspecies". The inclusion of the raw data is a great help. John Kane Kingston ON Canada -----Original Message----- From: daily.puja at gmail.com Sent: Tue, 19 Apr 2016 08:16:54 -0400 To: jrkrideau at inbox.com Subject: Re: [R] Indicator Species analysis; trouble with multipatt Thanks for the