53 research outputs found

    Supplement 1. Ant species occurrence data, ant abundance data, and environmental variables for regression analysis.

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    <h2>File List</h2><blockquote> <p><a href="tbspecies.txt">tbspecies.txt</a> -- (MD5: 26a77c828649475ba59510d0fc2452bc)</p> <p><a href="tbabundance.txt">tbabundance.txt</a> -- (MD5: 06314ecd127474788b5970eadb4caa82)</p> <p><a href="tbenvvars.txt">tbenvvars.txt</a> -- (MD5: 1dec3e3ce91d155f0509a7709193c462)</p> </blockquote><h2>Description</h2><blockquote> <p>tbspecies.txt is a tab-delimited text file with three columns. The first row is column headings. Each row is a species occurrence in a sample. samplecode is a unique code for a sample. Note that samples that contained no ants are not in this file. To get sample sizes at each site, see Appendix A. elevation(m) is the elevation of the site, in meters, and can be used to group samples by site. species is the species name; the same names are used for the species list in Appendix B. </p> <p>tbabundance.txt is a tab-delimited text file with two columns. The first row is column headings. Each row is a sample and all samples are in the dataset. elevation(m) is the elevation of the site, in meters, and can be used to group samples by site. abundance is the total number of ant workers in the sample. </p> <p>tbenvvars.txt is a tab-delimited text file with 18 columns. The first row is column headings. Each row is a site and there are seven sites in the dataset. Elevation(m) is the elevation of the site, in meters. MeanLog(abundance+1) is the mean of Log(abundance+1) where abundance is the total number of ant workers in the sample. Mean(SpeciesDensity) is the mean of number of species per sample. Sobs(MaoTau) is the observed species richness across all samples at a site, rarefied to 1170 species occurrences at the five lowest sites. ICEMean is the Incidence-based Coverage Estimator of asymptotic species richness, rarefied to 1170 species occurrences at the five lowest sites. MDE2900 is the mid-domain effect prediction using an upper bound of 2900m, rarefied to 1170 species occurrences at the five lowest sites. MDE2050 is the mid-domain effect prediction using an upper bound of 2050m, rarefied to 1170 species occurrences at the five lowest sites. Log(Area) is the log-transformed elevation-specific regional area, estimated from a digital elevation model as the proportional area in each 100 m elevation band on the Atlantic slope of Costa Rica. Rain(mm) is estimated annual rainfall. MeanRH is estimated relative humidity. MeanTemp is mean daily average temperature. MinTemp is mean daily minimum temperature. MaxTemp is mean daily maximum temperature. SoilN is soil nitrogen level. SoilP is soil phosphorus level. AlphaMean is Fisher's Alpha diversity index, calculated using EstimateS 8.0 and rarefied to 1170 species occurrences at the five lowest sites. ShannonMean is the exponential Shannon diversity index, calculated using EstimateS 8.0 and rarefied to 1170 species occurrences at the five lowest sites. SimpsonMean is the Simpson diversity index, calculated using EstimateS 8.0 and rarefied to 1170 species occurrences at the five lowest sites.</p> </blockquote

    Appendix A. Analytic estimators for rarefaction (interpolation) of Hill numbers of order q = 0, q = 1, and q = 2, given a reference sample.

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    Analytic estimators for rarefaction (interpolation) of Hill numbers of order q = 0, q = 1, and q = 2, given a reference sample

    Appendix A. Methods used to sample the ant community of La Selva Biological Station.

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    Methods used to sample the ant community of La Selva Biological Station

    Supplement 1. Data matrices and R source code of the software used in the paper.

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    <h2>File List</h2><div> <p><a href="RareNMtests.zip">RareNMtests.zip</a> (MD5: 4fd3828969780f87ee17ac2c5ce60640)</p> <p><a href="Example_of_negative_binomial_sampling_error.pdf">Example_of_negative_binomial_sampling_error.pdf</a> (MD5: 25738f0fe874ae2ea3ce38a7e931d7d5)</p> <p><a href="Benchmark_tests.R">Benchmark_tests.R</a> (MD5: 77b9f48830fbbc922c70ad9a782dd740)</p> <p><a href="Chiapas_dataset.csv">Chiapas_dataset.csv</a> (MD5: 1183bdcf5ae0a155731729fbc2648d0b)</p> </div><h2>Description</h2><div> <p>rareNMtests.zip-R package, with functions to implement ecological and biogeographical null model tests for comparing rarefaction curves. </p> <p>Example_of_negative_binomial_sampling_error.pdf – R code to exemplify how a negative binomial error is added to the abundance counts every time a sample is randomly drawn from the simulated assemblage in the <i>BiogTest</i> randomization algorithm. </p> <p>Benchmark_tests.R – R code used to run all benchmark tests.</p> <p>Chiapas_dataset.csv – Data set of 224 circular 0.1-ha plots from tropical montane cloud forests in three mountainous regions of southern Mexico.</p> </div

    Supplement 1. Inventory of species occurrences of ants at La Selva Biological Station in both viewable and downloadable form.

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    <h2>File List</h2><blockquote> <p><a href="ants.htm">ants.htm</a> --formatted for ease of viewing </p><p><a href="ants.txt">ants.txt </a> -- formatted for ease of downloading and reanalysis</p> </blockquote><h2>Description</h2>This file contains the complete species list for the ant fauna of La Selva Biological Station, with abundance data partitioned by the eight methods used in the inventory. There are 11 variables: Subfamily, Species, Barger, Berlese, Fogging, Longino, Malaise, Other, Thompson, Winkler, and Total. The first row of the data file contains column labels. Subfamily and Species are alpha character fields; the rest are integers. Species is the species name. For published species, the Species field contains genus, specific epithet, author, and year. For manuscript names, the author is followed by "ms" (manuscript names have no taxonomic standing and are not made taxonomically available by appearing here). Morphospecies codes are not followed by author or year. Barger, Berlese, Fogging, Longino, Malaise, Other, Thompson, and Winkler are the number of samples in which workers of a species occurred, for each sampling method, respectively. Total is the total number of samples in which workers of a species occurred. Species with a value of zero in the total column have been collected in this survey only as males or queens

    Geographic (A) and elevational (B) distribution of study sites.

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    <p>Geographic (A) and elevational (B) distribution of study sites.</p

    Ant abundance variables as a function of species richness among 41 Central American wet forest sites.

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    <p>Number of Species = number in 100 samples (taxon subset; see text). Symbols differentiate low and high elevation sites (elevation rounded to nearest 100 m). A. Log(Abundance) = average of 100 log[<i>n</i>+1] values where <i>n</i> = number of workers in 1 m<sup>2</sup>. B. Percent of samples containing the single most abundant species at each site. The curve shows the fitted quadratic model.</p

    Ant abundance and richness variables as a function of elevation among 41 Central American wet forest sites.

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    <p>A. Log(Abundance) = average of 100 log[<i>n</i>+1] values where <i>n</i> = number of workers in 1 m<sup>2</sup>. B. Percent of samples containing ants. C. Species Richness = number of species in 100 samples (taxon subset; see text). D. Abundance per species = Abundance as defined in panel A/Richness as defined in panel C. LOESS curves are included for A and C, using default parameters in R 3.0.2.</p
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