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Estimate. S: Biodiversity Estimation. Estimate. S 9. 1. User's Guide. Last Revised June 1.
Copyright 2. 01. 3 by Robert K. Colwell, Department of Ecology & Evolutionary Biology, University of Connecticut, Storrs, CT 0. USAWebsite: http: //purl.
Table of Contents. Introduction Samples and Species, Abundance and Incidence Single and Multiple Datasets The Fundamental Design of Estimate. S: Diversity The Fundamental Design of Estimate. S: Shared Species and Similarity.
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Preparing a Data Input File for Estimate. S Estimate. S Filetypes: The Load Data Input Screen The Four Input Filetypes Filetype 1. Sample- based incidence or abundance data: One set of replicated sampling units (classic Estimate. S input) Filetype 2. Individual- based abundance data: One individual- based abundance sample Filetype 4.
Species (rows) by Samples(columns) Format 2. Samples (rows) by Species (columns) Format 3. Species, Sample, Abundance triplets Format 4. Sample, Species. , Abundance triplets Format 5. Estimate. S computes a variety of biodiversity statistics, including rarefaction and extrapolation, estimators of species richness, diversity indices, Hill numbers, and similarity measures. Car Insurance 17 Year Old Male Ontario read more. Some estimators and indices require countsof individuals (or gene copies) for each species in single sample, or in each of a set of samples. Such data are called individual- based abundance data.
When a dataset consists of species abundance data for a set of related samples (sample- based abundance data), the dataset can be treated, sample- by- sample, as individual- based abundance data, or converted to sample- based incidence data. When comparing the biotic (species or higher taxa) similarity of two or more localities (or habitats, treatments, seasons, etc.), you can do so either using abundance data or by using summed incidence data (frequencies of occurence, pooled among samples) for each or two or more sample sets.
Each dataset may consist of either individual- based abundance data (a single sample of abundance data) or sample- based incidence or abundance data (several related samples of incidence or abundance data). More information here. The Fundamental Design of Estimate. S: Diversity Estimate. S helps you account for the inevitable confounding effects of sample size (or sampling effort) on biodiversity data by several different strategies. Consider a reference sample: either a single, individual- based abundance sample of n individuals, or a set of t related sampling units for which incidence data have been recorded.
Based on a reference sample (as defined above), Estimate. S computes several widely- used statistical estimators of asymptotic species richness, the true number of species in the assemblage sampled. These estimators aim to reduce the effect of undersampling, which inevitably biases the observed species count. More information here. Rarefaction. Rarefaction is a resampling framework that selects, at random, 1, 2, .., n individuals or i= 1, 2, .., t sampling units (generally without replacement) until all individuals or sampling units in the reference sample have been accumulated. For each level of rarefaction, Estimate.
S computes a large number of biodiversity statistics. For species richness, exact analytical methods are used to compute the expected number of species (and its unconditional standard deviation) for each level of accumulation.
For other diversity measures, Estimate. S resamples individuals or sampling units stochastically, based on a random- number- driven algorithm. The resampling process is repeated many times, and the means (and conditional standard deviations) among resamples for each level of accumulation are reported.
The effects of differences in sample size on diversity statistics for two or more samples can usually be substantially reduced by comparing a the same level of species accumulation. More information here.
Extrapolation. Rarefaction, in effect, represents an interpolation between the value of a diversity measure assessed for the reference sample and zero (for individual- based abundance data) or the diversity of a typical single sampling unit (for sample- based indidence data). For species richness (only) Estimate.
Low- Fat Dietary Pattern and Risk of Cardiovascular Disease. Howard, Ph. D, Med. Star Research Institute, 6. New Hampshire Ave, Suite 2. Hyattsville, MD 2.
Author Contributions: Dr Howard had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis. Study concept and design: Van Horn, Manson, Stefanick, Lewis, Margolis, Prentice, Robbins, Rossouw, Snetselaar, Stevens, Tinker, Trevisan, Anderson, Bassford, Black, Greenland, Hays. Acquisition of data: Howard, Van Horn, Hsia, Manson, Stefanick, Wassertheil- Smoller, La.
Croix, Langer, Lasser, Lewis, Limacher, Margolis, Mysiw, Ockene, Parker, Perri, Phillips, Prentice, Robbins, Sarto, Schatz, Snetselaar, Stevens, Tinker, Trevisan, Assaf, Bassford, Beresford, Black, Brunner, Brzyski, Caan, Chlebowski, Gass, Granek, Greenland, Hays, Heber, Heiss, Hendrix, Hubbell, Johnson, Kotchen. Analysis and interpretation of data: Howard, Van Horn, Hsia, Manson, Stefanick, Wassertheil- Smoller, Kuller, La. Croix, Lewis, Limacher, Mysiw, Perri, Prentice, Rossouw, Snetselaar, Tinker, Trevisan, Vitolins, Anderson, Black, Chlebowski, Greenland. Drafting of the manuscript: Howard, Van Horn, Stefanick, Rossouw, Trevisan, Vitolins.
Critical revision of the manuscript for important intellectual content: Howard, Van Horn, Hsia, Manson, Stefanick, Wassertheil- Smoller, Kuller, La. Croix, Langer, Lasser, Lewis, Limacher, Margolis, Mysiw, Ockene, Parker, Perri, Phillips, Prentice, Robbins, Rossouw, Sarto, Schatz, Snetselaar, Stevens, Tinker, Trevisan, Anderson, Assaf, Bassford, Beresford, Black, Brunner, Brzyski, Caan, Chlebowski, Gass, Granek, Greenland, Hays, Heber, Heiss, Hendrix, Hubbell, Johnson, Kotchen. Statistical analysis: Van Horn, Kuller, La. Croix, Prentice. Obtained funding: Howard, Van Horn, Manson, Stefanick, Wassertheil- Smoller, Langer, Lewis, Ockene, Prentice, Robbins, Rossouw, Snetselaar, Stevens, Trevisan, Assaf, Beresford, Black, Brunner, Greenland, Heiss, Hendrix, Hubbell.
Administrative, technical, or material support: Van Horn, Hsia, Manson, Stefanick, La. Croix, Langer, Lasser, Lewis, Limacher, Margolis, Mysiw, Ockene, Perri, Phillips, Prentice, Robbins, Rossouw, Snetselaar, Stevens, Trevisan, Anderson, Assaf, Bassford, Black, Brunner, Brzyski, Granek, Hays, Heber, Heiss, Hendrix, Hubbell, Johnson, Kotchen. Study supervision: Howard, Van Horn, Manson, Stefanick, Wassertheil- Smoller, La. Croix, Limacher, Ockene, Parker, Perri, Prentice, Robbins, Stevens, Trevisan, Anderson, Assaf, Beresford, Black, Brunner, Caan, Chlebowski, Hays, Heiss, Hendrix, Johnson. Critical input to representation of the intervention program: Tinker. Financial Disclosures: Dr Howard has served on the advisory boards of Merck, Shering Plough, the Egg Nutrition Council, and General Mills, and has received research support from Merck and Pfizer. Dr Assaf is an employee of Pfizer.
Dr Black has received research grants from Pfizer and Astra. Zeneca, was on the speaker's bureaus for Pfizer, Novartis, Sanofi- Aventis, Bristol- Myers Squibb, Searle, Pharmacia, and Boehringer, and served as a consultant or on an advisory board for Myogen, Merck Sharp and Dohme, Novartis, Mylan- Bertek, Pfizer, Bristol- Myers Squibb, and Sanofi- Aventis. No other disclosures were reported. Funding/Support: Funding was provided by the National Heart, Lung, and Blood Institute, US Department of Health and Human Services. While the WHI hormone therapy and calcium- vitamin D trials received study medications from pharmaceutical companies, the diet trial received no outside nonfederal support. Role of the Sponsor: The National Heart, Lung, and Blood Institute has representation on the WHI Steering Committee, which governed the design and conduct of the study, the interpretation of the data, and preparation and approval of manuscripts.
The National Heart, Lung, and Blood Institute Project Office reviewed the manuscript. Independent Statistical Analyses: All statistical analyses for the study were performed by statisticians at the Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, under the direction of the principal investigator of the Coordinating Center, Dr Prentice. WHI Investigators: For a complete list of the WHI investigators, see the companion article in this issue, .
Acknowledgment: We thank Mary Pettinger, Fred Hutchinson Cancer Research Center, for data analysis and Rachel Schaperow, Med. Star Research Institute, for editorial assistance.