Jackknife Estimator of Species Richness with S-PLUS

An estimate of the number of species, S , usually called species richness by ecologists, in an area is one of the basic statistics used to ascertain biological diversity. Traditionally ecologists have used the number of species observed in a sample, S_0 , to estimate S , realizing that S_0 is a lower bound for S . One alternative to S_0 is to use a nonparametric procedure such as jackknife resampling. For species richness, a closed form of the jackknife estimator is available. Typically statistical software contains only the traditional iterative form of the jackknife estimator. The purpose of this article is to propose an S-PLUS function for calculating the noniterative first order jackknife estimator of species richness and some associated plots and statistics.

Jackknife Estimator of Species Richness with S-PLUS

An estimate of the number of species, S , usually called species richness by ecologists, in an area is one of the basic statistics used to ascertain biological diversity. Traditionally ecologists have used the number of species observed in a sample, S0 , to estimate S , realizing that S0 is a lower bound for S . One alternative to S0 is to use a nonparametric procedure such as jackknife resampling. For species richness, a closed form of the jackknife estimator is available. Typically statistical software contains only the traditional iterative form of the jackknife estimator. The purpose of this article is to propose an S-PLUS function for calculating the noniterative first order jackknife estimator of species richness and some associated plots and statistics

BOOTSTRAP CONFIDENCE INTERVALS FROM ADAPTIVE SAMPLING OF AN INSECT POPULATION

We construct 90% normal, percentile, and bias-corrected and accelerated confidence intervals using a finite population bootstrapping algorithm based on adaptive sampling in an agroecosystem. We evaluate the interval estimates based on sampling simulations of a spatially arranged population of plots that contain counts of beet webworms and based on an adaptive condition that generates small networks. The sampling distributions of the original sample estimates and of the bootstrap estimates were generally similar and symmetric. The simulation coverages were from 84% to 90% and similar under any of the sample sizes and any of the three confidence interval types. This study also serves as an example of how adaptive sampling may be used to estimate population characteristics of insects in agroecosystems

Nonparametric estimation of stage transition time from stage frequency data

LD2668 .R4 STAT 1987 P66Master of ScienceStatistic

VALIDITY OF 95% t-CONFIDENCE INTERVALS UNDER SOME TRANSECT SAMPLING STRATEGIES

Soil pH data were used to assess the capture rates of 95 % t-confidence intervals based on five different transect sampling strategies. Two different sampling methods were considered, deterministic and two-stage simple random sampling . The data used were pH readings at 15 and 30 centimeter depths from two local agricultural fields in the Manhattan, Kansas area. The data provided three distinct populations with three different distributions - skewed left, symmetric, and bimodal. The total number of transects randomly sampled was 2, 5, and 10. The total number of points sampled along each transect was 2, 7 and 14. The 95% t-confidence intervals were simulated 5000 times using five different transect sampling strategies, and the capture rates of the population mean were recorded. Box plots of the capture rates for the five transect sampling strategies were constructed and compared. In most cases the deterministic sampling method had capture rates that underestimated the 95 % confidence level, whereas the two-stage sampling strategies produced capture rates which were conservative or closer to the 95 % confidence level. The variances of the capture rates for the two-stage sampling strategies were relatively small in comparison to the deterministic sampling strategies. In conclusion, the two-stage simple random sampling method along with the Satterthwaite degrees of freedom are recommended when using transect sampling

CONDITIONING PLOTS AND DESIGNED EXPERIMENTS

Conditioning plots (coplots) are useful graphics for displaying values of response variables conditional on the values of given (conditioning) variables. We present a principles guide for construction of coplots when the data or statistics come from studies based on designed experiments, and illustrate the usefulness of these coplots in interpreting results. We have found coplots to be useful in our statistical consulting work, and illustrate our approach so that others may find them useful. Coplots in traditional and in trellis displays are provided

PROSESS: a protein structure evaluation suite and server

PROSESS (PROtein Structure Evaluation Suite and Server) is a web server designed to evaluate and validate protein structures generated by X-ray crystallography, NMR spectroscopy or computational modeling. While many structure evaluation packages have been developed over the past 20 years, PROSESS is unique in its comprehensiveness, its capacity to evaluate X-ray, NMR and predicted structures as well as its ability to evaluate a variety of experimental NMR data. PROSESS integrates a variety of previously developed, well-known and thoroughly tested methods to evaluate both global and residue specific: (i) covalent and geometric quality; (ii) non-bonded/packing quality; (iii) torsion angle quality; (iv) chemical shift quality and (v) NOE quality. In particular, PROSESS uses VADAR for coordinate, packing, H-bond, secondary structure and geometric analysis, GeNMR for calculating folding, threading and solvent energetics, ShiftX for calculating chemical shift correlations, RCI for correlating structure mobility to chemical shift and PREDITOR for calculating torsion angle-chemical shifts agreement. PROSESS also incorporates several other programs including MolProbity to assess atomic clashes, Xplor-NIH to identify and quantify NOE restraint violations and NAMD to assess structure energetics. PROSESS produces detailed tables, explanations, structural images and graphs that summarize the results and compare them to values observed in high-quality or high-resolution protein structures. Using a simplified red–amber–green coloring scheme PROSESS also alerts users about both general and residue-specific structural problems. PROSESS is intended to serve as a tool that can be used by structure biologists as well as database curators to assess and validate newly determined protein structures. PROSESS is freely available at http://www.prosess.ca

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Influence of Prairie Dogs on Vegetation in Kansas Shortgrass Prairie

We quantified plant species richness, frequency, percent cover and percent bare ground on black-tailed prairie dog colonies and non-colonized areas in southwest Kansas in 1996 and 1997. In 1996 field sampling occurred after 12 months of below-average precipitation, while field sampling in 1997 occurred after 10 months of above-average precipitation. In 1996 prairie dog colonies were characterized by lower percentages of grass cover and higher percentages of forb cover than non-colonized sites, but there was no difference in percent bare ground. In 1997 percent grass cover, forb cover and bare ground was similar for prairie dog colonies and non-colonized areas. A preliminary analysis indicates that plant species richness of prairie dog colonies was similar to that of non-colonized areas. In 1996 four perennial grasses, two perennial forbs and one annual forb differed in frequency among the treatments. In 1997 seven perennial grasses, seven perennial forbs, six annual or biennial forbs and one annual grass differed in frequency among the treatments