Showing papers by "Anne Chao published in 2006"

Abundance-based similarity indices and their estimation when there are unseen species in samples.

Abstract: A wide variety of similarity indices for comparing two assemblages based on species incidence (i.e., presence/absence) data have been proposed in the literature. These indices are generally based on three simple incidence counts: the number of species shared by two assemblages and the number of species unique to each of them. We provide a new probabilistic derivation for any incidence-based index that is symmetric (i.e., the index is not affected by the identity ordering of the two assemblages) and homogeneous (i.e., the index is unchanged if all counts are multiplied by a constant). The probabilistic approach is further extended to formulate abundance-based indices. Thus any symmetric and homogeneous incidence index can be easily modified to an abundance-type version. Applying the Laplace approximation formulas, we propose estimators that adjust for the effect of unseen shared species on our abundance-based indices. Simulation results show that the adjusted estimators significantly reduce the biases of the corresponding unadjusted ones when a substantial fraction of species is missing from samples. Data on successional vegetation in six tropical forests are used for illustration. Advantages and disadvantages of some commonly applied indices are briefly discussed.

A statistical approach to estimate soil ciliate diversity and distribution based on data from five continents

Abstract: A total of 359 soil samples collected from five continents (Africa, Asia, Australia, Europe and South America) were investigated for the presence/absence of soil ciliate species. Merging records by species identity, we have compiled a master data list (species by sample matrix). In the list, a total of 964 soil ciliate species (644 described and 320 undescribed) are recorded. The species distributions within the 359 samples and across the five continents are examined. The frequency distribution of the species over samples is used for global diversity estimation. A statistical ACE (abundance-based coverage estimation) model which links observed data to unseen species is applied to assess regional and global soil ciliate species richness. The model, whose reliability was tested by its power to predict the number of new species in additional samples from Africa, may resolve the controversial issue on global species diversity of soil ciliates. Although an accurate point estimate is not feasible due to severe undersampling, the statistical model enables us to obtain a minimum regional diversity and global species diversity. A consistent finding over all five continents is that at least half of the species diversity is still undiscovered. Our model also yields a global soil ciliate diversity of at least 1900 species, that is, doubles the number of currently known species, and thus diversity is relatively high. This is consistent with the finding of Foissner, who used a probability-based method. Soil ciliate distributions between continent pairs are analyzed by adjusted abundance-based similarity/overlap indices. These new indices account for the effect of unseen species and also reduce the bias generated by undersampling. The adjusted abundance-based Jaccard (or Sorensen) index shows that there is about 30% (18% for Sorensen) dis-similarity between any two continents, supporting the moderate endemicity model. The results are discussed with respect to protist species distribution, that is, whether they are cosmopolitan or of restricted distribution.

Application of laplace's boundary‐mode approximations to estimate species and shared species richness

Abstract: Summary The Laplace method for approximating integrals is a useful technique in a number of research fields. This paper shows that it also has interesting applications in biological and ecological statistical inferences. When sample abundance or replicated incidence (i.e., presence or absence) records of each species are available, the expected low-order frequency counts in heterogeneous communities can be approximated by the Laplace method when the species discovery or detection probabilities are bounded from below by a constant. The approximation formulae as applied to one community can then be used to derive estimators of species richness and to examine their performance. The approach is also extended to obtain simple and new estimators for the number of shared species in two communities. The replicated species incidence data recorded by competing teams of the Hong Kong Big Bird Race for the years 1999 and 2000 are used to estimate the number of resident birds in Hong Kong and to illustrate the method of estimation.

Analgesic use in intubated patients during acute resuscitation.

Abstract: Background: Pain relief can often be overlooked during a busy trauma resuscitation, especially in patients who are intubated. We sought to investigate qualitative and quantitative aspects of analgesic use in intubated patients during the acute phase of resuscitation. Methods: We evaluated a retrospective cohort of consecutive adult patients who were intubated during the acute trauma resuscitation (first 6 hours) from January 2001 to May 2002 at a Level I trauma center in the United States. Patient demographics, injuries, vital signs, medications, trauma bay procedures, and disposition status were analyzed. Analgesia was recorded as the type of analgesic, route of administration, elapsed time to receive the first analgesic, total dosage, and time intervals between two successive doses. Fisher's exact test, Χ 2 test, and ANOVA were used to analyze data. Results: A total of 120 patients were included. Sixty-one (51%) patients received analgesia during their stay in the emergency department. Using logistic regression analysis, patients who more likely to receive analgesia were those who did not require immediate surgical operation and were transferred to the intensive care unit (odds ratio [OR] = 3.91; 95% CI = 1.75-8.76) and those who were admitted during the hours of 8 AM to 6 PM (OR= 3.17; CI = 1.40-7.16). Among those patients receiving analgesia, 30 (25%) patients received analgesia within 30 minutes upon arrival. The mean time of receiving the first analgesia dose was 57 minutes. The average morphine equivalent dose given to the patients was 15.7 mg. The most frequently given single dose was 100 μg of intravenous fentanyl. Most of the analgesics (37%) were given between 30 to 60 minutes apart. Conclusion: Our findings suggest that patients who are intubated during the acute resuscitation probably receive inadequate analgesia. The inadequacy appears to be in the timing and repetition of administration, rather than the dose. Patients who were transferred early to the intensive care unit were more likely to receive analgesics.