Statistics

Replication probabilities and p-rep

by Thom Baguley

Baguley, T. (2012). Replication probabilities and p-rep. Online Supplement 3 to Serious stats: A guide to advanced statistics for the behavioral sciences. Basingsoke: Palgrave. Retrieved from: http://www.palgrave.com/psychology/baguley/students/supplements.html

Companion blog:

http://seriousstats.wordpress.com/

Pseudo-R2 and related measures

by Thom Baguley

Baguley, T. (2012). Pseudo-R2 and related measures. Online Supplement 4 to Serious stats: A guide to advanced statistics for the behavioral sciences. Basingsoke: Palgrave. Retrieved from: http://www.palgrave.com/psychology/baguley/students/supplements.html

Companion blog:

http://seriousstats.wordpress.com/

Meta-analysis

by Thom Baguley

Baguley, T. (2012). Meta-analysis. Online Supplement 1 to Serious stats: A guide to advanced statistics for the behavioral sciences. Basingsoke: Palgrave. Retrieved from: http://www.palgrave.com/psychology/baguley/students/supplements.html

Companion blog:

http://seriousstats.wordpress.com/

Dealing with missing data

by Thom Baguley

Baguley, T. (2012). Meta-analysis. Online Supplement 2 to Serious stats: A guide to advanced statistics for the behavioral sciences. Basingsoke: Palgrave. Retrieved from: http://www.palgrave.com/psychology/baguley/students/supplements.html

Companion blog:

http://seriousstats.wordpress.com/

Loglinear models

by Thom Baguley

Baguley, T. (2012). Loglinear models. Online Supplement 4 to Serious stats: A guide to advanced statistics for the behavioral sciences. Basingsoke: Palgrave. Retrieved from: http://www.palgrave.com/psychology/baguley/students/supplements.html

Companion blog:

http://seriousstats.wordpress.com/

The Multivariate Watson Distribution: Maximum-Likelihood Estimation and other Aspects

by Suvrit Sra

A Bayesian mixture modeling approach for assessing the effects of correlated exposures in case-control studies

by Frank de Vocht

Frank de Vocht, Nicola Cherry, jon Wakefield

Predisposition to a disease is usually caused by cumulative effects of a multitude of exposures and lifestyle factors... more Predisposition to a disease is usually caused by cumulative effects of a multitude of exposures and lifestyle factors in combination with individual susceptibility. Failure to include all relevant variables may result in biased risk estimates and decreased power, whereas inclusion of all variables may lead to computational difficulties, especially when variables are correlated. We describe a Bayesian Mixture Model (BMM) incorporating a variable-selection prior and compared its performance with logistic multiple regression model (LM) in simulated case–control data with up to twenty exposures with varying prevalences and correlations. In addition, as a practical example we re analyzed data on male infertility and occupational exposures (Chaps-UK). BMM mean-squared errors (MSE) were smaller than of the LM, and were independent of the number of model parameters. BMM type I errors were minimal (less than or equal to1), whereas for the LM this increased with the number of parameters and correlation between exposures. The numbers of type II errors were comparable. Re analysis of Chaps-UK data demonstrated more convincingly than by using a LM that occupational exposure to glycol ethers and VOCs are likely risk factors for male infertility. This BMM proves an appealing alternative to standard logistic regression when dealing with the analysis of (correlated) exposures in case–control studies.

Jones, T. and Hillier, L. (2012). Sexuality education school policy for Australian GLBTIQ students. Sex Education, ifirst http://www.tandfonline.com/doi/abs/10.1080/14681811.2012.677211 Accessed 10.05.12.

by Tiffany Jones

Education is state-run in Australia, and within each of the eight states and territories there are both government and... more Education is state-run in Australia, and within each of the eight states and territories there are both government and independent schooling systems. This paper details the position of gay, lesbian, bisexual, transgender, intersex and queer (GLBTIQ) students within Australian education policy documents nationally, focusing on the three largest states and educational sectors in Australia. Survey data are used to report on the schooling experiences of over 3000 Australian GLBTIQ young people aged 14–21 years. Data from interviews with key policy informants identify both the obstacles to implementing policies, and how such obstacles have been overcome. Much official policy sees sexuality education as promoting inclusive, protective and affirming messages around GLBTIQ students. There exist significant correlations between policy and a variety of well-being and psycho-social outcomes for GLBTIQ students, including lowered incidence of homophobic abuse and suicide, and the creation of supportive school environments. Ideal policy visions are outlined, along with practical recommendations of relevance to a variety of stakeholders.

Assessment of patients' level of satisfaction with cleft treatment using the cleft evaluation profile

by Sabri Musa

OBJECTIVES: Determination of the psychosocial status and assessment of the level of satisfaction in Malaysian cleft... more OBJECTIVES: Determination of the psychosocial status and assessment of the level of satisfaction in Malaysian cleft palate patients and their parents. DESIGN: Cross-sectional study. PARTICIPANTS AND METHODS: Sixty cleft lip and palate patients (12 to 17 years of age) from Hospital Universiti Sains Malaysia and their parents were selected. The questionnaires used were the Child Interview Schedule, the Parents Interview Schedule, and the Cleft Evaluation Profile (CEP), administered via individual interviews. RESULTS: Patients were teased because of their clefts and felt their self-confidence was affected by the cleft condition. They were frequently teased about cleft-related features such as speech, teeth, and lip appearance. Parents also reported that their children were being teased because of their clefts and that their children's self-confidence was affected by the clefts. Both showed a significant level of satisfaction with the treatment provided by the cleft team. There was no significant difference between the responses of the patients and their parents. The features that were found to be most important for the patients and their parents, in decreasing order of priority, were teeth, nose, lips, and speech. CONCLUSIONS: Cleft lip and/or palate patients were teased because of their clefts, and it affected their self-confidence. The Cleft Evaluation Profile is a reliable and useful tool to assess patients' level of satisfaction with treatment received for cleft lip and/or palate and can identify the types of cleft-related features that are most important for the patients.

Morphological Variation in the Dusky Fruit Bat, Penthetor lucasi

by M.T. Abdullah, PhD

Dusky fruit bats morphology Dusky fruit bats morphology

A morphometric analysis of Rhinolophus species complex. 2008.

by M.T. Abdullah, PhD

DFA and CVA analyses were used to differentiate Malaysian Rhinolophus species complex. DFA and CVA analyses were used to differentiate Malaysian Rhinolophus species complex.

Phylogenetic Analysis of the Malaysian Rhinolopus and Hipposideros using mtDNA cytochrome b gene. PJTAS 34(2):281-294.

by M.T. Abdullah, PhD

Read Abdullah (2003)

The phylogenetic relationships among 10 species of Rhinolophus and 10 species of Hipposideros from Borneo and... more The phylogenetic relationships among 10 species of Rhinolophus and 10 species of Hipposideros from Borneo and Peninsular Malaysia were successfully inferred from the partial mitochondrial DNA (mtDNA) cytochrome (cyt) b sequences. Of the 413 nucleotide positions examined, there were 171 positions (41.4%), of which 164 positions (95.9%) were parsimoniously informative. The phylogenetic trees reconstruction using neighbour-joining (NJ), unweighted maximum parsimony (MP) and maximum likelihood (ML) methods suggest the monophyletic clustering of these families. The interspecific relationships within Rhinolophidae were completely resolved, while those within Hipposideridae were not fully resolved, as supported by the low bootstrap values. Overall, the phylogenetic analysis using partial mtDNA cyt b gene was useful to discriminate these complicated taxa and successfully revealed the misidentification of several specimens before due to their similar morphologies.

Keywords: Cytochrome b, Hipposideros, mitochondrial DNA, phylogenetics, Rhinolophus

Preliminary Morphometric Analysis of Aethalops aequalis. 2012

by M.T. Abdullah, PhD

Read Vijaya et al. (2012)

Aethalops aequalis was previously recorded as a subspecies of A. alecto in Borneo. They are difficult to distinguish... more Aethalops aequalis was previously recorded as a subspecies of A. alecto in Borneo. They are difficult to distinguish by external morphology as Malaysian Aethalops species are similar in size. The objective of this study was to characterize the morphological differences within the Malaysian A. aequalis populations based upon the evaluation of seven selected populations in Borneo. To this end, 11 skull and 11 dental characters were examined and analyzed using SPSS software. Six of these characters were found to be polymorphic across populations, with CM1 being the strongest character in most of the extracted functions followed by IM1, both of which are dental characters that relate to the lower jaw length. Character CM1 was generally shorter in most of the Southwest Sarawak populations compared to the Northeast Sarawak and Sabah populations. Aethalops aequalis from Sabah and Sarawak possessed a single skull morphotype and mountain isolation is, or has not yet been a sufficient barrier to lead to morphological divergence. The body and skull sizes were not affected by altitude or elevations, with A. aequalis possessing a single morphotype in Malaysian Borneo. In conclusion, little morphological variation was detected within and among the different geographical populations of A. aequalis in Sabah and Sarawak. The few differences found are likely to have arisen via natural selection driven adaptation to the new environment.

Morphometrical Variations of Malaysian Hipposideros Species. 2012

by M.T. Abdullah, PhD

Read Vijaya et al (2012)

A study on the morphometrical variations among four Malaysian Hipposideros species was conducted using voucher... more A study on the morphometrical variations among four Malaysian Hipposideros species was conducted using voucher specimens deposited in Universiti Malaysia Sarawak (UNIMAS) Zoological Museum and the Department of Widlife and National Park (DWNP) Kuala Lumpur. Twenty two individuals from four species of Hipposideros ater, H. bicolor, H. cineraceus and H. dyacorum were morphologically measured, in which a total of 27 linear parameters of body, skull and dentals of each were appropriately recorded. The statistical data were later subjected to discriminant function analysis (DFA) and canonical variate analysis (CVA) using SPSS version 15.0 and unweighted pair-group method average (UPGMA) cluster analysis using Minitab version 14.4. The highest character loadings observed in Function l, Function 2 and Function 3 were the forearm length (FA), the third digit second phalanx length (D3P2L) and the palatal length (PL) with standardised canonical discriminant function coefficient values of 21.910, 5.770 and 5.095, respectively. These three characters were identified as the best diagnostic features for discriminating these closely related species of Hipposideros. Hence, this morphometric approach could be a promising tool as an alternative to the molecular
DNA analysis for identification of Chiroptera species.

A Predictive Model to Differentiate the Fruit Bats Cynopterus brachyotis and C. cf. brachyotis Forest (Chiroptera: Pteropodidae) from Malaysia Using Multivariate Analysis. 2012

by M.T. Abdullah, PhD

Read also Abdullah (2003)

Field discrimination of Cynopterus brachyotis and C. cf. brachyotis Forest (as designated by Francis 2008) in southern... more Field discrimination of Cynopterus brachyotis and C. cf. brachyotis Forest (as designated by Francis 2008) in southern Thailand, Peninsular Malaysia, and Borneo is problematic. These 2 forms are sympatric in this region but are confined to different habitat types: C. brachyotis inhabits open habitats, orchards, and agricultural areas, while C. cf. brachyotis Forest is confined to primary and old secondary forests. In this study, we attempted to develop prediction models to identify both C. brachyotis and C. cf. brachyotis Forest in this region based on multivariate statistics. Two predictive models were generated using a canonical discriminant function, and it was found that 5 characters can be used to accurately identify museum vouchers of C. brachyotis and C. cf. brachyotis Forest. Four characters are needed for field identification of these 2 forms of Cynopterus in southern Thailand, Peninsular Malaysia, and Borneo. A review of the current taxonomy and classification indicated that there is a need to describe the 6 existing forms of the C. brachyotis complex in the Indo-Malayan region. This will aid conservationists, field ecologists, and taxonomists in taxonomic- and conservation-related decisions about this species complex.

Molecular phylogenetics and systematics of five genera of Malaysian murine rodents (Maxomys, Sundamys, Leopoldamys, Niviventer and Rattus) inferred from partial mitochondrial cytochrome c oxidase subunit I (COI) gene.

by M.T. Abdullah, PhD

Nur Aida Md Tamrin and M. T. Abdullah. 2011. Journal of Science and Technology in the Tropics 7: 75-86. (SCOPUS-indexed).

We genetically analysed 50 specimens of Murinae from Peninsular Malaysia and Sarawak, assigned to 12 species.... more We genetically analysed 50 specimens of Murinae from Peninsular Malaysia and Sarawak, assigned to 12 species. Phylogenetic analyses of partial mitochondrial cytochrome c oxidase subunit I (476 base pairs) using four methods, namely, neighbour-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian method resulted in similar statistically supported clades with minimal change in branching order. The analyses discovered that there were intermediate form of Maxomys species within M. whiteheadi and M. ochraceiventer populations. They display same external morphology as M. whiteheadi but genetically closer to M. ochraceiventer. Craniodental measurements showed significant differences between the three populations. Rattus and Sundamys appeared not fully resolved while Leopoldamys and Niviventer were steadily clustered. The intraspecific geographic variation in some species agrees with previous studies on the vicariance scenario and diversification of flora and fauna in Malaysia and Borneo.

Nur Aida Md Tamrin and M. T. Abdullah. 2011. Journal of Science and Technology in the Tropics 7: 75-86. (SCOPUS-indexed).

Biogeography of fruit bats in Southeast Asia. Les S. Hall, Gordon G. Grigg, Craig Moritz, Besar Ketol, Isa Sait, Wahab Marni and M.T. Abdullah.

by M.T. Abdullah, PhD

Should read Abdullah (2003).

We studied on the biogeography and diversity of fruit bats in Southeast Asia, from Borneo to Asian Mainland.The... more We studied on the biogeography and diversity of fruit bats in Southeast Asia, from Borneo to Asian Mainland.The patterns of distribution of distribution, diversity and abundance are related to ecological and biogeographical factors and possible past Pleistocene events.

Les S. Hall, Gordon G. Grigg, Craig Moritz, Besar Ketol, Isa Sait, Wahab Marni and M.T. Abdullah. 2004. Sarawak Museum Journal 81: 191-284.

A morphological analysis of Malaysian Kerivoula (Chiroptera, Vespertilionidae).

by M.T. Abdullah, PhD

Related study by Faisal Anwali Khan et al. 2010

Recent identification of new species within the genus Kerivoula from the Southeast Asian region has indicated that... more Recent identification of new species within the genus Kerivoula from the Southeast Asian region has indicated that this genus was understudied and currently underestimated in terms of its species diversity. Thus, this morphological study was carried out to record and analyse the morphological characters of available specimens of Malaysian Kerivoula from the Museum of Zoology, Universiti Malaysia Sarawak. Thirty-one external, skull and dental characters were taken and analysed using the multivariate analysis, dicriminant function analysis. As the result, six groupings of Kerivoula was identified, namely K. intermedia, K. hardwickii, K. pellucida, K. lenis and K. papillosa which were divided into two distinctive groupings of K. papillosa type large (K.
papillosa type L, hereafter) and K. papillosa type small (K. papillosa type S, hereafter). Variable dentary length was identified as the best predictor to characterize each group of Kerivoula. The
separation of the K. papillosa specimens into two separate morphotypes were characterised by their different sizes whereby the former group was larger in size compared to the latter. It is suggested that each represents an independent species even though both morphotypes occur sympatrically. The homogenising effect of the previous environmental events might have been the primary factor of the sympatric occurrence of both morphotypes. Nevertheless, further study regarding ecology, morphology and genetics should be carried out to provide a better insight regarding the cryptic population of K. papillosa in Borneo and Malaysia.

Hasan, N.H., Abdullah, M.T. 2011. Mammal Study 36: 87-97.

Assessing the probability of detection of horizontal gene transfer events in bacterial populations

by Jeffrey Townsend

How Likely is Simpson's Paradox?

by Marios Pavlides

The American Statistician. August 1, 2009, 63(3): 226-233. doi:10.1198/tast.2009.09007.

What proportion of all 2×2×2 contingency tables exhibit Simpson’s Paradox? An exact answer is obtained for large... more What proportion of all 2×2×2 contingency tables exhibit Simpson’s Paradox? An exact answer is obtained for large sample sizes and extended to 2×2×ℓ tables by Monte Carlo approximation. Conditional probabilities of the occurrence of Simpson’s Paradox are also derived. If the observed cell proportions satisfy a Simpson reversal, the posterior probability that the population parameters satisfy the same reversal is obtained. This Bayesian analysis is applied to the well-known Simpson reversal of the 1995–1997 batting averages of Derek Jeter and David Justice.