gamclass - Functions and Data for a Course on Modern Regression and Classification

Functions and data are provided that support a course that emphasizes statistical issues of inference and generalizability. The functions are designed to make it straightforward to illustrate the use of cross-validation, the training/test approach, simulation, and model-based estimates of accuracy. Methods considered are Generalized Additive Modeling, Linear and Quadratic Discriminant Analysis, Tree-based methods, and Random Forests.

Last updated 1 years ago

4.82 score 44 scripts 314 downloads

hwde - Models and Tests for Departure from Hardy-Weinberg Equilibrium and Independence Between Loci

Fits models for genotypic disequilibria, as described in Huttley and Wilson (2000) <doi:10.1093/genetics/156.4.2127>, Weir (1996) and Weir and Wilson (1986). Contrast terms are available that account for first order interactions between loci. Also implements, for a single locus in a single population, a conditional exact test for Hardy-Weinberg equilibrium.

Last updated 1 years ago

3.74 score 11 scripts 281 downloads

qra - Quantal Response Analysis for Dose-Mortality Data

Functions are provided that implement the use of the Fieller's formula methodology, for calculating a confidence interval for a ratio of (commonly, correlated) means. See Fieller (1954) <doi:10.1111/j.2517-6161.1954.tb00159.x>. Here, the application of primary interest is to studies of insect mortality response to increasing doses of a fumigant, or, e.g., to time in coolstorage. The formula is used to calculate a confidence interval for the dose or time required to achieve a specified mortality proportion, commonly 0.5 or 0.99. Vignettes demonstrate link functions that may be considered, checks on fitted models, and alternative choices of error family. Note in particular the betabinomial error family. See also Maindonald, Waddell, and Petry (2001) <doi:10.1016/S0925-5214(01)00082-5>.

Last updated 1 years ago

3.48 score 1 scripts 264 downloads

hddplot - Use Known Groups in High-Dimensional Data to Derive Scores for Plots

Cross-validated linear discriminant calculations determine the optimum number of features. Test and training scores from successive cross-validation steps determine, via a principal components calculation, a low-dimensional global space onto which test scores are projected, in order to plot them. Further functions are included that are intended for didactic use. The package implements, and extends, methods described in J.H. Maindonald and C.J. Burden (2005) <https://journal.austms.org.au/V46/CTAC2004/Main/home.html>.

Last updated 1 years ago

3.00 score 10 scripts 251 downloads

tTOlr - Likelihood Ratio Statistics for One or Two Sample T-Tests

Likelihood ratio and maximum likelihood statistics are provided that can be used as alternatives to p-values Colquhoun (2017) <doi:10.1098/rsos.171085>. Arguments can be either p-values or t-statistics. together with degrees of freedom. For the function 'tTOlr', the argument 'twoSided' has the default 'twoSided = TRUE'.

Last updated 1 years ago

2.30 score 2 scripts 162 downloads

DAAGbio - Data Sets and Functions, for Demonstrations with Expression Arrays and Gene Sequences

Data sets and functions, for the display of gene expression array (microarray) data, and for demonstrations with such data.

Last updated 1 years ago

2.15 score 14 scripts 349 downloads