In ekstroem/MESS: Miscellaneous Esoteric Statistical Scripts

The MESS package contains a mix of functions.

There is no real connection between the function except they have all been created by the same person, and they range from computational functions, graphical functions, statistical analysis functions, utility functions, and function that extend other packages.

This vignette gives an overview of the package and shows some examples.

Overview

Statistical analysis

--------------------- ---------------------------------------------- QIC.geeglm Quasi Information Criterion adaptive.weights Compute weights for use with adaptive lasso. common.shared Compute a common shared environment matrix drop1.geeglm Drop All Possible Single Terms to a geeglm Model Using Wald or Score Test drop1.geem Drop All Possible Single Terms to a geem Model Using Wald or Score Test extended.shared Compute a common shared environment matrix feature.test Inference for features identified by the Lasso geekin Fit a generalized estimating equation (GEE) model with fixed additive correlation structure gkgamma Goodman-Kruskal's gamma statistic for a two-dimensional table mfastLmCpp Fast marginal simple regresion analyses onemargintest Two-sided table test with fixed margins power_binom_test Power Calculations for Exact Test of a simple null hypothesis in a Bernoulli experiment power_mcnemar_test Power Calculations for Exact and Asymptotic McNemar Test in a 2 by 2 table power_t_test Power calculations for one and two sample t tests with unequal sample size prepost.test Pretest-posttest RCT for quantitative observations with possible missing values --------------------- ----------------------------------------------

Utility functions

--------------------- ---------------------------------------------- age Compute the age of a person from two dates. auc Compute the area under the curve for two vectors. categorize A table function to use with magrittr pipes cmd Correlation matrix distance expand_table Expand table or matrix to data frame fac2num Convert factor to numeric vector filldown Fill down NA with the last observed observation ht Show the head and tail of an object lower.tri.vector Split Matrix by Clusters and Return Lower Triangular Parts as Vector ordered.clusters Check if unique elements of a vector appear in contiguous clusters qdiag Fast extraction of matrix diagonal qpcr Gene expression from real-time quantitative PCR quadform Fast quadratic form computation repmat Fast replication of a matrix rmvt.pedigree Simulate residual multivariate t-distributed data from a polygenic model rmvtnorm.pedigree Simulate residual multivariate Gaussian data from a polygenic model round_percent Round vector of number to percentages scorefct Internal functions for the MESS package screen_variables Screen variable before penalized regression segregate.genes Segregate genes through a pedigree sinv Invert a symmetric positive-definite matrix tracemp Fast computation of trace of matrix product write.xml Write a data frame in XML format --------------------- ----------------------------------------------

Graphics

--------------------- ---------------------------------------------- col.alpha Add and set alpha channel for RGB color col.shade Shade an RGB color col.tint Tint an RGB color panel.hist Panel plot of histogram and density curve panel.r2 Panel plot of R2 values for pairs residualplot.default Plots a standardaized residual rootonorm Hanging rootogram for normal distribution wallyplot.default Plots a Wally plot --------------------- ----------------------------------------------

Datasets

--------------------- ---------------------------------------------- bdstat Danish live births and deaths bees Bee data. Number of different types of bees caught. clotting Blood clotting for 158 rats earthquakes Earthquakes in 2015 greenland Average yearly summer air temperature for Tasiilaq, Greenland happiness Happiness score and tax rates for 148 countries icecreamads Ice cream consumption and advertising kwdata Non-parametric Kruskal Wallis data example lifeexpect Estimated life expectancy for Danish newborns matched Flu hospitalization nh4 Ammonia nitrogen found in river picea Ozone concentration damage to picea spruce qpcr Gene expression from real-time quantitative PCR rainman Perception of points in a swarm smokehealth Effect of smoking on self reported health soccer Danish national soccer players superroot2 Gene expression data from two-color dye-swap experiment --------------------- ----------------------------------------------

ekstroem/MESS documentation built on July 28, 2023, 4:02 a.m.