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Miscellaneous Esoteric Statistical Scripts - an R package
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DESCRIPTION Added a version of residual plot that uses ggplot2 instead of base R … Aug 16, 2019
NAMESPACE Added a version of residual plot that uses ggplot2 instead of base R … Aug 16, 2019
NEWS.md Removed dev code for bayes factors temporarily Aug 15, 2019
README.md Correlation variable selection Jan 28, 2019

README.md

MESS

Development version of the R package MESS (Miscellaneous Esoteric Statistical Scripts). This package contains a collection of various semi-useful functions that I have written and over the years.

There is no real overall theme to the functions in the package but I have tried to group the contents in the overview below.

To install the development version of MESS run the following command from within R (this requires that the devtools package is already installed on the system.)

devtools::install_github('ekstroem/MESS')

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Package overview

The list below is far from complete.

Statistical functions

  • cmd - Correlation matrix distance. A measure of the similarity of two matrices of equal dimensions.
  • drop1.geeglm - A drop1 extension for geeglm objects
  • gkgamma - compute Goodman-Kruskal's gamma statistic for a two-dimensional table of ordered categories
  • monte_carlo_chisq_test - Monte Carlo tests of 2x2 tables with fixed margin(s). Also works for r x c tables.
  • mfastLmCpp - fast computation of simple regression slopes for each predictor represented by a column in a matrix
  • ks_cumtest - One-sample Kolmogorov-Smirnov discrete cumulative comparison.
  • qic -
  • rud - Randomized treatments for an RCT based on an urn model
  • screenr -

Power calculations are - for better or worse - part of my job, and while I generally recommend researchers to simulate their design and test procedure, there are some benefits to be gained from asymptotic approximations in standard designs.

In time these will be moved to the Austin package, but for now they still reside in MESS.

  • power_prop_test extends the standard power.prop.test function to accommodate different group sizes.
  • power_t_test extends the standard power.t.test function to accommodate different group sizes and/or variances.
  • power_mcnemar_test - power calculations for exact and asymptotic McNemar test in a 2 by 2 table
  • power_binom_test - power calculations for exact test of a simple null hypothesis in a Bernoulli experiment

Graphical functions

  • col.shade
  • col.tint
  • col.alpha
  • rootonorm - plot Tukey's hanging root-o-gram for comparison of a histogram to a normal distribution.
  • wallyplot - plot a Wally plot for evaluation of a residual plot.

Utility functions

  • age - computes the age in years of a person from two date (birth date and current date)
  • auc - computes the area under the curve for two vectors (x-values and y-values). Can handle ranges and missing observations
  • categorize - produce tables using a data argument
  • colCumSum - fast computation of column cumulative sums for matrices
  • expand_table - Expand table or matrix to data frame where each observation in the table becomes a single observation in the data frame with corresponding information for each for each combination of the table dimensions.
  • fac2num - convert a factor to numerical. I keep forgetting the simple code for this so ended up writing a function that could do it.
  • filldown - Fill down missing values in a vector with the latest non-missing value. A last measurement carried forward function. And fast.
  • lower.tri.vector -
  • write.xml - save a data frame as an xml file

Computational functions

  • conditional_rowMeans - a function similar to rowMeans but it only returns the mean if a prespecified number of observations is available.
  • pairwise_Schur_product - compute Schur products (element-wise) of all pairwise combinations of columns in matrix
  • qdiag - fast extraction of matrix diagonal
  • quadform - fast computation of a quadratic form t(X) %*% M %*% X
  • repmat - fast replication of a matrix. Can be replicated both row-wise and columns-wise.
  • sinv - invert a symmetric positive-definite matrix. Some speedup can be gained if we know the matrix is symmetric
  • tracemp - fast computation of trace of matrix product trace(t(A) %*% B)

Datasets

  • bdstat - Monthly live births and deaths in Denmark from January 1901 to March 2013
  • earthquakes - Information on earthquakes worldwide in 2015 with a magnitude greater than 3 on the Richter scale.
  • happiness - Data on happiness, taxation rates, countris and continents
  • kwdata - example data to show that Krushkal-Wallis' test examines more than differences in medians.
  • soccer - List of players on the Danish national soccer team
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