# Miscellaneous Esoteric Statistical Scripts

## Documentation for package ‘MESS’ version 0.5.7

- DESCRIPTION file.

## Help Pages

A B C D E F G H I K L M N O P Q R S T U W

MESS-package | Collection of miscellaneous useful and semi-useful functions

## -- A --

adaptive.weights | Compute weights for use with adaptive lasso.
add_torows | Fast addition of vector to each row of matrix
age | Compute the age of a person from two dates.
auc | Compute the area under the curve for two vectors.

## -- B --

bdstat | Danish live births and deaths
bees | Bee data. Number of different types of bees caught.
bin | Fast binning of numeric vector into equidistant bins

## -- C --

categorize | A table function to use with magrittr pipes
clotting | Blood clotting for 158 rats
cmd | Correlation matrix distance
col.alpha | Add and set alpha channel for RGB color
col.shade | Shade an RGB color
col.tint | Tint an RGB color
colCumSum | Apply cumsum to each column of matrix
common.shared | Compute a common shared environment matrix
common.shared.pedigree | Compute a common shared environment matrix
common.shared.pedigreeList | Compute a common shared environment matrix
conditional_rowMeans | Form row means conditional on number of non-missing
cumsumbinning | Binning based on cumulative sum with reset above threshold

## -- D --

dCor | Fast distance correlation matrix
dCov | Fast distance covariance 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

## -- E --

earthquakes | Earthquakes in 2015
expand_table | Expand table or matrix to data frame
extended.shared | Compute a common shared environment matrix
extended.shared.pedigree | Compute a common shared environment matrix
extended.shared.pedigreeList | Compute a common shared environment matrix

## -- F --

fac2num | Convert factor to numeric vector
feature.test | Inference for features identified by the Lasso
filldown | Fill down NA with the last observed observation
founder.shared | Compute a common shared environment matrix
founder.shared.pedigree | Compute a common shared environment matrix
founder.shared.pedigreeList | Compute a common shared environment matrix

## -- G --

geekin | Fit a generalized estimating equation (GEE) model with fixed additive correlation structure
gkgamma | Goodman-Kruskal's gamma statistic for a two-dimensional table
greenland | Average yearly summer air temperature for Tasiilaq, Greenland

## -- H --

happiness | Happiness score and tax rates for 148 countries
ht | Show the head and tail of an object
hwe_frequencies | Fast estimation of allele and genotype frequencies under Hardy-Weinberg equilibrium

## -- I --

icecreamads | Ice cream consumption and advertising

## -- K --

ks_cumtest | Kolmogorov-Smirnov goodness of fit test for cumulative discrete data
kwdata | Non-parametric Kruskal Wallis data example

## -- L --

lifeexpect | Estimated life expectancy for Danish newborns
lower.tri.vector | Split Matrix by Clusters and Return Lower Triangular Parts as Vector

## -- M --

matched | Flu hospitalization
maximum_subarray | Fast computation of maximum sum subarray
MESS | Collection of miscellaneous useful and semi-useful functions
mfastLmCpp | Fast marginal simple regresion analyses
monte_carlo_chisq_test | Two-sided table test with fixed margins

## -- N --

nh4 | Ammonia nitrogen found in river

## -- O --

ordered.clusters | Check if unique elements of a vector appear in contiguous clusters

## -- P --

pairwise.cor.test | Pairwise Tests for Association/Correlation Between Paired Samples
pairwise_combination_indices | Compute all pairwise combinations of indices
pairwise_Schur_product | Compute Schur products (element-wise) of all pairwise combinations of columns in matrix
panel.hist | Panel plot of histogram and density curve
panel.r2 | Panel plot of R2 values for pairs
picea | Ozone concentration damage to picea spruce
plr | Fast computation of several simple linear regressions
plr.matrix | Fast computation of several simple linear regressions
plr.numeric | Fast computation of several simple linear regressions
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_prop_test | Power Calculations for Two-Sample Test for Proportions with unequal sample size
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
print.geekin | Fit a generalized estimating equation (GEE) model with fixed additive correlation structure

## -- Q --

qdiag | Fast extraction of matrix diagonal
QIC | Quasi Information Criterion
QIC.geeglm | Quasi Information Criterion
QIC.geekin | Quasi Information Criterion
QIC.ordgee | Quasi Information Criterion
qpcr | Gene expression from real-time quantitative PCR
quadform | Fast quadratic form computation

## -- R --

rainman | Perception of points in a swarm
repmat | Fast replication of a matrix
residualplot | Plots a standardized residual
residualplot.default | Plots a standardized residual
residualplot.glm | Plots a standardized residual
residualplot.lm | Plots a standardized residual
residual_plot | Plots a standardized residual
residual_plot.default | Plots a standardized residual
residual_plot.glm | Plots a standardized residual
residual_plot.lm | Plots a standardized residual
rmvt.pedigree | Simulate residual multivariate t-distributed data from a polygenic model
rmvtnorm.pedigree | Simulate residual multivariate Gaussian data from a polygenic model
rnorm_perfect | Simulate values from a perfect normal distribution
rootogram | Hanging rootogram for normal distribution
rootonorm | Hanging rootogram for normal distribution
round_percent | Round vector of number to percentages
rud | Simulate randomized urn design

## -- S --

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
smokehealth | Effect of smoking on self reported health
soccer | Danish national soccer players
superroot2 | Gene expression data from two-color dye-swap experiment

## -- T --

tracemp | Fast computation of trace of matrix product

## -- U --

usd | Unbiased standard deviation

## -- W --

wallyplot | Plots a Wally plot
wallyplot.default | Plots a Wally plot
wallyplot.lm | Plots a Wally plot
write.xml | Write a data frame in XML format