Miscellaneous Functions from M. Kohl

Contains several functions for statistical data analysis; e.g. for sample size and power calculations, computation of confidence intervals and tests, and generation of similarity matrices.


News

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NEWS to package MKmisc

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Version 1.3

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  • added function normDiffCI to compute confidence intervals for the difference of two means.
  • extended the print function for confidence intervals. Now, optional additional information is also printed.
  • added function hsu.t.test to compute the Hsu two-sample t-test.
  • added function power.hsu.t.test to compute power of the Hsu two-sample t-test, or determine parameters to obtain a target power.
  • added function mod.t.test to compute moderated t-test based on package limma
  • added function mod.oneway.test to compute moderated 1-way ANOVA based on package limma
  • added function pairwise.mod.t.test to compute pairwise moderated t-tests.

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Version 1.2

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  • added as.numeric in the computation of AUC to avoid integer overflow as reported by Mike Harwood
  • added function power.welch.t.test to compute power of the Welch two-sample t-test, or determine parameters to obtain a target power.

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Version 1.1

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  • added new function glog, glog10, glog2, inv.glog, inv.glog10, inv.glog2 to compute the generalized logarithm and its inverse
  • added new function melt.long to transform a data.frame form wide to long form
  • added new functions to scale axes in ggplot2 plots by glog and neglog
  • extended function perfMeasures by argument cutoff, predictions are no longer restricted to [0,1]
  • added new function optCutoff to compute optimal cutoff for various performance measures for binary classification

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Version 1.0

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  • added a vignette

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Version 0.999

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  • added new function perfMeasures to compute various performance measures for binary classification
  • added new function thyroid for plotting TSH, fT3, fT4
  • removed upper bound n = 100 in modified wilson confidence interval (thanks to Andri Signorell for detecting this inconsistency)

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Version 0.998

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  • extended function normCI - now mean or sd can be known
  • added print function for confidence intervals

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Version 0.997

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  • added function risks to compute RR, OR, etc.
  • added function rrCI to compute an approximate confidence interval for the relative risk (RR).

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Version 0.996

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  • extended function or2rr
  • added function normCI for computing confidence intervals for mean and sd of a normal distribution

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Version 0.995

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  • added function sIQR for computing standardized IQR

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Version 0.994

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  • added function power.nb.test for computing sample size or power for comparing two negative binomial rates

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Version 0.993

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  • added function madCI for computing confidence intervals for MAD

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Version 0.992

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  • corrected bug in quantileCI reported by Rogier Donders (estimate always median independent of specified prob)

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Version 0.991

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  • added function simCorVars to simulate a pair of variables with a prespecified correlation

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Version 0.99

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  • added function to compute t-test based on multiple imputed datasets
  • moved packages stats and graphics from Depends to Imports and added respective imports directives to NAMESPACE file
  • added grDevices to Imports
  • use of importFrom in NAMESPACE file except for package stats
  • added Amelia to Suggests

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Version 0.98

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  • added function predValues to compute PPV and NPV
  • added function ssize.pcc to calculate sample sizes for developing classifiers using high-dimensional data
  • provide a more detailed description of the package in the DESCRIPTION file

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Version 0.97

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  • corrected copy and paste error in documentation of quantileCI.
  • added function or2rr to transform OR to RR.
  • CITATION file now uses bibentry
  • added argument minLength to quantileCI and medianCI

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Version 0.96

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  • corrected a bug identified by Steven Kern in the modified Jeffreys interval for binomial proportions.

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Version 0.95

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  • added functions quantileCI and medianCI to compute confidence intervals for quantiles
  • moved RColorBrewer and robustbase from Depends to Imports
  • corrected some minor bugs in traceBack and corDist

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Version 0.94

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  • added function stringSim to compute optimal global and local alignment scores (Needleman-Wunsch and Smith-Waterman algorithm with constant gap penalties)
  • added function traceBack to compute an optimal alignment based on the trace back matrix included in objects of class stringDist or stringSim
  • corrected bug in function stringDist: wrong initialisation for Levenshtein distance

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Version 0.93

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  • added function power.diagnostic.test to compute power resp. sample size for a diagnostic test by approach of Flahault et al. (2005) incorporating the correction of Chu and Cole (2007)

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Version 0.92

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  • added an additional Parameter to function AUC, which can be used to suppress switching of the AUC values from x to 1-x if x < 0.5 (a request by Yuta Tanoue)

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Version 0.91

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  • added function stringDist to compute Hamming and Levenshtein distance of two strings (sequences)

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Version 0.9

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  • extended simPlot and corPlot by argument "lab.both.axes" which also to add labels on both axes (a request by Sunghee OH).
  • example to HLgof.test was wrong as pointed out by Dan O'Shea. This was corrected and the function slightly modified (intercept is no longer added inside of HLgof.test for the le Cessie-van Houwelingen-Copas-Hosmer unweighted sum of squares test for global goodness of fit)

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Version 0.8

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  • added function simPlot for plotting similarity matrices (a slight modification of function corPlot)

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Version 0.7

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  • added NEWS file
  • modified function oneWayAnova: instead of lm and anova now oneway.test is used allowing for unequal variances
  • added functions AUC, pairwise.auc and AUC.test as well as pairwise.fun and HLgof.test
  • added NAMESPACE file

Reference manual

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install.packages("MKmisc")

1.5 by Matthias Kohl, 2 months ago


http://www.stamats.de/


Browse source code at https://github.com/cran/MKmisc


Authors: Matthias Kohl [aut, cre]


Documentation:   PDF Manual  


LGPL-3 license


Imports stats, utils, graphics, grDevices, RColorBrewer, robustbase, ggplot2, scales, limma

Suggests gplots, Amelia, knitr, rmarkdown, exactRankTests, foreach, parallel, doParallel


Suggested by RFLPtools.


See at CRAN