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MKmisc - 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.

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7.75 score 12 stars 1 dependents 155 scripts 869 downloads

MKinfer - Inferential Statistics

Computation of various confidence intervals (Altman et al. (2000), ISBN:978-0-727-91375-3; Hedderich and Sachs (2018), ISBN:978-3-662-56657-2) including bootstrapped versions (Davison and Hinkley (1997), ISBN:978-0-511-80284-3) as well as Xiao (Xiao (2018), <doi:10.17654/TS054010021>), Hsu (Hedderich and Sachs (2018), ISBN:978-3-662-56657-2), permutation (Janssen (1997), <doi:10.1016/S0167-7152(97)00043-6>), bootstrap (Davison and Hinkley (1997), ISBN:978-0-511-80284-3), intersection-union (Sozu et al. (2015), ISBN:978-3-319-22005-5) and multiple imputation (Barnard and Rubin (1999), <doi:10.1093/biomet/86.4.948>) t-test; furthermore, computation of intersection-union z-test as well as multiple imputation Wilcoxon tests. Graphical visualizations: volcano plot, Bland-Altman plots (Bland and Altman (1986), <doi:10.1016/S0140-6736(86)90837-8>; Shieh (2018), <doi:10.1186/s12874-018-0505-y>), mean difference plot (Boehning et al. (2008), <doi:10.1177/0962280207081867>), plot of test statistic for permutation and bootstrap tests as well as objects of class htest.

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7.47 score 7 stars 4 dependents 118 scripts 991 downloads

MKdescr - Descriptive Statistics

Computation of standardized interquartile range (IQR), Huber-type skipped mean (Hampel (1985), <doi:10.2307/1268758>), robust coefficient of variation (CV) (Arachchige et al. (2020), <doi:10.1080/02664763.2020.1808599>), robust signal to noise ratio (SNR), z-score, standardized mean difference (SMD), z-factor (Zhang et al. (1999), <doi:10.1177/108705719900400206>) as well as functions that support graphical visualization such as boxplots based on quartiles (not hinges), negative logarithms and generalized logarithms for 'ggplot2' (Wickham (2016), ISBN:978-3-319-24277-4).

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6.81 score 4 stars 5 dependents 89 scripts 1.2k downloads

MKpower - Power Analysis and Sample Size Calculation

Power analysis and sample size calculation for Welch, Hsu (Hedderich and Sachs (2018), ISBN:978-3-662-56657-2) and Xiao (Xiao (2018), <doi:10.17654/TS054010021>) as well as permutation (Janssen (1997), <doi:10.1016/S0167-7152(97)00043-6>) and bootstrap (Davison and Hinkley (1997), ISBN:978-0-511-80284-3) t-tests including Monte-Carlo simulations of empirical power and type-I-error. Monte-Carlo simulations of empirical power and type-I-error for conditional two-sample tests. Power and sample size calculation for Wilcoxon rank sum and signed rank tests via Monte-Carlo simulations. Power and sample size required for the evaluation of a diagnostic test(-system) (Flahault et al. (2005), <doi:10.1016/j.jclinepi.2004.12.009>; Dobbin and Simon (2007), <doi:10.1093/biostatistics/kxj036>) as well as for a single proportion (Fleiss et al. (2003), ISBN:978-0-471-52629-2; Piegorsch (2004), <doi:10.1016/j.csda.2003.10.002>; Thulin (2014), <doi:10.1214/14-ejs909>), comparing two negative binomial rates (Zhu and Lakkis (2014), <doi:10.1002/sim.5947>), ANCOVA (Shieh (2020), <doi:10.1007/s11336-019-09692-3>), reference ranges (Jennen-Steinmetz and Wellek (2005), <doi:10.1002/sim.2177>), multiple primary endpoints (Sozu et al. (2015), ISBN:978-3-319-22005-5), and AUC (Hanley and McNeil (1982), <doi:10.1148/radiology.143.1.7063747>).

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6.27 score 10 stars 37 scripts 793 downloads

distrEx - Extensions of Package 'distr'

Extends package 'distr' by functionals, distances, and conditional distributions.

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6.25 score 16 dependents 127 scripts 3.6k downloads

RandVar - Implementation of Random Variables

Implements random variables by means of S4 classes and methods.

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6.07 score 6 dependents 76 scripts 2.1k downloads

MKomics - Omics Data Analysis

Similarity plots based on correlation and median absolute deviation (MAD); adjusting colors for heatmaps; aggregate technical replicates; calculate pairwise fold-changes and log fold-changes; compute one- and two-way ANOVA; simplified interface to package 'limma' (Ritchie et al. (2015), <doi:10.1093/nar/gkv007> ) for moderated t-test and one-way ANOVA; Hamming and Levenshtein (edit) distance of strings as well as optimal alignment scores for global (Needleman-Wunsch) and local (Smith-Waterman) alignments with constant gap penalties (Merkl and Waack (2009), ISBN:978-3-527-32594-8).

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5.18 score 3 stars 51 scripts 318 downloads

RobAStBase - Robust Asymptotic Statistics

Base S4-classes and functions for robust asymptotic statistics.

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4.93 score 3 dependents 69 scripts 3.5k downloads

ROptEst - Optimally Robust Estimation

R infrastructure for optimally robust estimation in general smoothly parameterized models using S4 classes and methods as described Kohl, M., Ruckdeschel, P., and Rieder, H. (2010), <doi:10.1007/s10260-010-0133-0>, and in Rieder, H., Kohl, M., and Ruckdeschel, P. (2008), <doi:10.1007/s10260-007-0047-7>.

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4.43 score 1 dependents 71 scripts 3.2k downloads

MKclass - Statistical Classification

Performance measures and scores for statistical classification such as accuracy, sensitivity, specificity, recall, similarity coefficients, AUC, GINI index, Brier score and many more. Calculation of optimal cut-offs and decision stumps (Iba and Langley (1991), <doi:10.1016/B978-1-55860-247-2.50035-8>) for all implemented performance measures. Hosmer-Lemeshow goodness of fit tests (Lemeshow and Hosmer (1982), <doi:10.1093/oxfordjournals.aje.a113284>; Hosmer et al (1997), <doi:10.1002/(SICI)1097-0258(19970515)16:9%3C965::AID-SIM509%3E3.0.CO;2-O>). Statistical and epidemiological risk measures such as relative risk, odds ratio, number needed to treat (Porta (2014), <doi:10.1093%2Facref%2F9780199976720.001.0001>).

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4.30 score 2 stars 20 scripts 201 downloads

RobLox - Optimally Robust Influence Curves and Estimators for Location and Scale

Functions for the determination of optimally robust influence curves and estimators in case of normal location and/or scale (see Chapter 8 in Kohl (2005) <https://epub.uni-bayreuth.de/839/2/DissMKohl.pdf>).

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3.98 score 69 scripts 3.5k downloads

RFLPtools - Tools to Analyse RFLP Data

Provides functions to analyse DNA fragment samples (i.e. derived from RFLP-analysis) and standalone BLAST report files (i.e. DNA sequence analysis).

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2.85 score 71 scripts 235 downloads