{
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  "Date": "2026-05-07",
  "Title": "Miscellaneous Functions from M. Kohl",
  "Authors@R": "person(\"Matthias\", \"Kohl\", role = c(\"aut\", \"cre\"),\nemail = \"Matthias.Kohl@stamats.de\",\ncomment = c(ORCID = \"0000-0001-9514-8910\"))",
  "Author": "Matthias Kohl [aut, cre] (0000-0001-9514-8910)",
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  "Description": "Contains several functions for statistical data analysis;\ne.g. for sample size and power calculations, computation of\nconfidence intervals and tests, and generation of similarity\nmatrices.",
  "License": "LGPL-3",
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    "glog10",
    "glog2",
    "heatmapCol",
    "HLgof.test",
    "hsu.t.test",
    "imputeSD",
    "inv.glog",
    "inv.glog10",
    "inv.glog2",
    "IQrange",
    "iqrCV",
    "iqrSNR",
    "madCI",
    "madMatrix",
    "madPlot",
    "meanAD",
    "medCV",
    "medianCI",
    "medSNR",
    "melt.long",
    "mi.t.test",
    "mod.oneway.test",
    "mod.t.test",
    "normCI",
    "normDiffCI",
    "oneWayAnova",
    "optCutoff",
    "or2rr",
    "pairwise.auc",
    "pairwise.fc",
    "pairwise.fun",
    "pairwise.logfc",
    "pairwise.mod.t.test",
    "perfMeasures",
    "perfScores",
    "power.diagnostic.test",
    "power.hsu.t.test",
    "power.nb.test",
    "power.welch.t.test",
    "predValues",
    "qboxplot",
    "qbxp.stats",
    "quantileCI",
    "repMeans",
    "risks",
    "rrCI",
    "scale_x_glog",
    "scale_x_glog10",
    "scale_x_glog2",
    "scale_x_neglog",
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    "scale_x_neglog2",
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    "scale_y_glog10",
    "scale_y_glog2",
    "scale_y_neglog",
    "scale_y_neglog10",
    "scale_y_neglog2",
    "simCorVars",
    "simPlot",
    "sIQR",
    "SNR",
    "ssize.pcc",
    "stringDist",
    "stringSim",
    "thyroid",
    "traceBack",
    "twoWayAnova"
  ],
  "_help": [
    {
      "page": "0MKmisc-package",
      "title": "Miscellaneous Functions from M. Kohl.",
      "topics": [
        "MKmisc-package",
        "MKmisc"
      ]
    },
    {
      "page": "AUC",
      "title": "Compute AUC",
      "topics": [
        "AUC"
      ]
    },
    {
      "page": "AUCtest",
      "title": "AUC-Test",
      "topics": [
        "AUC.test"
      ]
    },
    {
      "page": "binomCI",
      "title": "Confidence Intervals for Binomial Proportions",
      "topics": [
        "binomCI"
      ]
    },
    {
      "page": "corDist",
      "title": "Correlation Distance Matrix Computation",
      "topics": [
        "corDist"
      ]
    },
    {
      "page": "corPlot",
      "title": "Plot of similarity matrix based on correlation",
      "topics": [
        "corPlot"
      ]
    },
    {
      "page": "CV",
      "title": "Compute CV",
      "topics": [
        "CV",
        "iqrCV",
        "medCV"
      ]
    },
    {
      "page": "cvCI",
      "title": "Confidence Intervals for Coefficient of Variation",
      "topics": [
        "cvCI"
      ]
    },
    {
      "page": "fiveNS",
      "title": "Five-Number Summaries",
      "topics": [
        "fiveNS"
      ]
    },
    {
      "page": "glog",
      "title": "Compute Generalized Logarithm",
      "topics": [
        "glog",
        "glog10",
        "glog2",
        "inv.glog",
        "inv.glog10",
        "inv.glog2"
      ]
    },
    {
      "page": "heatmapCol",
      "title": "Generate colors for heatmaps",
      "topics": [
        "heatmapCol"
      ]
    },
    {
      "page": "HLgofTest",
      "title": "Hosmer-Lemeshow goodness of fit tests.",
      "topics": [
        "HLgof.test"
      ]
    },
    {
      "page": "hsu.t.test",
      "title": "Hsu Two-Sample t-Test",
      "topics": [
        "hsu.t.test",
        "hsu.t.test.default",
        "hsu.t.test.formula"
      ]
    },
    {
      "page": "imputeSD",
      "title": "Impute Standard Deviations for Changes from Baseline",
      "topics": [
        "imputeSD"
      ]
    },
    {
      "page": "IQrange",
      "title": "The Interquartile Range",
      "topics": [
        "IQrange",
        "sIQR"
      ]
    },
    {
      "page": "madMatrix",
      "title": "Compute MAD between colums of a matrix or data.frame",
      "topics": [
        "madMatrix"
      ]
    },
    {
      "page": "madPlot",
      "title": "Plot of similarity matrix based on MAD",
      "topics": [
        "madPlot"
      ]
    },
    {
      "page": "meanAD",
      "title": "The Mean Absolute Deviation",
      "topics": [
        "meanAD"
      ]
    },
    {
      "page": "melt.long",
      "title": "Transform data.frame to Long Form",
      "topics": [
        "melt.long"
      ]
    },
    {
      "page": "mi.t.test",
      "title": "Multiple Imputation Student's t-Test",
      "topics": [
        "mi.t.test",
        "mi.t.test.default"
      ]
    },
    {
      "page": "mod.oneway.test",
      "title": "Moderated 1-Way ANOVA",
      "topics": [
        "mod.oneway.test"
      ]
    },
    {
      "page": "mod.t.test",
      "title": "Moderated t-Test",
      "topics": [
        "mod.t.test"
      ]
    },
    {
      "page": "normCI",
      "title": "Confidence Intervals for Mean and Standard Deviation",
      "topics": [
        "normCI"
      ]
    },
    {
      "page": "normDiffCI",
      "title": "Confidence Intervals for Difference of Means",
      "topics": [
        "normDiffCI"
      ]
    },
    {
      "page": "oneWayAnova",
      "title": "A function for Analysis of Variance",
      "topics": [
        "oneWayAnova"
      ]
    },
    {
      "page": "optCutoff",
      "title": "Compute the Optimal Cutoff for Binary Classification",
      "topics": [
        "optCutoff"
      ]
    },
    {
      "page": "or2rr",
      "title": "Transform OR to RR",
      "topics": [
        "or2rr"
      ]
    },
    {
      "page": "pairwiseAUC",
      "title": "Compute pairwise AUCs",
      "topics": [
        "pairwise.auc"
      ]
    },
    {
      "page": "pairwiseFC",
      "title": "Compute pairwise fold changes",
      "topics": [
        "pairwise.fc"
      ]
    },
    {
      "page": "pairwiseFun",
      "title": "Compute pairwise values for a given function",
      "topics": [
        "pairwise.fun"
      ]
    },
    {
      "page": "pairwiselogFC",
      "title": "Compute pairwise log-fold changes",
      "topics": [
        "pairwise.logfc"
      ]
    },
    {
      "page": "pairwise.mod.t.test",
      "title": "Pairwise Moderated t-Tests",
      "topics": [
        "pairwise.mod.t.test"
      ]
    },
    {
      "page": "perfMeasures",
      "title": "Compute Performance Measures and Scores for Binary Classification",
      "topics": [
        "perfMeasures",
        "perfScores"
      ]
    },
    {
      "page": "power.diagnostic.test",
      "title": "Power calculations for a diagnostic test",
      "topics": [
        "power.diagnostic.test"
      ]
    },
    {
      "page": "power.hsu.t.test",
      "title": "Power calculations for two sample Hsu t test",
      "topics": [
        "power.hsu.t.test"
      ]
    },
    {
      "page": "power.nb.test",
      "title": "Power calculation for comparing two negative binomial rates",
      "topics": [
        "power.nb.test"
      ]
    },
    {
      "page": "power.welch.t.test",
      "title": "Power calculations for two sample Welch t test",
      "topics": [
        "power.welch.t.test"
      ]
    },
    {
      "page": "predValues",
      "title": "Compute PPV and NPV.",
      "topics": [
        "predValues"
      ]
    },
    {
      "page": "print.confint",
      "title": "Print Method for Confidence Intervals",
      "topics": [
        "print.confint"
      ]
    },
    {
      "page": "qboxplot",
      "title": "Box Plots",
      "topics": [
        "qboxplot",
        "qboxplot.default",
        "qboxplot.formula"
      ]
    },
    {
      "page": "qbxp.stats",
      "title": "Box Plot Statistics",
      "topics": [
        "qbxp.stats"
      ]
    },
    {
      "page": "quantileCI",
      "title": "Confidence Intervals for Quantiles",
      "topics": [
        "madCI",
        "medianCI",
        "quantileCI"
      ]
    },
    {
      "page": "repMeans",
      "title": "Compute mean of replicated spots",
      "topics": [
        "repMeans"
      ]
    },
    {
      "page": "risks",
      "title": "Compute RR, OR, etc.",
      "topics": [
        "risks"
      ]
    },
    {
      "page": "rrCI",
      "title": "Compute Approximate Confidence Interval for RR.",
      "topics": [
        "rrCI"
      ]
    },
    {
      "page": "simCorVars",
      "title": "Simulate correlated variables.",
      "topics": [
        "simCorVars"
      ]
    },
    {
      "page": "simPlot",
      "title": "Plot of a similarity matrix.",
      "topics": [
        "simPlot"
      ]
    },
    {
      "page": "SNR",
      "title": "Compute SNR",
      "topics": [
        "iqrSNR",
        "medSNR",
        "SNR"
      ]
    },
    {
      "page": "ssize.pcc",
      "title": "Sample Size Planning for Developing Classifiers Using High Dimensional Data",
      "topics": [
        "ssize.pcc"
      ]
    },
    {
      "page": "stringDist",
      "title": "Function to compute distances between strings",
      "topics": [
        "stringDist"
      ]
    },
    {
      "page": "stringSim",
      "title": "Function to compute similarity scores between strings",
      "topics": [
        "stringSim"
      ]
    },
    {
      "page": "thyroid",
      "title": "Plot TSH, fT3 and fT4 with respect to reference range.",
      "topics": [
        "thyroid"
      ]
    },
    {
      "page": "traceBack",
      "title": "Function to trace back",
      "topics": [
        "traceBack"
      ]
    },
    {
      "page": "transformations",
      "title": "New Transformations for Use with ggplot2 Package",
      "topics": [
        "glog10_trans",
        "glog2_trans",
        "glog_trans",
        "neglog10_trans",
        "neglog2_trans",
        "neglog_breaks",
        "neglog_trans",
        "scale_x_glog",
        "scale_x_glog10",
        "scale_x_glog2",
        "scale_x_neglog",
        "scale_x_neglog10",
        "scale_x_neglog2",
        "scale_y_glog",
        "scale_y_glog10",
        "scale_y_glog2",
        "scale_y_neglog",
        "scale_y_neglog10",
        "scale_y_neglog2"
      ]
    },
    {
      "page": "twoWayAnova",
      "title": "A function for Analysis of Variance",
      "topics": [
        "twoWayAnova"
      ]
    }
  ],
  "_readme": "https://github.com/stamats/mkmisc/raw/HEAD/README.md",
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    "cpp11",
    "DEoptimR",
    "farver",
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    "glue",
    "gtable",
    "isoband",
    "labeling",
    "lifecycle",
    "limma",
    "R6",
    "RColorBrewer",
    "rlang",
    "robustbase",
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    "scales",
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      "source": "MKmisc.Rmd",
      "filename": "MKmisc.html",
      "title": "Package MKmisc",
      "author": "Matthias Kohl",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Descriptive Statistics",
        "IQR",
        "Mean Absolute Deviation",
        "Five Number Summary",
        "Coefficient of Variation (CV)",
        "Signal to Noise Ratio (SNR)",
        "Box- and Whisker-Plot",
        "OR, RR and Other Risk Measures",
        "Generalized Logarithm",
        "Simulate Correlated Variables",
        "Plot TSH, fT3 and fT4 Values",
        "Generalized and Negative Logarithm as Transformations",
        "Change Data from Wide to Long",
        "Confidence Intervals",
        "Binomial Proportion",
        "Mean and SD",
        "Difference in Means",
        "Coefficient of Variation",
        "Quantiles, Median and MAD",
        "Relative Risk",
        "Sample Size",
        "Welch Two-Sample t-Test",
        "Hsu Two-Sample t-Test",
        "Two Negative Binomial Rates",
        "Moderated Tests Based on Package limma",
        "Moderated t-Test",
        "Moderated 1-Way ANOVA",
        "Pairwise moderated t-tests",
        "Multiple Imputation t-Test",
        "Imputation of Standard Deviations for Changes from Baseline",
        "AUC",
        "Estimation",
        "Testing",
        "Pairwise",
        "Pairwise Comparisons",
        "FC and logFC",
        "Arbitrary Criteria",
        "Binary Classification",
        "PPV and NPV",
        "Performance Measures and Scores",
        "Optimal Cutoff",
        "Hosmer-Lemeshow and le Cessie-van Houwelingen-Copas-Hosmer",
        "Sample Size Calculation",
        "Omics Data",
        "Aggregating Technical Replicates",
        "1- and 2-Way ANOVA",
        "Correlation Distance Matrix",
        "MAD Matrix",
        "Similarity Matrices",
        "Colors for Heatmaps",
        "String Alignment",
        "String Distances",
        "String Similarities",
        "Optimal Alignment",
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      "created": "2018-03-08 07:15:21",
      "modified": "2019-09-07 05:15:08",
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