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codapack_structure.yaml
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CoDaPack Menu:
- Data:
- Transformation:
- ALR:
id: "TransformationALR"
- CLR:
id: "TransformationCLR"
- Raw-ILR:
id: "TransformationRawILR"
- ILR-Raw:
id: "TransformationILRRaw"
- Operations:
- Centering:
id: "CenterData"
- Subcomposition/Closure:
id: "ClosureData"
- Perturbation:
id: "PerturbateData"
- Power Transformation:
id: "PowerData"
- Manipulate:
- Discretize/Segment Variable:
id: "Discretize"
- Calculate New Variable:
id: "CalculateNewVar"
- Sort Data:
id: "SortData"
- Numeric to Categoric:
id: "Numeric2Categoric"
- Categoric to Numeric:
id: "Categoric2Numeric"
- Change Category Labels:
id: "ChangeGroupName"
- Filters:
- Categorical Filter:
id: "Filter"
- Advanced Filter:
id: "AdvancedFilter"
- Create New Table:
id: "CreateNewTable"
- Add Numeric Variables:
id: "AddNumericVariables"
- Delete Variables:
id: "DeleteVariables"
- Irregular Data:
- Zero Patterns:
id: "ZeroPatterns"
code: "r"
script: "cdp_zpatterns.R"
controls:
- boolean: "Show means"
- boolean: "Show percentages"
- boolean:
label: "Add Pattern"
value: true
- boolean:
label: "Plot Pattern"
value: true
- select:
name: "Label"
values: ["0", "NA"]
- Set Detection Limit:
id: "SetDetectionLimit"
- Separator
- Multiplicative Zero Replacement:
id: "NonParametricZeroReplacement"
code: "r"
script: "cdp_nonparametric_zero_repl.R"
controls:
- numeric:
name: "DL proportion"
value: 0.65
- Bayesian Multiplicative Zero Replacement:
id: "BayesianMultiplicativeZeroReplacement"
code: "r"
script: "cdp_bayesian_multiplicative_repl.R"
controls:
- select:
name: "Method"
values: ["GBM", "SQ", "BL", "CZM"]
- Log-Ratio EM Zero Replacement:
id: "LogRatioEMZeroReplacement"
code: "r"
script: "cdp_lrnormal_zero_repl.R"
controls:
- select:
name: "Initial Cov"
values: ["multRepl", "complete.obs"]
- numeric:
name: "DL proportion"
value: 0.65
- boolean: "Robust"
- Log-Ratio EM Missing Imputation:
id: "LogRatioEMMissingReplacement"
code: "r"
script: "cdp_lrnormal_missing.R"
controls:
- boolean: "Robust"
- Log-Ratio EM Zero Repl. & Missing Imp.:
id: "LogRatioEMZeroMissingReplacement"
code: "r"
script: "cdp_lrnormal_zero_repl_missing.R"
controls:
- select:
name: "Initial Cov"
values: ["multRepl", "complete.obs"]
- numeric:
name: "DL proportion"
value: 0.65
- boolean: "Robust"
- Separator
- Atypicality Index:
id: "Outliers"
code: "r"
script: "cdp_outliers.R"
controls:
- numeric:
name: "Confidence level"
value: 0.95
- Statistics:
- Compositional Statistics Summary:
id: "CompStatsSummary"
- Classical Statistics Summary:
id: "ClasStatsSummary"
- Separator
- Multivariate Analysis:
- Regression:
- X real, Y composition:
id: "RegressionCoDaResponse"
code: "r"
script: "cdp_regression_coda_response.R"
options: ["2selectors"]
textA: "Explanatory variables"
textB: "Response composition"
controls:
- basis:
name: "Response partition"
selector: "Y"
- boolean: "Residuals"
- boolean: "Fitted values"
- X composition, Y real:
id: "RegressionCoDaExplanaotory"
code: "r"
script: "cdp_regression_coda_explanatory.R"
options: ["2selectors"]
textA: "Explanatory composition"
textB: "Response variable"
controls:
- basis:
name: "Explanatory partition"
selector: "X"
- boolean: "Residuals"
- boolean: "Fitted values"
- X real, Y real:
id: "RegressionReal"
code: "r"
script: "cdp_regression_real.R"
options: ["2selectors"]
textA: "Explanatory variables"
textB: "Response variable"
controls:
- boolean: "Residuals"
- boolean: "Fitted values"
- data: "Predict new data"
- Cluster:
- K-means:
id: "KMeans"
code: "r"
script: "cdp_kmeans.R"
controls:
- label: "Number of clusters"
- numeric:
name: "Mininum"
value: 2
- numeric:
name: "Maximum"
value: 10
- select:
name: "Optimality"
values: ["Calinski index", "Average Silhouette"]
- string:
name: "Cluster name"
value: "Cluster"
- Manova:
id: "Manova"
code: "r"
script: "cdp_manova.R"
options: ["groups"]
controls:
- boolean: "Residuals"
- boolean: "Test pairs"
- select:
name: "Test"
values: ["Pillai", "Wilks", "Hotelling-Lawley", "Roy", "Spherical"]
- boolean: "Sum-Squares"
- Discriminant Analysis:
id: "DiscriminantAnalysis"
code: "r"
script: "cdp_discriminant_analysis.R"
options: ["groups"]
controls:
- boolean: "Uniform prior"
- boolean: "Discriminant score"
- boolean: "Posterior probability"
- boolean: "Maximum posterior classification"
- data: "Predict new data"
- Log-Ratio Normality Test:
id: "LogRatioNormalityTest"
- Univariate Normality Test:
id: "UnivariateNormalityTest"
code: "r"
script: "cdp_univariate_normality_test.R"
controls:
- select:
name: "Method"
values: ["Shapiro-Wilk", "Kolmogorov-Smirnov"]
- Graphs:
- Ternary/Quaternary Plot:
id: "TernaryQuaternaryPlot"
- Ternary/Quaternary PC Plot:
id: "TernaryQuaternaryPCPlot"
- Ternary Predictive Region:
id: "PredictiveRegionPlot"
- Ternary Center Confidence Region:
id: "CenterConfidenceRegionPlot"
- Ternary Plot Builder:
id: "TernaryQuaternaryPlotEmpty"
- Separator
- Geometric Mean Barplot:
id: "GeometricMeanBarplot"
code: "r"
script: "cdp_geometric_mean_barplot.R"
options: ["groups"]
controls:
- select:
name: "Arranged by"
values: ["parts", "groups"]
- CLR-biplot:
id: "CLRBiplot"
- ILR/CLR-biplot:
id: "ILRCLRBiplot"
- Balance Dendrogram:
id: "BalanceDendrogram"
- Separator
- Boxplot:
id: "Boxplot"
code: "r"
script: "cdp_boxplot.R"
options: ["groups"]
controls:
- boolean: "Add geometric mean"
- boolean: "Add arithmetic mean"
- Scatterplot:
id: "ScatterPlot"
code: "r"
script: "cdp_scatterplot.R"
options: ["groups"]
controls:
- boolean: "Set same scale"
- Mosaic plot:
id: "MosaicPlot"
code: "r"
script: "cdp_mosaic_plot.R"
options: ["only_categoric"]
controls: []