Machine Learning and Visualization
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Documentation for package ‘rtemis’ version 1.0.0
Help Pages
A C D E F G I L M N O P R S T U W X misc
| rtemis-package | 'rtemis': Advanced Machine Learning and Visualization |
-- A --
| available_algorithms | Available Algorithms |
| available_clustering | Available Algorithms |
| available_decomposition | Available Algorithms |
| available_draw | Available Draw Functions |
| available_supervised | Available Algorithms |
| available_themes | Print available 'rtemis' themes |
-- C --
| calibrate | Calibrate 'Classification' & 'ClassificationRes' Models |
| check_data | Check Data |
| choose_theme | Select an rtemis theme |
| classification_metrics | Classification Metrics |
| class_imbalance | Class Imbalance |
| clean_colnames | Clean column names |
| clean_names | Clean names |
| cluster | Perform Clustering |
| col2grayscale | Color to Grayscale |
| color_adjust | Adjust HSV Color |
-- D --
| ddb_collect | Collect a lazy-read duckdb table |
| ddb_data | Read CSV using DuckDB |
| ddSci | Format Numbers for Printing |
| decomp | Perform Data Decomposition |
| describe | Describe rtemis object |
| describe.factor | Describe factor |
| df_movecolumn | Move data frame column |
| df_nunique_perfeat | Unique values per feature |
| draw_3Dscatter | Interactive 3D Scatter Plots |
| draw_bar | Interactive Barplots |
| draw_box | Interactive Boxplots & Violin plots |
| draw_calibration | Draw calibration plot |
| draw_confusion | Plot confusion matrix |
| draw_dist | Draw Distributions using Histograms and Density Plots |
| draw_fit | True vs. Predicted Plot |
| draw_graphD3 | Plot graph using 'networkD3' |
| draw_graphjs | Plot network using 'threejs::graphjs' |
| draw_heatmap | Interactive Heatmaps |
| draw_leaflet | Plot interactive choropleth map using 'leaflet' |
| draw_pie | Interactive Pie Chart |
| draw_protein | Plot an amino acid sequence with annotations |
| draw_pvals | Barplot p-values using draw_bar |
| draw_roc | Draw ROC curve |
| draw_scatter | Interactive Scatter Plots |
| draw_spectrogram | Interactive Spectrogram |
| draw_survfit | Draw a survfit object |
| draw_table | Simple HTML table |
| draw_ts | Interactive Timeseries Plots |
| draw_varimp | Interactive Variable Importance Plot |
| draw_volcano | Volcano Plot |
| draw_xt | Plot timeseries data |
| dt_describe | Describe data.table |
| dt_inspect_types | Inspect column types |
| dt_keybin_reshape | Long to wide key-value reshaping |
| dt_merge | Merge data.tables |
| dt_names_by_attr | List column names by attribute |
| dt_nunique_perfeat | Number of unique values per feature |
| dt_pctmatch | Get N and percent match of values between two columns of two data.tables |
| dt_pctmissing | Get percent of missing values from every column |
| dt_set_autotypes | Set column types automatically |
| dt_set_cleanfactorlevels | Clean factor levels of data.table _*in-place*_ |
| dt_set_clean_all | Clean column names and factor levels _*in-place*_ |
| dt_set_logical2factor | Convert data.table logical columns to factors |
| dt_set_one_hot | Convert data.table's factor to one-hot encoding _*in-place*_ |
-- E --
| exc | Exclude columns by character or numeric vector. |
-- F --
| features | Get features from tabular data |
| feature_matrix | Convert tabular data to feature matrix |
| feature_names | Get feature names |
-- G --
| getcharacternames | Get names by string matching or class |
| getdatenames | Get names by string matching or class |
| getfactornames | Get names by string matching or class |
| getlogicalnames | Get names by string matching or class |
| getnames | Get names by string matching or class |
| getnamesandtypes | Get data.frame names and types |
| getnumericnames | Get names by string matching or class |
| get_factor_names | Get factor names |
| get_mode | Get the mode of a factor or integer |
| get_palette | Get Color Palette |
-- I --
| inc | Select (include) columns by character or numeric vector. |
| index_col_by_attr | Index columns by attribute name & value |
| init_project_dir | Initialize Project Directory |
| inspect | Inspect rtemis object |
| inspect_type | Inspect character and factor vector |
| is_constant | Check if vector is constant |
-- L --
| labelify | Format text for label printing |
-- M --
| massGLM | Mass-univariate GLM Analysis |
| matchcases | Match cases by covariates |
| mgetnames | Get names by string matching multiple patterns |
-- N --
| names_by_class | List column names by class |
-- O --
| one_hot2factor | Convert one-hot encoded matrix to factor |
| outcome | Get the outcome as a vector |
| outcome_name | Get the name of the last column |
-- P --
| plot.MassGLM | Plot MassGLM using volcano plot |
| plot_manhattan | Manhattan plot |
| plot_manhattan.MassGLM | Manhattan plot |
| plot_roc | Plot ROC curve |
| plot_true_pred | Plot True vs. Predicted Values |
| plot_varimp | Plot Variable Importance |
| preprocess | Preprocess Data |
| preprocess.class_tabular.Preprocessor | Preprocess Data |
| preprocess.class_tabular.PreprocessorConfig | Preprocess Data |
| preprocessed | Get preprocessed data from 'Preprocessor'. |
| present | Present rtemis object |
| present.list | Present list of Supervised or SupervisedRes objects |
| previewcolor | Preview color |
-- R --
| read | Read tabular data from a variety of formats |
| read_config | Read 'SuperConfig' from TOML file |
| regression_metrics | Regression Metrics |
| resample | Resample data |
| rnormmat | Random Normal Matrix |
| rtemis | 'rtemis': Advanced Machine Learning and Visualization |
| rtemis_colors | rtemis Color System |
| rtversion | Get rtemis version and system info |
| runifmat | Random Uniform Matrix |
-- S --
| setdiffsym | Symmetric Set Difference |
| setup_CART | Setup CART Hyperparameters |
| setup_CMeans | Setup CMeansConfig |
| setup_DBSCAN | Setup DBSCANConfig |
| setup_ExecutionConfig | Setup Execution Configuration |
| setup_GAM | Setup GAM Hyperparameters |
| setup_GLM | Setup GLM Hyperparameters |
| setup_GLMNET | Setup GLMNET Hyperparameters |
| setup_GridSearch | Setup Grid Search Config |
| setup_HardCL | Setup HardCLConfig |
| setup_ICA | setup_ICA |
| setup_Isomap | Setup Isomap config. |
| setup_Isotonic | Setup Isotonic Hyperparameters |
| setup_KMeans | Setup KMeansConfig |
| setup_LightCART | Setup LightCART Hyperparameters |
| setup_LightGBM | Setup LightGBM Hyperparameters |
| setup_LightRF | Setup LightRF Hyperparameters |
| setup_LightRuleFit | Setup LightRuleFit Hyperparameters |
| setup_LinearSVM | Setup LinearSVM Hyperparameters |
| setup_NeuralGas | Setup NeuralGasConfig |
| setup_NMF | Setup NMF config. |
| setup_PCA | Setup PCA config. |
| setup_Preprocessor | Setup Preprocessor |
| setup_RadialSVM | Setup RadialSVM Hyperparameters |
| setup_Ranger | Setup Ranger Hyperparameters |
| setup_Resampler | Setup Resampler |
| setup_SuperConfig | Setup SuperConfig |
| setup_TabNet | Setup TabNet Hyperparameters |
| setup_tSNE | Setup tSNE config. |
| setup_UMAP | Setup UMAP config. |
| set_outcome | Move outcome to last column |
| size | Size of object |
-- T --
| table_column_attr | Tabulate column attributes |
| theme_black | Themes for draw_* functions |
| theme_blackgrid | Themes for draw_* functions |
| theme_blackigrid | Themes for draw_* functions |
| theme_darkgray | Themes for draw_* functions |
| theme_darkgraygrid | Themes for draw_* functions |
| theme_darkgrayigrid | Themes for draw_* functions |
| theme_lightgraygrid | Themes for draw_* functions |
| theme_mediumgraygrid | Themes for draw_* functions |
| theme_white | Themes for draw_* functions |
| theme_whitegrid | Themes for draw_* functions |
| theme_whiteigrid | Themes for draw_* functions |
| train | Train Supervised Learning Models |
-- U --
| uniprot_get | Get protein sequence from UniProt |
-- W --
| write_toml | Write to TOML file |
-- X --
| xtdescribe | Describe longitudinal dataset |
| xt_example | Example longitudinal dataset |
-- misc --
| %BC% | Binary matrix times character vector |