# Machine Learning and Visualization

## Documentation for package ‘rtemis’ version 1.2.7

- DESCRIPTION file
- Package README

## Help Pages

A C D E F G I M N O P R S T U W X misc

rtemis-package | 'rtemis': Advanced Machine Learning and Visualization

## -- A --

apply_decomp | Apply Decomposition to New Data
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
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
decomp | Perform Data Decomposition
describe | Describe object
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
get_varimp | Get variable importance

## -- 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

## -- 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
numeric_features | Get numeric features from tabular data

## -- 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
previewcolor | Preview color

## -- R --

read | Read tabular data from a variety of formats
read_config | Read an rtemis config from file
regression_metrics | Regression Metrics
resample | Resample data
rnormmat | Random Normal Matrix
roc_curve | ROC curve coordinates
rtemis | 'rtemis': Advanced Machine Learning and Visualization
rtemis_conditions | rtemis error conditions
rtemis_data_error | rtemis error conditions
rtemis_dim_error | rtemis error conditions
rtemis_error | rtemis error conditions
rtemis_file_exists | rtemis error conditions
rtemis_file_not_found | rtemis error conditions
rtemis_input_error | rtemis error conditions
rtemis_io_error | rtemis error conditions
rtemis_length_error | rtemis error conditions
rtemis_level_mismatch | rtemis error conditions
rtemis_missing_data | rtemis error conditions
rtemis_null_input | rtemis error conditions
rtemis_outcome_error | rtemis error conditions
rtemis_range_error | rtemis error conditions
rtemis_runtime_error | rtemis error conditions
rtemis_type_error | rtemis error conditions
rtemis_unsupported_error | rtemis error conditions
rtemis_value_error | rtemis error conditions
rtversion | Get rtemis version and system info
runifmat | Random Uniform Matrix

## -- S --

setdiffsym | Symmetric Set Difference
setup_CART | Setup CART Hyperparameters
setup_ClusterConfig | Setup ClusterConfig
setup_CMeans | Setup CMeansConfig
setup_DBSCAN | Setup DBSCANConfig
setup_DecomposeConfig | Setup DecomposeConfig
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_SuperConfigLive | Setup SuperConfigLive
setup_TabNet | Setup TabNet Hyperparameters
setup_tSNE | Setup tSNE config.
setup_UMAP | Setup UMAP config.
set_outcome | Move outcome to last column
set_positive_class | Set positive class
show_color_key | Show rtemis color key
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_config | Write an rtemis config to a JSON file

## -- X --

xtdescribe | Describe longitudinal dataset
xt_example | Example longitudinal dataset

## -- misc --

%BC% | Binary matrix times character vector