R: Advanced Toolset for Efficient Time Series Dissimilarity Analysis

# Advanced Toolset for Efficient Time Series Dissimilarity Analysis

## Documentation for package ‘distantia’ version 2.0.3

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

A C D E F H I M P S T U Z

## -- A --

albatross | Flight Path Time Series of Albatrosses in the Pacific
auto_distance_cpp | (C++) Sum Distances Between Consecutive Samples in a Time Series
auto_sum_cpp | (C++) Sum Distances Between Consecutive Samples in Two Time Series
auto_sum_full_cpp | (C++) Sum Distances Between All Consecutive Samples in Two Time Series
auto_sum_path_cpp | (C++) Sum Distances Between All Consecutive Samples in the Least Cost Path Between Two Time Series

## -- C --

cities_coordinates | Coordinates of 100 Major Cities
cities_temperature | Long Term Monthly Temperature in 20 Major Cities
color_continuous | Default Continuous Color Palette
color_discrete | Default Discrete Color Palettes
cost_matrix_diagonal_cpp | (C++) Compute Orthogonal and Diagonal Least Cost Matrix from a Distance Matrix
cost_matrix_diagonal_weighted_cpp | (C++) Compute Orthogonal and Weighted Diagonal Least Cost Matrix from a Distance Matrix
cost_matrix_orthogonal_cpp | (C++) Compute Orthogonal Least Cost Matrix from a Distance Matrix
cost_path_cpp | Least Cost Path
cost_path_diagonal_bandwidth_cpp | (C++) Orthogonal and Diagonal Least Cost Path Restricted by Sakoe-Chiba band
cost_path_diagonal_cpp | (C++) Orthogonal and Diagonal Least Cost Path
cost_path_orthogonal_bandwidth_cpp | (C++) Orthogonal Least Cost Path
cost_path_orthogonal_cpp | (C++) Orthogonal Least Cost Path
cost_path_slotting_cpp | (C++) Least Cost Path for Sequence Slotting
cost_path_sum_cpp | (C++) Sum Distances in a Least Cost Path
cost_path_trim_cpp | (C++) Remove Blocks from a Least Cost Path
covid_counties | County Coordinates of the Covid Prevalence Dataset
covid_prevalence | Time Series of Covid Prevalence in California Counties

## -- D --

distance | Distance Between Two Numeric Vectors
distances | Distance Methods
distance_bray_curtis_cpp | (C++) Bray-Curtis Distance Between Two Vectors
distance_canberra_cpp | (C++) Canberra Distance Between Two Binary Vectors
distance_chebyshev_cpp | (C++) Chebyshev Distance Between Two Vectors
distance_chi_cpp | (C++) Normalized Chi Distance Between Two Vectors
distance_cosine_cpp | (C++) Cosine Dissimilarity Between Two Vectors
distance_euclidean_cpp | (C++) Euclidean Distance Between Two Vectors
distance_hamming_cpp | (C++) Hamming Distance Between Two Binary Vectors
distance_hellinger_cpp | (C++) Hellinger Distance Between Two Vectors
distance_jaccard_cpp | (C++) Jaccard Distance Between Two Binary Vectors
distance_ls_cpp | (C++) Sum of Pairwise Distances Between Cases in Two Aligned Time Series
distance_manhattan_cpp | (C++) Manhattan Distance Between Two Vectors
distance_matrix | Data Frame to Distance Matrix
distance_matrix_cpp | (C++) Distance Matrix of Two Time Series
distance_russelrao_cpp | (C++) Russell-Rao Distance Between Two Binary Vectors
distance_sorensen_cpp | (C++) Sørensen Distance Between Two Binary Vectors
distantia | Dissimilarity Analysis of Time Series Lists
distantia_aggregate | Aggregate 'distantia()' Data Frames Across Parameter Combinations
distantia_boxplot | Distantia Boxplot
distantia_cluster_hclust | Hierarchical Clustering of Dissimilarity Analysis Data Frames
distantia_cluster_kmeans | K-Means Clustering of Dissimilarity Analysis Data Frames
distantia_dtw | Dynamic Time Warping Dissimilarity Analysis of Time Series Lists
distantia_dtw_plot | Two-Way Dissimilarity Plots of Time Series Lists
distantia_ls | Lock-Step Dissimilarity Analysis of Time Series Lists
distantia_matrix | Convert Dissimilarity Analysis Data Frame to Distance Matrix
distantia_model_frame | Dissimilarity Model Frame
distantia_spatial | Spatial Representation of 'distantia()' Data Frames
distantia_stats | Summary Statistics of Dissimilarity Data Frame
distantia_time_delay | Time Delay Between Time Series

## -- E --

eemian_coordinates | Site Coordinates of Nine Interglacial Sites in Central Europe
eemian_pollen | Pollen Counts of Nine Interglacial Sites in Central Europe

## -- F --

fagus_coordinates | Site Coordinates of Fagus sylvatica Stands
fagus_dynamics | Time Series Data from Three Fagus sylvatica Stands
f_binary | Data Transformation: Convert Zoo Object to Binary
f_clr | Data Transformation: Rowwise Centered Log-Ratio
f_detrend_difference | Data Transformation: Detrending and Differencing
f_detrend_linear | Data Transformation: Linear Detrending of Zoo Time Series
f_detrend_poly | Data Transformation: Polynomial Linear Detrending of Zoo Time Series
f_hellinger | Data Transformation: Rowwise Hellinger Transformation
f_list | Lists Available Transformation Functions
f_log | Data Transformation: Log
f_percent | Data Transformation: Rowwise Percentages
f_proportion | Data Transformation: Rowwise Proportions
f_proportion_sqrt | Data Transformation: Rowwise Square Root of Proportions
f_rescale_global | Data Transformation: Global Rescaling to a New Range
f_rescale_local | Data Transformation: Local Rescaling to a New Range
f_scale_global | Data Transformation: Global Centering and Scaling
f_scale_local | Data Transformation: Local Centering and Scaling
f_trend_linear | Data Transformation: Linear Trend of Zoo Time Series
f_trend_poly | Data Transformation: Polynomial Linear Trend of Zoo Time Series

## -- H --

honeycomb_climate | Rainfall and Temperature in The Americas
honeycomb_polygons | Hexagonal Grid

## -- I --

importance_dtw_cpp | (C++) Contribution of Individual Variables to the Dissimilarity Between Two Time Series (Robust Version)
importance_dtw_legacy_cpp | (C++) Contribution of Individual Variables to the Dissimilarity Between Two Time Series (Legacy Version)
importance_ls_cpp | (C++) Contribution of Individual Variables to the Dissimilarity Between Two Aligned Time Series

## -- M --

momentum | Contribution of Individual Variables to Time Series Dissimilarity
momentum_aggregate | Aggregate 'momentum()' Data Frames Across Parameter Combinations
momentum_boxplot | Momentum Boxplot
momentum_dtw | Dynamic Time Warping Variable Importance Analysis of Multivariate Time Series Lists
momentum_ls | Lock-Step Variable Importance Analysis of Multivariate Time Series Lists
momentum_model_frame | Importance Model Frame
momentum_spatial | Spatial Representation of 'momentum()' Data Frames
momentum_stats | Summary Statistics of Importance Data Frame
momentum_to_wide | Momentum Data Frame to Wide Format

## -- P --

permute_free_by_row_cpp | (C++) Unrestricted Permutation of Complete Rows
permute_free_cpp | (C++) Unrestricted Permutation of Cases
permute_restricted_by_row_cpp | (C++) Restricted Permutation of Complete Rows Within Blocks
permute_restricted_cpp | (C++) Restricted Permutation of Cases Within Blocks
psi_auto_distance | Cumulative Sum of Distances Between Consecutive Cases in a Time Series
psi_auto_sum | Auto Sum
psi_cost_matrix | Cost Matrix
psi_cost_path | Least Cost Path
psi_cost_path_sum | Sum of Distances in Least Cost Path
psi_distance_lock_step | Lock-Step Distance
psi_distance_matrix | Distance Matrix
psi_dtw_cpp | (C++) Psi Dissimilarity Score of Two Time-Series
psi_equation | Normalized Dissimilarity Score
psi_equation_cpp | (C++) Equation of the Psi Dissimilarity Score
psi_ls_cpp | (C++) Psi Dissimilarity Score of Two Aligned Time Series
psi_null_dtw_cpp | (C++) Null Distribution of Dissimilarity Scores of Two Time Series
psi_null_ls_cpp | (C++) Null Distribution of the Dissimilarity Scores of Two Aligned Time Series

## -- S --

subset_matrix_by_rows_cpp | (C++) Subset Matrix by Rows

## -- T --

tsl_aggregate | Aggregate Time Series List Over Time Periods
tsl_burst | Multivariate TSL to Univariate TSL
tsl_colnames_clean | Clean Column Names in Time Series Lists
tsl_colnames_get | Get Column Names from Time Series Lists
tsl_colnames_prefix | Append Prefix to Column Names of Time Series List
tsl_colnames_set | Set Column Names in a Time Series List
tsl_colnames_suffix | Append Suffix to Column Names of Time Series List
tsl_count_NA | Count NA Cases in Time Series Lists
tsl_diagnose | Diagnose Issues in Time Series Lists
tsl_handle_NA | Handle NA Cases in Time Series Lists
tsl_Inf_to_NA | Handle NA Cases in Time Series Lists
tsl_init | Transform Raw Time Series Data to Time Series List
tsl_initialize | Transform Raw Time Series Data to Time Series List
tsl_join | Join Time Series Lists
tsl_names_clean | Clean Time Series Names in a Time Series List
tsl_names_get | Get Time Series Names from Time Series Lists
tsl_names_set | Set Time Series Names in a Time Series List
tsl_names_test | Tests Naming Issues in Time Series Lists
tsl_NaN_to_NA | Handle NA Cases in Time Series Lists
tsl_ncol | Get Number of Columns in Time Series Lists
tsl_nrow | Get Number of Rows in Time Series Lists
tsl_plot | Plot Time Series List
tsl_repair | Repair Issues in Time Series Lists
tsl_resample | Resample Time Series Lists to a New Time
tsl_simulate | Simulate a Time Series List
tsl_smooth | Smoothing of Time Series Lists
tsl_stats | Summary Statistics of Time Series Lists
tsl_subset | Subset Time Series Lists by Time Series Names, Time, and/or Column Names
tsl_time | Time Features of Time Series Lists
tsl_time_summary | Time Features of Time Series Lists
tsl_to_df | Transform Time Series List to Data Frame
tsl_transform | Transform Values in Time Series Lists

## -- U --

utils_as_time | Ensure Correct Class for Time Arguments
utils_block_size | Default Block Size for Restricted Permutation in Dissimilarity Analyses
utils_boxplot_common | Common Boxplot Component of 'distantia_boxplot()' and 'momentum_boxplot()'
utils_check_args_distantia | Check Input Arguments of 'distantia()'
utils_check_args_matrix | Checks Input Matrix
utils_check_args_momentum | Check Input Arguments of 'momentum()'
utils_check_args_path | Checks Least Cost Path
utils_check_args_tsl | Structural Check for Time Series Lists
utils_check_args_zoo | Checks Argument x
utils_check_distance_args | Check Distance Argument
utils_check_list_class | Checks Classes of List Elements Against Expectation
utils_clean_names | Clean Character Vector of Names
utils_cluster_hclust_optimizer | Optimize the Silhouette Width of Hierarchical Clustering Solutions
utils_cluster_kmeans_optimizer | Optimize the Silhouette Width of K-Means Clustering Solutions
utils_cluster_silhouette | Compute Silhouette Width of a Clustering Solution
utils_coerce_time_class | Coerces Vector to a Given Time Class
utils_color_breaks | Auto Breaks for Matrix Plotting Functions
utils_digits | Number of Decimal Places
utils_distantia_df_split | Split Dissimilarity Analysis Data Frames by Combinations of Arguments
utils_drop_geometry | Remove Geometry Column from SF Data Frames
utils_global_scaling_params | Global Centering and Scaling Parameters of Time Series Lists
utils_is_time | Test if Vector is a Valid Time Class
utils_line_color | Handles Line Colors for Sequence Plots
utils_line_guide | Guide for Time Series Plots
utils_matrix_guide | Color Guide for Matrix Plot
utils_matrix_plot | Plot Distance or Cost Matrix and Least Cost Path
utils_new_time | New Time for Time Series Aggregation
utils_new_time_type | New Time for Time Series Aggregation
utils_optimize_loess | Optimize Loess Models for Time Series Resampling
utils_optimize_spline | Optimize Spline Models for Time Series Resampling
utils_prepare_df | Convert Data Frame to a List of Data Frames
utils_prepare_matrix | Convert Matrix to Data Frame
utils_prepare_matrix_list | Convert List of Matrices to List of Data Frames
utils_prepare_time | Handles Time Column in a List of Data Frames
utils_prepare_vector_list | Convert List of Vectors to List of Data Frames
utils_prepare_zoo_list | Convert List of Data Frames to List of Zoo Objects
utils_rescale_vector | Rescale Numeric Vector to a New Data Range
utils_time_keywords | Valid Aggregation Keywords
utils_time_keywords_dictionary | Dictionary of Time Keywords
utils_time_keywords_translate | Translate User Time Keywords Into Valid Ones
utils_time_units | Data Frame with Supported Time Units
utils_tsl_pairs | Data Frame with Pairs of Time Series in Time Series Lists

## -- Z --

zoo_aggregate | Aggregate Cases in Zoo Time Series
zoo_name_clean | Clean Name of a Zoo Time Series
zoo_name_get | Get Name of a Zoo Time Series
zoo_name_set | Set Name of a Zoo Time Series
zoo_permute | Random or Restricted Permutation of Zoo Time Series
zoo_plot | Plot Zoo Time Series
zoo_resample | Resample Zoo Objects to a New Time
zoo_simulate | Simulate a Zoo Time Series
zoo_smooth_exponential | Exponential Smoothing of Zoo Time Series
zoo_smooth_window | Rolling Window Smoothing of Zoo Time Series
zoo_time | Get Time Features from Zoo Objects
zoo_to_tsl | Convert Individual Zoo Objects to Time Series List
zoo_vector_to_matrix | Coerce Coredata of Univariate Zoo Time Series to Matrix