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AnimalSequences (version 0.2.0)

Analyse Animal Sequential Behaviour and Communication

Description

All animal behaviour occurs sequentially. The package has a number of functions to format sequence data from different sources, to analyse sequential behaviour and communication in animals. It also has functions to plot the data and to calculate the entropy of sequences.

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Version

Install

install.packages('AnimalSequences')

Monthly Downloads

180

Version

0.2.0

License

Apache License (>= 2.0)

Maintainer

Alex Mielke

Last Published

September 23rd, 2024

Functions in AnimalSequences (0.2.0)

sequence_duration_summary

Summarize Sequence Durations
median_seq_length

Calculate the Median Length of Sequences
sequence_length_summary_element

Summarize Sequence Lengths by Element
sequences_to_long

Convert Sequences to Long Format
sequence_length_summary

Summarize Sequence Lengths
sequence_length_summary_covariate

Summarize Sequence Lengths by Covariate
shuffle_sequences_across

Shuffle Elements Across All Sequences
zipf_plot

Create a Zipf's Law Plot
menzerath_plot

Create a Menzerath-Altmann Plot
count_distinct_elements_per_list_item

Count Distinct Elements per List Item
temporal_overlap

Temporal Overlap
count_distinct_elements_per_list_item_shuffled

Count Distinct Elements per List Item in Shuffled Sequences
min_max_seq_length

Calculate the Minimum and Maximum Length of Sequences
shuffle_sequences_within

Shuffle Elements Within Each Sequence
transition_chisq

Perform a Chi-Squared Test for Transition Counts
sd_seq_length

Calculate the Standard Deviation of Sequence Lengths
transition_entropy

Calculate Transition Entropy for Sequences
find_most_similar_columns

Find Most Similar Columns in a Distance Matrix
perform_clustering

Perform Various Clustering Methods
redundancy

Calculate Observed and Expected Redundancy of Sequences
transition_predictions

Transition Predictions
generate_sequence

Generate a Sequence of Elements
plot_seq_length_distribution

Plot the Distribution of Sequence Lengths
transition_test

Perform a Statistical Test for Transition Probabilities
cooccurrence_matrix

Calculate Co-occurrence Matrix for Sequences
calculate_transition_counts

Calculate Transition Counts from Sequences
calculate_conditional_entropy

Calculate Conditional Entropy of B given A in Bits
compare_distinct_elements_per_list_item

Compare True and Shuffled Distinct Elements per List Item
cluster_elements

Cluster Elements Using Hierarchical Clustering
count_distinct_elements

Count Distinct Elements in Sequences
average_seq_length

Calculate the Average Length of Sequences
calculate_distance_matrix

Calculate Distance Matrix from Co-occurrence Matrix
association_metrics

Calculate Association Metrics for Sequences
calculate_transition_probs

Calculate Transition Probabilities from Sequences
element_duration

Calculate Individual Element Durations
long_to_sequences

Convert Long Format to Sequences
element_covariate_network

Plot the network of elements and covariates based on the long format of sequences
element_covariate

Calculate Element-Covariate Conditional Probabilities
element_position

Calculate Median Position of Each Element in Sequences