Package: AnimalSequences 0.2.0

Alex Mielke

AnimalSequences: Analyse Animal Sequential Behaviour and Communication

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.

Authors:Alex Mielke [aut, cre]

AnimalSequences_0.2.0.tar.gz
AnimalSequences_0.2.0.tar.gz(r-4.5-noble)AnimalSequences_0.2.0.tar.gz(r-4.4-noble)
AnimalSequences_0.2.0.tgz(r-4.4-emscripten)AnimalSequences_0.2.0.tgz(r-4.3-emscripten)
AnimalSequences.pdf |AnimalSequences.html✨
AnimalSequences/json (API)

# Install 'AnimalSequences' in R:
install.packages('AnimalSequences', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

On CRAN:

Conda-Forge:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 264 downloads 39 exports 74 dependencies

Last updated 5 months agofrom:33a78e8c01. Checks:2 OK. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKFeb 21 2025
R-4.5-linuxOKFeb 21 2025

Exports:association_metricsaverage_seq_lengthcalculate_conditional_entropycalculate_distance_matrixcalculate_transition_countscalculate_transition_probscluster_elementscompare_distinct_elements_per_list_itemcooccurrence_matrixcount_distinct_elementscount_distinct_elements_per_list_itemcount_distinct_elements_per_list_item_shuffledelement_covariateelement_covariate_networkelement_durationelement_positionfind_most_similar_columnsgenerate_sequencelong_to_sequencesmedian_seq_lengthmenzerath_plotmin_max_seq_lengthperform_clusteringplot_seq_length_distributionredundancysd_seq_lengthsequence_duration_summarysequence_length_summarysequence_length_summary_covariatesequence_length_summary_elementsequences_to_longshuffle_sequences_acrossshuffle_sequences_withintemporal_overlaptransition_chisqtransition_entropytransition_predictionstransition_testzipf_plot

Dependencies:apclustercachemclasscliclustercolorspacecpp11dbscanDEoptimRdiptestdplyrfansifarverfastmapflexmixfpcgenericsggforceggplot2ggraphggrepelgluegraphlayoutsgridExtragtableigraphisobandjaneaustenrjsonlitekernlablabelinglatticelifecyclemagrittrMASSMatrixmclustmemoisemgcvmodeltoolsmunsellnaivebayesnlmennetpillarpkgconfigpolyclipprabcluspurrrR6rangerRColorBrewerRcppRcppArmadilloRcppEigenrlangrobustbasescalesSnowballCstringistringrsystemfontstibbletidygraphtidyrtidyselecttidytexttokenizerstweenrutf8vctrsviridisviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Calculate Association Metrics for Sequencesassociation_metrics
Calculate the Average Length of Sequencesaverage_seq_length
Calculate Conditional Entropy of B given A in Bitscalculate_conditional_entropy
Calculate Distance Matrix from Co-occurrence Matrixcalculate_distance_matrix
Calculate Transition Counts from Sequencescalculate_transition_counts
Calculate Transition Probabilities from Sequencescalculate_transition_probs
Cluster Elements Using Hierarchical Clusteringcluster_elements
Compare True and Shuffled Distinct Elements per List Itemcompare_distinct_elements_per_list_item
Calculate Co-occurrence Matrix for Sequencescooccurrence_matrix
Count Distinct Elements in Sequencescount_distinct_elements
Count Distinct Elements per List Itemcount_distinct_elements_per_list_item
Count Distinct Elements per List Item in Shuffled Sequencescount_distinct_elements_per_list_item_shuffled
Calculate Element-Covariate Conditional Probabilitieselement_covariate
Plot the network of elements and covariates based on the long format of sequenceselement_covariate_network
Calculate Individual Element Durationselement_duration
Calculate Median Position of Each Element in Sequenceselement_position
Find Most Similar Columns in a Distance Matrixfind_most_similar_columns
Generate a Sequence of Elementsgenerate_sequence
Convert Long Format to Sequenceslong_to_sequences
Calculate the Median Length of Sequencesmedian_seq_length
Create a Menzerath-Altmann Plotmenzerath_plot
Calculate the Minimum and Maximum Length of Sequencesmin_max_seq_length
Perform Various Clustering Methodsperform_clustering
Plot the Distribution of Sequence Lengthsplot_seq_length_distribution
Calculate Observed and Expected Redundancy of Sequencesredundancy
Calculate the Standard Deviation of Sequence Lengthssd_seq_length
Summarize Sequence Durationssequence_duration_summary
Summarize Sequence Lengthssequence_length_summary
Summarize Sequence Lengths by Covariatesequence_length_summary_covariate
Summarize Sequence Lengths by Elementsequence_length_summary_element
Convert Sequences to Long Formatsequences_to_long
Shuffle Elements Across All Sequencesshuffle_sequences_across
Shuffle Elements Within Each Sequenceshuffle_sequences_within
Temporal Overlaptemporal_overlap
Perform a Chi-Squared Test for Transition Countstransition_chisq
Calculate Transition Entropy for Sequencestransition_entropy
Transition Predictionstransition_predictions
Perform a Statistical Test for Transition Probabilitiestransition_test
Create a Zipf's Law Plotzipf_plot