Package: timeordered 1.0.1

timeordered: Time-Ordered and Time-Aggregated Network Analyses

Approaches for incorporating time into network analysis. Methods include: construction of time-ordered networks (temporal graphs); shortest-time and shortest-path-length analyses; resource spread calculations; data resampling and rarefaction for null model construction; reduction to time-aggregated networks with variable window sizes; application of common descriptive statistics to these networks; vector clock latencies; and plotting functionalities. The package supports <doi:10.1371/journal.pone.0020298>.

Authors:Benjamin Wong Blonder [aut, cre]

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timeordered.pdf |timeordered.html✨
timeordered/json (API)

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

Peer review:

Bug tracker:https://github.com/bblonder/timeordered/issues

Datasets:
  • ants - Ant interaction data

On CRAN:

2.92 score 3 stars 28 scripts 373 downloads 32 exports 13 dependencies

Last updated 2 months agofrom:087481bb3f. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 15 2024
R-4.5-winOKOct 15 2024
R-4.5-linuxOKOct 15 2024
R-4.4-winOKOct 15 2024
R-4.4-macOKOct 15 2024
R-4.3-winOKOct 15 2024
R-4.3-macOKOct 15 2024

Exports:applynetworkfunctioncontact_randomizationedge_randomizationgeneratelatenciesgeneratenetworkslicesgeneratetimeaggregatednetworkgeneratetimedeltasgeneratetimelagsgeneratetonetworkgeneratetonetworkfromvelgeneratevertexedgelistmaxpointsmidpointsplotnetworkslicesplottanetplottonetrandom_timesrandomize_edges_helperrandomized_contactsrandomized_edgesrandomizeidentitiesrandomizetimesrandomly_permuted_timesrarefyshortesthoppathshortesttimepathspreadanalysisswaptime_reversaltotal_randomizationtransformspreadbyindividualvertex_randomization

Dependencies:clicpp11glueigraphlatticelifecyclemagrittrMatrixpkgconfigplyrRcpprlangvctrs

Readme and manuals

Help Manual

Help pageTopics
Ant interaction dataants
Applies a function (typically a descriptive statistic) to multiple time-aggregated networksapplynetworkfunction
Generates vector-clock latencies for each individual at each time.generatelatencies
Generates multiple time-aggregated networks from a time-ordered networkgeneratenetworkslices
Constructs a weighted time-aggregated network from a time-ordered network by aggregating interactions occurring between a start and stop time. Weights are stored as E(g)$weight.generatetimeaggregatednetwork
Constructs matrix of sequential time windows suitable for slicing time ordered networksgeneratetimedeltas
Constructs matrix of increasingly large time windows suitable for assessing how window size affects time aggregated networksgeneratetimelags
Generates a time-ordered network from an interaction list.generatetonetwork
Generates a time-ordered network from a data frame listing all directed edges. An internal function.generatetonetworkfromvel
Generates a data frame listing all directed edges in a time-ordered network from an observed interaction list. An internal function.generatevertexedgelist
Determines the maximum value of each row of a matrix; used as a convenience function for plotting.maxpoints
Determines the mean value of each row of a matrix; used as a convenience function for plotting.midpoints
Plots a time-aggregated networkplotnetworkslices
Plots a time-aggregated network.plottanet
Plots a time-ordered network.plottonet
Does all the work for 'edge_randomization' and 'randomized_edges'. An internal function.randomize_edges_helper
Resamples data based on vertex identity.randomizeidentities
Resamples data based on event time.randomizetimes
Randomize temporal networkscontact_randomization edge_randomization randomized_contacts randomized_edges randomly_permuted_times random_times time_reversal total_randomization vertex_randomization
Simulates the effect of insufficient sampling by data rarefaction.rarefy
Determines a path (shortest by the least number of unique vertices) between two vertices at two times.shortesthoppath
Determines a path (shortest by the least time) between a vertex at a start time and another vertex at any later time.shortesttimepath
Simulates the perfect spread of a resource on a time-ordered network.spreadanalysis
Swaps two elements in a data frame. An internal function.swap
A helper function to assess differences in spreading potential by vertex.transformspreadbyindividual