Package: streamDAG 1.5-9

streamDAG: Analytical Methods for Stream DAGs

Provides indices and tools for directed acyclic graphs (DAGs), particularly DAG representations of intermittent streams. A detailed introduction to the package can be found in the publication: "Non-perennial stream networks as directed acyclic graphs: The R-package streamDAG" (Aho et al., 2023) <doi:10.1016/j.envsoft.2023.105775>, and in the introductory package vignette.

Authors:Ken Aho [aut, cre], Arya Legg [dtc, ctb], Rob Ramos [dtc], Maggi Kraft [dtc], Charles T. Bond [dtc], Rebecca L. Hale [dtc]

streamDAG_1.5-9.tar.gz
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streamDAG.pdf |streamDAG.html✨
streamDAG/json (API)

# Install 'streamDAG' in R:
install.packages('streamDAG', repos = c('https://moondog1969.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/moondog1969/streamdag/issues

Datasets:

On CRAN:

4.40 score 4 scripts 561 downloads 47 exports 32 dependencies

Last updated 2 months agofrom:38b434600a. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 04 2024
R-4.5-winWARNINGNov 04 2024
R-4.5-linuxWARNINGNov 04 2024
R-4.4-winWARNINGNov 04 2024
R-4.4-macWARNINGNov 04 2024
R-4.3-winWARNINGNov 04 2024
R-4.3-macWARNINGNov 04 2024

Exports:AA.multarc.pa.from.nodesassign_pa_to_segmentsassortavg.efficiencybern.lengthbeta.posteriorbiv.berndegree.distsdelete.arcs.padelete.nodes.padinvbetaefficiency.matrixget.AIMS.dataglobal.efficiencyglobal.summaryhararyI.DICSLimp.closenessislelocal.summarymax_rmin_rmulti.path.visibilityn.sourcesn.tot.pathspath.lengths.sinkpath.visibilitypinvbetaplot_degree.distprint.network_to_sfR.boundsrinvbetasink.Gsize.intact.to.arcsize.intact.to.nodesize.intact.to.sinksourcesspath.lengthsspatial.plotspatial.plot.sfSTIC.RFimputestream.orderstreamDAGsvector_segments

Dependencies:asbiocachemclicodetoolscpp11deSolvedigestdoRNGfastmapforeachgluegWidgets2gWidgets2tcltkigraphiteratorsitertoolslatticelifecyclemagrittrMatrixmemoisemissForestmultcompViewmvtnormpixmappkgconfigplotrixrandomForestrlangrngtoolsscatterplot3dvctrs

Introduction to streamDAG

Ken Aho

Rendered fromstreamDAG.Rmdusingknitr::rmarkdownon Nov 04 2024.

Last update: 2024-10-04
Started: 2023-05-30

Readme and manuals

Help Manual

Help pageTopics
Arcs of a directed graphA
Raise an adjacency matrix to some powerA.mult
Nodal coordinates for graphs in the AIMS projectAIMS.node.coords
Obtain arc stream activity outcomes based on bounding nodesarc.pa.from.nodes
Assortativityassort
Botter and Durighetto Bernoulli stream lengthbern.length
Posterior Beta and Inverse-beta summariesbeta.posterior
Bivariate Bernoulli Distributionbiv.bern
Stream segment presence absence data for Dry Cr. Idahodc_arc_pres_abs
Lengths of Dry Creek stream (arc) segmentsdc_lengths
Stream node presence absence data for Dry Cr. Idahodc_node_pres_abs
Potential degree distributionsdegree.dists
Delete arcs based on presence absence datadelete.arcs.pa
Delete nodes based on presence absence datadelete.nodes.pa
Inverse Beta Distributiondinvbeta pinvbeta rinvbeta
Local and global efficiencyavg.efficiency efficiency.matrix global.efficiency
Loads AIMS dataset associated with a particular AIMS graphget.AIMS.data
Coordinates of nodes at Gibson Jack Creek, Idaho for a 2016 surveygj_coords16
Lengths of Gibson Jack stream (arc) segmentsgj_lengths gj_lengths_piezo_full
Stream node presence absence data for Gibson Jack Idahogj_node_pres_abs
Stream node presence absence data for Gibson Jack Cr. Idaho, for a 2016 surveygj_node_pres_abs16
Global Summaryglobal.summary
Harary Indexharary
Generalized DAG indicesI.D
Integral connectivity scale length (ICSL)ICSL
Improved Closeness Centralityimp.closeness
Detects and defines islands in a streamDAGisle
Lengths of Johnson Draw stream (arc) segmentsjd_lengths jd_lengths_2023 jd_lengths_full
Stream node presence absence data for Johnson Draw Idahojd_node_pres_abs
Coordinates of nodes in the Konza Praire datasetkon_coords
Lengths of Murphy Cr. stream (arc) segmentskon_lengths
local (nodal) summaries of a DAGlocal.summary
Stream segment presence absence data for Murphy Cr. Idahomur_arc_pres_abs
Coordinates of nodes at Murphy Ck. Idahomur_coords
Lengths of Murphy Cr. stream (arc) segmentsmur_lengths
Stream node presence absence data for Murphy Cr. Idahomur_node_pres_abs
Simulated seasonal arc presence absence data for Murphy Crmur_seasons_arc_pa
Identify source and sink nodesn.sources sources
Path Lengthspath.lengths.sink
Path Visibilitiesmulti.path.visibility path.visibility visibility
Plot degree distributionsplot_degree.dist
Bounds for the correlation of two (or more) Benrnoulli random variablesmax_r min_r R.bounds
Size of the intact network above an arcsize.intact.to.arc
Size of intact network that feeds into the sink or a particular nodesize.intact.to.node size.intact.to.sink
Shortest path lengths and number of pathsn.tot.paths spath.lengths
Spatial plot of an igraph object or stream shapefilespatial.plot spatial.plot.sf
A wrapper for missForest for random forest STIC imputationSTIC.RFimpute
Strahler or Shreve stream order of a stream DAGsink.G stream.order
Stream DAG datasetsstreamDAGs
Functions for overlaying networks on shapefilesassign_pa_to_segments print.network_to_sf vector_segments