streamDAGs: Stream DAG datasets
In streamDAG: Analytical Methods for Stream DAGs

streamDAGs

R Documentation

Stream DAG datasets

Description

The function contains a number of stream direct acyclic graph datasets written in igraph format. See: graph_from_literal. Many of the graphs were based on sampling regimes for the National Science Foundation Aquatic Intermittency Effects on Microbiomes in Streams (AIMS) project.

Usage

streamDAGs(graph = c("dc_piezo_full", "dc_full", "gj_full16", "gj_synoptic_2023", 
"gj_full", "gj_piezo_full", "jd_piezo_full", "jd_piezo_full_2023","jd_full", 
"konza_full", "KD0521", "KD0528", "KD0604", "mur_full", "td_full", "wh_full", 
"pr_full"))

Arguments

graph

Currently, one of "dc_piezo_full", "dc_full", "gj_full16", "gj_full16", "gj_synoptic_2023", "gj_full", "gj_piezo_full", "jd_piezo_full", "jd_piezo_full_2023", "jd_full", "konza_full", "KD0521", "KD0528", "KD0604", "mur_full", "pr_full", "td_full", or "wh_full" (see Details below).

Details

Currently, the following graph options exist. Note that many of the graphs have associated datasets. Obtaining these datasets is now greatly simplified through the use of get.AIMS.data (code steps shown below are unnecessary).

"dc_piezo_full" codifies the Dry Creek stream network in southwestern Idaho for STIC (Stream Temperature, Intermittency, and Conductivity) sensors, confluences, and piezometer locations (outlet coordinates: 43.71839^\circN, 116.13747^\circW).
- Network spatial coordinates for this graph can be subset from AIMS.node.coords using: AIMS.node.coords$site == "DC".
- Nodal surface water presence/absence data for this graph can be obtained directly from dc_node_pres_abs.
- Arc lengths for this graph can be obtained directly from dc_lengths.
"dc_full" codifies the Dry Creek stream network in southwestern Idaho but only for STICs and confluences, not piezometer locations (outlet coordinates: 43.71839^\circN, 116.13747^\circW).
- Network spatial coordinates for this graph can be subset from AIMS.node.coords using: AIMS.node.coords$site == "DC" & AIMS.node.coords$STIC_inferred_PA.
- Nodal surface water presence/absence data for this graph can be obtained using dc <- streamDAGs("dc_full") followed by dc_node_pres_abs[attributes(V(dc))$names].
"gj_full16" codifies nodes established at the Gibson Jack drainage in southeast Idaho, as defined in 2016 (outlet coordinates: 42.767180^\circN, 112.480240^\circW).
"gj_full" codifies nodes established at the Gibson Jack drainage in southeast Idaho for STIC sensors in 2022-2023, along with confluence locations. Piezometer locations not included (outlet coordinates: 42.767180^\circN, 112.480240^\circW).
- Network spatial coordinates for this graph can be subset from AIMS.node.coords using: AIMS.node.coords$site == "GJ" & AIMS.node.coords$STIC_inferred_PA.
- Nodal surface water presence/absence data for this graph can be obtained from: gj_node_pres_abs using gj <- streamDAGs("gj_full"); vnames <- attributes(V(gj))$names; w <- which(names(gj_node_pres_abs)[-1] %in% vnames) + 1; node.pa <- gj_node_pres_abs[,c(1,w)].
- Arc lengths for this graph can be obtained from gj_lengths_piezo_full using gj <- streamDAGs("gj_full"); anames <- attributes(E(gj))$vnames; enames <- gsub("\|", " -> ", anames); m <- match(enames, gj_lengths_piezo_full[,1]) gj_lengths_piezo_full[m,].
"gj_piezo_full" codifies nodes established at the Gibson Jack drainage in southeast Idaho, by the the AIMS team which include longterm STICs and piezometers, along with confluence locations (outlet coordinates: 42.767180^\circN, 112.480240^\circW).
- Network spatial coordinates for this graph can be subset from AIMS.node.coords using: AIMS.node.coords$site == "GJ" & (AIMS.node.coords$STIC_inferred_PA | AIMS.node.coords$piezo).
- Nodal surface water presence/absence data for this graph can be obtained using gj <- streamDAGs("gj_piezo_full") followed by gj_node_pres_abs[attributes(V(gj))$names].
- Arc lengths for this graph can be obtained from gj_lengths_piezo_full using gj <- streamDAGs("gj_piezo_full"); anames <- attributes(E(gj))$vnames; enames <- gsub("\|", " -> ", anames); m <- match(enames, gj_lengths_piezo_full[,1]); gj_lengths_piezo_full[m,].
"gj_synoptic_2023" codifies nodes established at the Gibson Jack drainage in southeast Idaho by the AIMS team during synoptic sampling in 2023, includes piezometers and additional sites to those sampled in "gj_full" (outlet coordinates: 42.767180^\circN, 112.480240^\circW).
"jd_piezo_full" codifies the Johnson Draw stream network in southwestern Idaho for both STIC and and piezometer locations (outlet coordinates: 43.12256^\circN, 116.77630^\circW).
- Network spatial coordinates for this graph can be subset from AIMS.node.coords using: AIMS.node.coords$site == "JD" & AIMS.node.coords$New_in_2023 == FALSE.
- Nodal surface water presence/absence data for this graph can be obtained from jd_node_pres_abs using jd <- streamDAGs("jd_piezo_full") followed by jd_node_pres_abs[attributes(V(jd))$names].
- Arc lengths can be subset from jd_lengths_2023 using something like: jd <- streamDAGs("jd_piezo_full"); anames <- attributes(E(jd))$vnames; nnames <- gsub("\\|", " -> ", anames); jd_lengths_2023[which(jd_lengths_2023[,1] %in% nnames ),].
"jd_piezo_full_2023" codifies the Johnson Draw stream network in southwestern Idaho for both STIC and and piezometer locations, along with new STIC locations added in 2023 (outlet coordinates: 43.12256^\circN, 116.77630^\circW).
- Network spatial coordinates for this graph can be subset from AIMS.node.coords using: AIMS.node.coords$site == "JD".
- Nodal surface water presence/absence data for this graph can be obtained from jd_node_pres_abs using jd <- streamDAGs("jd_piezo_full_2023") followed by jd_node_pres_abs[attributes(V(jd))$names].
- Arc lengths can be subset from jd_lengths_2023 using something like: jd <- streamDAGs("jd_piezo_full_2023"); anames <- attributes(E(jd))$vnames; nnames <- gsub("\\|", " -> ", anames); jd_lengths_2023[which(jd_lengths_2023[,1] %in% nnames ),].
"jd_full" codifies the Johnson Draw stream network in southwestern Idaho, but only for STICs, not piezometers (outlet coordinates: 43.12256^\circN, 116.77630^\circW).
- Network spatial coordinates for this graph can be subset from AIMS.node.coords using: AIMS.node.coords$site == "JD" & AIMS.node.coords$STIC_inferred_PA.
- Nodal surface water presence/absence data for this graph can be obtained using jd <- streamDAGs("jd_full") followed by jd_node_pres_abs[attributes(V(jd))$names].
- Arc lengths can be obtained from jd_lengths.
"konza_full" provides codification of a complete intermittent stream network of Konza Prairie in the northern Flint Hills region of Kansas (outlet coordinates: 39.11394^\circN, 96.61153^\circW).
- Network spatial coordinates for this graph can be obtained directly from kon_coords
- Arc lengths can be obtained from kon_lengths.
Options "KD0521","KD0528", and "KD0604" provide networks for Konza Prairie at 05/21/2021 (before spring snow melt), 05/28/2021 (during spring snow melt) and 06/04/2021 (drying following snow melt), respectively.
"mur_full" is an igraph codification of the complete Murphy Creek dataset from the Owyhee Mountains in SW Idaho (outlet coordinates: 43.256^\circN, 116.817^\circW) established in 2019 by Warix et al. (2021), also see Aho et al. (2023).
- Network spatial coordinates for the graph can be obtained directly from mur_coords
- Nodal surface water presence/absence data for this graph can be obtained from mur_node_pres_abs
- Arc lengths can be obrtained from mur_lengths.
"pr_full" codifies the Painted Rock stream network in northern Alabama (outlet coordinates: 34.96867^\circN, 86.16544^\circW).
- Network spatial coordinates for this graph can be subset from AIMS.node.coords using: AIMS.node.coords$site == "PR".
"td_full" codifies the Talladega stream network in central Alabama (outlet coordinates: 33.76218^\circN, 85.59552^\circW).
- Network spatial coordinates for this graph can be subset from AIMS.node.coords using: AIMS.node.coords$site == "TD".
"wh_full" codifies the Weyerhauser stream network in western Alabama (outlet coordinates: 32.98463^\circN, 88.01227^\circW).
- Network spatial coordinates for this graph can be obtained from AIMS.node.coords using: AIMS.node.coords$site == "WH".

Value

Returns a graph object of class igraph.

Author(s)

Ken Aho, Maggie Kraft, Rob Ramos, Rebecca L. Hale, Charles T. Bond, Arya Legg

References

Aho, K., Derryberry, D., Godsey, S. E., Ramos, R., Warix, S., & Zipper, S. (2023). The communication distance of non-perennial streams. EarthArvix doi: 10.31223/X5Q367

Warix, S. R., Godsey, S. E., Lohse, K. A., & Hale, R. L. (2021), Influence of groundwater and topography on stream drying in semi-arid headwater streams. Hydrological Processes, 35(5), e14185.