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