Metric Graph creating disconnected graph from fully connected spatial object

[Sylvanben]

Hi,

I am an inla user who has started to work on rivers so I am trying to learn this new technique. I am trying to creating a graph based on a river shapefile but I am having issues where metric graph is saying the graph is disconnected, however as far as I can tell, the underlying spatial object is continuous (processed with SF and converted to SP object). The metric graph object says there are 3 sections of floating lines, ranging from 2-9 segments. However, when I plot these they are clearly joined to the network in the underlying SP object which was used to create the graph, here is the code and I can provide the shapefile if someone can offer some help, thank you:

Metric Graph

##6/11/24

#devtools::install_github("davidbolin/MetricGraph", ref="devel")
#remotes::install_github("davidbolin/rspde", ref = "devel")

library(rSPDE)
library(INLA)
library(fmesher)
library(MetricGraph)
library(sf)
library(dplyr)
library(ggplot2)
library(viridis)

Load yggplot2# Load your river network and catchment shapefiles

river_network <- st_read(here::here("SpatialData/EPA River Network Moy.shp"))

Remove the Z and M dimensions (if present)

river_network <- st_zm(river_network)%>%
st_cast("LINESTRING") %>%
st_make_valid()

river_network <- river_network %>%
mutate(length_km=as.numeric(st_length(river_network))/1000)

invalid_geoms <- !st_is_valid(river_network)
sum(invalid_geoms)
t<-river_network[invalid_geoms, ]

Now transform the CRS to your target CRS (Irish Transverse Mercator)

river_network <- st_transform(river_network, crs = "+proj=tmerc +lat_0=53.5 +lon_0=-8 +k=0.99982 +x_0=600000 +y_0=750000 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=km +no_defs +type=crs")

Check the transformed object

print(river_network)

nrow(river_network)

SIMPLIFYING NETWORK HERE, REMOVE IF CAUSING ISSUES OR TOO SIMPLIFIED

river_network <- st_simplify(st_make_valid(river_network), dTolerance = 0.1) # Simplify by 100 meters

removing disconnected river segments -------------------------

library(igraph)
library(viridis)

touching_list = st_touches(river_network)
g = graph_from_adj_list(touching_list)
c = components(g)
table(c$membership)
hist(river_network$groups <- c$membership)
length(unique(river_network$groups))
river_network<-river_network %>% mutate(area=st_area(geometry))
#SELECT MAIN SPATIAL OBJECT --
river_network<-river_network %>% filter(groups==1)

##the SF object isnt working but the sp object is for some reason
river_network_sp <- as(river_network, "Spatial")

Create the MetricGraph object ---------------------------------------------------

graph <- metric_graph$new(river_network_sp, longlat = F, perform_merges = F)

Plot components to inspect disconnections

graph$plot(vertex_size = 0) #, color_components = TRUE

##use segment length as weights when caluclating spatial correlation
##not working because metric graph drop 3 segments -------------------------------
graph$set_edge_weights(weights = river_network$length_km)

_>Error in graph$set_edge_weights(weights = river_network$length_km) :

The length of 'weights' must be either 1 or 3902_

[davidbolin]

Hi, sure please send the shape file and I can take a look. You can try

graph <- metric_graph$new(river_network_sp)

and see if you get the same issue. You can also try setting perform_merges = TRUE and adjust the tolerance argument. However, the graph creating might take some time in this case if you have a large river network.