In KevinSee/PITcleanr: Cleans up PIT tag capture histories

The user may also be interested in getting the flowlines (i.e., the stream or river network), for their sites of interest. PITcleanr provide the function queryFlowlines() to accomplish that. queryFlowlines() downloads an NHDPlus v2 stream layer from USGS using the suggested nhdplusTools R package. It requires the spatial location of sites as an sf object (such as the output of extractSites()), and a site code identified as the "root" site. The root site might correspond with your tagging or release location and is provided to the root_site_code argument. The function starts from the root_site_code and downloads all flowlines upstream from there, with a minimum stream order set by min_strm_order.

If flowlines downstream of the root_site_code site are required, set the argument dwnstrm_sites = TRUE (default is FALSE). This might be useful if the user is interesting in analyzing or modeling sites downstream of the release site. If you're not interested in analyzing/modeling downstream sites you can set dwnstrm_sites = FALSE which may speed up the function considerably.

The user can also control the minimum stream order of the downstream flowlines by setting the dwn_min_stream_order_diff argument. Note: smaller stream orders correspond to smaller streams. This can be useful if the user is not interested or wants to prevent downloading all sorts of tiny streams downstream of a tagging or release location; the dwn_min_stream_order_diff is an attempt to constrain the amount of flowlines downloaded downstream of the root_site_code which can be sizable. The dwn_min_stream_order_diff corresponds to the difference between the stream order of the root_site_code site and the minimum stream order desired in the downstream flowlines. In our example, our root_site_code is located on a stream order of 5 (Wenatchee River) and dwn_min_stream_order_diff = 2, in this case only downstream flowlines of at least 5-2 = 3 will be downloaded. The extent of the downstream flowlines is further constrained by the sites_sf object. The queryFlowlines() function returns a list consisting of:

flowlines: the flowlines upstream of the root_site_code
basin: the polygon containing the upstream flowlines
dwn_flowlines: the flowlines downstream of the root_site_code, if dwnstrm_sites = T

Depending on the spatial extent of your flowlines, the queryFlowlines() function may take awhile. Here we create a list of objects, nhd_list. We then use the function rbind() to combine the nhd$flowlines and nhd$dwn_flowlines into a single flowlines simple feature object. More information on the nhdplusTools R package can be found here.

# query the flowlines
nhd_list = queryFlowlines(sites_sf = sites_sf,
                          root_site_code = "TUM",
                          min_strm_order = 2,
                          dwnstrm_sites = T,
                          dwn_min_stream_order_diff = 2)

# join the upstream and downstream flowlines
flowlines = nhd_list$flowlines %>%
    rbind(nhd_list$dwn_flowlines)