In KevinSee/PITcleanr: Cleans up PIT tag capture histories

The queryPtagisMeta() and buildConfig() functions in PITcleanr return information from all INT and MRR sites in PTAGIS. However, the user may only be interested in detections from site codes found within their complete tag history output, e.g., your cth_file. The extractSites() function does just that: extracts the site codes found in the complete tag history. In addition, the detections can be filtered by a minimum and/or maximum detection date, and the results are returned as either a tibble, or as a simple (spatial) feature sf object. Setting the min_date argument could be useful if the user is not interested in detections at sites prior to your study period e.g., detections that occur prior to fish arriving at your tagging or release location.

In this example, we create a new object sites_sf, return it as an sf object (by setting as_sf = T) and only return sites from those detections that occurred after May 1, 2018. We also extract sites only from the Wenatchee subbasin and remove a couple sites that we perhaps don't care about. More information on simple features (sf objects) can be found here.

sites_sf = extractSites(cth_file,
                        as_sf = T,
                        min_date = "20180501")

# focus on sites within Wenatchee subbasin, and drop a few sites we don't care about
sites_sf <- sites_sf %>%
  # all sites in the Wenatchee have a river kilometer that starts with 754
  filter(str_detect(rkm, "^754."),
         type != "MRR",
         site_code != "LWE") |> 
  mutate(across(site_code,
                ~ recode(.,
                         "TUF" = "TUM")))

The user could create their own sf object of detection sites, either by hand in R, or by using GIS software to create a shapefile or geopackage that can then be read into R using the st_read() function in the sf package. If the user chooses this path, the file must contain at least a column called site_code, whose values should be the same site codes found in the configuration file. Other columns are optional. The extractSites() function returns an sf object with the following columns (gleaned from the configuration file):

• site_code
• site_name
• site_type
• type
• rkm
• site_description

extractSites() will also accept a configuration file as an argument, if the user wants to pass one of their own in. Such a file should contain all the columns listed above.

KevinSee/PITcleanr documentation built on Feb. 27, 2024, 11:03 p.m.