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2_observations.yml
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2_observations.yml
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target_default: 2_observations
packages:
- sf
- tidyverse
- lwgeom
- smoothr
- igraph
- purrr
- dataRetrieval
- readr
- readxl
- lubridate
- purrr
sources:
- 2_observations/src/crosswalk_functions.R
- 2_observations/src/data_munge_functions.R
- 2_observations/src/subset_closest.R
- 2_observations/src/pull_ngwos_dat.R
- 2_observations/src/munge_flow_dat.R
- 2_observations/src/munge_diversion_data.R
- 2_observations/src/munge_surface_area_data.R
- 2_observations/src/flag_seg_matches.R
targets:
2_observations:
depends:
- 2_observations/out/drb_temp_summary.csv
- 2_observations/out/drb_flow_summary.csv
- 2_observations/out/realsat_monthly_surface_area.csv.ind
- 2_observations/out/interpolated_daily_reservoir_water_budget_components.csv.ind
- 2_observations/out/reservoir_releases_by_type_drb.csv.ind
- 2_observations/out/reservoir_diversions.csv.ind
2_observations/out/NGWOS_sites_data.rds.ind:
command: retrieve_ngwos(
out_ind = target_name,
sites_ind = '2_observations/in/NGWOS_site_metadata.xlsx.ind')
# identify sites that we feel confident calling "NGWOS" sites for experiment purposes
ngwos_sites:
command: filter_ngwos(ngwos_ind = '2_observations/out/NGWOS_sites_data.rds.ind')
holdout_water_years:
command: c(I(1980:1984), I(2011:2015), I(2021))
#seg_id_nats; Birch Run is a Christina basin headwater; Willowemoc is a northern site upstream of all reservoirs
holdout_reach_ids:
command: c('Willowemoc Creek' = 1455,
'Callicoon' = 1578,
'Beltzville' = 1703,
'Beltzville' = 1697,
'Birch Run' = 2007,
'Trenton' = 1498,
'Schuylkill @PHL' = 2338,
'Maurice River' = 3570)
# temperature data and sites info comes from the national NWIS temperature pull: https://github.com/USGS-R/2wp-temp-observations
2_observations/out/crosswalk_site_reach.rds.ind:
command: crosswalk_sites_to_reaches(
out_ind = target_name,
temp_sites_ind = '2_observations/in/stream_sites_us.rds.ind',
flow_sites_ind = '2_observations/in/observation_summary.rds.ind',
boundary_ind = '1_network/out/boundary.rds.ind',
network_ind = '1_network/out/network.rds.ind')
# do some QA on site-to-reach matches
# NHDPlusV2 - NHM crosswalk, download and indicate
2_observations/out/GFv1_NHDv2_xwalk.csv.ind:
command: fetch_xwalk(
out_ind = target_name,
url = I("https://raw.githubusercontent.com/USGS-R/drb-network-prep/c45f469098dfb245a2d686b807a58afa00b9d0b2/2_process/out/GFv1_NHDv2_xwalk.csv"))
# refgages - download and indicate
2_observations/out/usgs_nldi_gages.geojson.ind:
command: fetch_refgages(
out_ind = target_name,
url = I('https://github.com/internetofwater/ref_gages/releases/download/v0.6/usgs_nldi_gages.geojson'))
# a subset of "useable" sites in DRB, munged by:
# 1) filtering by bird and fish distance
2_observations/out/drb_filtered_sites.rds.ind:
command: subset_sites(
out_ind = target_name,
crosswalk_ind = '2_observations/out/crosswalk_site_reach.rds.ind',
fish_dist = I(20000),
bird_dist = I(250))
# flag site-to-reach matches using a number of techniques,
# including cross-referencing refgages, independently matching
# to NHD reaches, looking at watershed size as it compares to reported
# NWIS value, and look for "tributary" in site name
2_observations/out/flagged_sitetoreach_matches.rds.ind:
command: site_to_reach_flags(
out_ind = target_name,
sites_ind = '2_observations/out/drb_filtered_sites.rds.ind',
cross_ind = '2_observations/out/GFv1_NHDv2_xwalk.csv.ind',
refgages_ind = '2_observations/out/usgs_nldi_gages.geojson.ind')
# compare the latest flagged sites to Lauren's manual/visual
# inspection of the originally flagged sites. Write "new flagged sites"
# that have not been manually inspected to a file and throw a warning.
2_observations/out/check_flagged_sites.rds.ind:
command: check_new_flags(
out_ind = target_name,
manualqa_ind = '2_observations/in/drb_filtered_sites_seg_match_QC.csv.ind',
siteqa_ind = '2_observations/out/flagged_sitetoreach_matches.rds.ind')
# use Lauren's "manual" decision about flagged sites to
# keep them in/out of dataset
2_observations/out/drb_filtered_sites_qa.rds.ind:
command: remove_bad_matches(
out_ind = target_name,
manualqa_ind = '2_observations/in/drb_filtered_sites_seg_match_QC.csv.ind',
sites_ind = '2_observations/out/drb_filtered_sites.rds.ind')
# write a summary of matched sites to track changes
2_observations/out/site_summary.csv:
command: summarize_sites(out_file = target_name, in_ind = '2_observations/out/drb_filtered_sites_qa.rds.ind')
# temperature observations that have been filtered to crosswalk
# this represent all DRB dat
2_observations/out/all_drb_temp_obs.rds.ind:
command: filter_temp_data_to_crosswalk(
dat_ind = '2_observations/in/daily_temperatures_qaqc.rds.ind',
cross_ind = '2_observations/out/crosswalk_site_reach.rds.ind',
out_ind = target_name)
# keep only data in the filtered sites above
2_observations/out/obs_temp_drb_raw.rds.ind:
command: filter_temp_data_to_sites(
sites_ind = '2_observations/out/drb_filtered_sites_qa.rds.ind',
dat_ind = '2_observations/out/all_drb_temp_obs.rds.ind',
out_ind = target_name)
# take mean of multiple obs/reach-dat to reduce duplicate vals
2_observations/out/obs_temp_drb.rds.ind:
command: munge_split_temp_dat(
dat_ind = '2_observations/out/obs_temp_drb_raw.rds.ind',
holdout_water_years = holdout_water_years,
holdout_reach_ids = holdout_reach_ids,
out_ind = target_name,
prioritize_nwis_sites = TRUE)
priority_sites:
command: c(I(c('01427207', '01417500', '01427000', '01426500', '01436690')))
# for priority sites, repull from NWIS, append any
# missing dates from "other" sources
2_observations/out/obs_temp_priority_sites.csv.ind:
command: get_priority_data(
out_ind = target_name,
dummy_date = I('2021-07-12'),
sites = priority_sites,
pcode = I('00010'),
statcd = I(c('00001', '00002', '00003')),
site_meta_ind = I('2_observations/out/crosswalk_site_reach.rds.ind'),
other_dat_ind = '2_observations/out/obs_temp_drb.rds.ind',
holdout_water_years = holdout_water_years,
holdout_reach_ids = holdout_reach_ids)
# ngwos reaches that should be withheld after 2017-10-01 for NGWOS experiment
ngwos_reaches:
command: get_ngwos_reaches(sites_ind = '2_observations/out/drb_filtered_sites.rds.ind', ngwos_sites)
# discharge data
2_observations/out/obs_flow_drb.rds.ind:
command: munge_split_flow(
out_ind = target_name,
dat_ind = '2_observations/in/daily_flow.rds.ind',
sites_ind = '2_observations/out/drb_filtered_sites_qa.rds.ind',
holdout_water_years = holdout_water_years,
holdout_reach_ids = holdout_reach_ids)
# for priority sites, repull from NWIS, append any
# missing dates from "other" sources
2_observations/out/obs_flow_priority_sites.csv.ind:
command: get_priority_data(
out_ind = target_name,
dummy_date = I('2021-06-17'),
sites = priority_sites,
pcode = I('00060'),
statcd = I('00003'),
site_meta_ind = I('2_observations/out/crosswalk_site_reach.rds.ind'),
holdout_water_years = holdout_water_years,
holdout_reach_ids = holdout_reach_ids)
2_observations/out/drb_temp_summary.csv:
command: summarize_dat(in_ind = '2_observations/out/obs_temp_drb.rds.ind', out_file = target_name)
2_observations/out/drb_flow_summary.csv:
command: summarize_dat(in_ind = '2_observations/out/obs_flow_drb.rds.ind', out_file = target_name)
# reservoir release data provided by NYC DEP
2_observations/out/reservoir_releases.csv.ind:
command: clean_release_dat(
in_ind = '2_observations/in/PCN_Spill_Release.xlsx.ind',
out_ind = target_name,
mgd_to_cms = I(0.0438125))
# modern reservoir releases that can be retrieved from NWIS.
# These are real-time releases that started in March 2021
2_observations/out/modern_reservoir_releases.rds.ind:
command: get_releases(
out_ind = target_name,
site_ids = I(c('01436499', '01417499', '01436599')),
reservoir_names = I(c('Cannonsville', 'Pepacton', 'Neversink')))
# reservoir diversion data
# you must download reservoir data from here: 'https://doimspp-my.sharepoint.com/:f:/g/personal/soliver_usgs_gov/EiawwIR59vdApLCkeyob4t0Bx86d2SoTic8ahCm6MH5wRA?e=KEk1zE'
# unzip downloaded folder to 2_observations/in
# such that the structure becomes
# 2_observations/in/reservoir_data
# WY2009 data/
# ...
# 01416900.WY2008.xls
# ...
2_observations/out/observed_daily_reservoir_water_budget_components.csv.ind:
command: read_munge_daily_diversions(out_ind = target_name)
2_observations/out/observed_monthly_reservoir_water_budget_components.csv.ind:
command: read_munge_monthly_diversions(
in_file = '2_observations/in/reservoir data/manually_extracted_diversions.csv',
out_ind = target_name)
# interpolate to daily values
# use daily observed values when available, populate same diversion value
# over month when monthly values vailable
2_observations/out/interpolated_daily_reservoir_water_budget_components.csv.ind:
command: interpolate_diversions_to_daily(
out_ind = target_name,
daily_ind = '2_observations/out/observed_daily_reservoir_water_budget_components.csv.ind',
monthly_ind = '2_observations/out/observed_monthly_reservoir_water_budget_components.csv.ind',
end_date = I('2020-12-31'),
mgd_to_cms = 0.0438, cfs_to_cms = 0.0283,
mg_to_cm = 3785.41, ft_to_m = 0.3048)
# reservoir surface area data
# You must download reservoir Monthly Shapefiles from here: 'http://umnlcc.cs.umn.edu/realsat/'.
# The reservoir reaLSAT ID can be found in the Base shapefile: ReaLSAT.shp.
# ReaLSAT.shp has no attribute information other than id --> the best way to find the reservoir
# id is to load the shapefile in ArcMap and zoom to where your reservoir is, visually id it by shape
# and then select the polygon to identify its reaLSAT id.
# The reservoir-specific shapefiles with surface-area data are zipped within larger monthly shapefiles.
# For each reaLSAT id, the corresponding monthly shapefile folder is numbered according
# to the LAST digit of the ID, e.g. the shapefile for 573567 is in the zipped monthly shapefile folder named '7'
# Download and unzip the monthly shapefile folder and place the reservoir-specific folder with its shapefile
# in 2_observations/in/realsat, such that the structure becomes:
# 2_observations/in/realsat/ID:
# in/realsat/573567/573567.shp
# in/realsat/573536/573536.shp
realsat_ids:
command: c(Pepacton = I('573567'), Cannonsville = I('573536'), Cannonsville = I('556766'))
2_observations/out/raw_realsat_reservoir_data.csv.ind:
command: retrieve_realsat_reservoir_data(
reservoir_ids = realsat_ids,
out_ind = target_name)
2_observations/out/realsat_monthly_surface_area.csv.ind:
command: combine_realsat_reservoir_data(
in_ind = '2_observations/out/raw_realsat_reservoir_data.csv.ind',
out_ind = target_name)
# combine all sources of releases to complete total release time series
# the manually extracted ODRM data is being used to cover the gaps between
# these data sources
2_observations/out/complete_reservoir_releases.csv.ind:
command: combine_release_sources(
out_ind = target_name,
hist_rel_ind = '2_observations/out/reservoir_releases.csv.ind',
usgs_rel_ind = '2_observations/out/observed_daily_reservoir_water_budget_components.csv.ind',
modern_rel_ind = '2_observations/out/modern_reservoir_releases.rds.ind',
manual_rel_ind = '2_observations/in/manually_extracted_odrm_data.csv.ind')
2_observations/out/reservoir_releases_by_type_drb.csv.ind:
command: combine_releases_by_type(
out_ind = target_name,
hist_rel_ind = '2_observations/out/reservoir_releases.csv.ind',
modern_rel_ind = '2_observations/out/modern_reservoir_releases.rds.ind')
2_observations/out/reservoir_diversions.csv.ind:
command: extract_diversions(
out_ind = target_name,
hist_ind = '2_observations/out/interpolated_daily_reservoir_water_budget_components.csv.ind',
mod_ind = '2_observations/out/modern_reservoir_releases.rds.ind')