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corroborating ws attr summaries and ts vars
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Lines changed: 92 additions & 41 deletions

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‎eml/eml_templates/attributes_ws_attr_summaries.txt‎

Lines changed: 40 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -1,15 +1,16 @@
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"attributeName" "attributeDefinition" "class" "unit" "dateTimeFormatString" "missingValueCode" "missingValueCodeExplanation" "details"
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"network" "short name for the data network associated with a MacroSheds site. See sites.csv" "character"
3-
"domain" "Short name for the data domain associated with a MacroSheds site. See sites.csv" "character"
4-
"site_code" "Short name for MacroSheds site. See sites.csv" "character"
3+
"domain" "short name for the data domain associated with a MacroSheds site. See sites.csv" "character"
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"site_code" "short name for MacroSheds site. See sites.csv" "character"
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"ws_area_ha" "watershed area (see Methods and Protocols)" "numeric" "hectare" "NA" "missing value" "watershed area is calculated using the R function sf::st_area() with inputs from either watershed boundary shapefiles provided by domains or watershed shapfiles delineated by macrosheds based on latitude and longitude of stream gauges"
6-
"cc_mean_annual_precip" "mean annual watershed-mean precipitation over the entire record (see attribution_and_intellectual_rights_ws_attr.csv)" "numeric" "millimeter" "NA" "missing value"
7-
"cc_mean_annual_temp" "mean annual watershed-mean temperature over the entire record (see attribution_and_intellectual_rights_ws_attr.csv)" "numeric" "celsius" "NA" "missing value"
6+
"cc_mean_annual_precip" "mean annual watershed-median precipitation over the entire record (see attribution_and_intellectual_rights_ws_attr.csv)" "numeric" "millimeter" "NA" "missing value"
7+
"cc_mean_annual_temp" "mean annual watershed-median temperature over the entire record (see attribution_and_intellectual_rights_ws_attr.csv)" "numeric" "celsius" "NA" "missing value"
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"vd_mean_sos" "mean watershed Start of Growing Season over the entire record (see attribution_and_intellectual_rights_ws_attr.csv)" "numeric" "dayOfYear" "NA" "missing value"
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"vd_mean_eos" "mean watershed End of Growing Season over the entire record (see attribution_and_intellectual_rights_ws_attr.csv)" "numeric" "dayOfYear" "NA" "missing value"
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"vd_mean_los" "mean watershed Length of Growing Season over the entire record (see attribution_and_intellectual_rights_ws_attr.csv)" "numeric" "number" "NA" "missing value"
11-
"va_mean_annual_gpp" "mean annual watershed-mean terrestrial gross primary production over the entire record (see attribution_and_intellectual_rights_ws_attr.csv)" "numeric" "kilogramsCarbonPerSquareMeter" "NA" "missing value"
12-
"va_mean_annual_npp" "mean annual watershed-mean terrestrial net primary production over the entire record (see attribution_and_intellectual_rights_ws_attr.csv)" "numeric" "kilogramsCarbonPerSquareMeter" "NA" "missing value"
11+
"vd_mean_mos" "mean watershed Maximum of Growing Season (max day of canopy photosynthesis) over the entire record (see attribution_and_intellectual_rights_ws_attr.csv)" "numeric" "number" "NA" "missing value"
12+
"va_mean_annual_gpp" "mean annual watershed-median terrestrial gross primary production over the entire record (see attribution_and_intellectual_rights_ws_attr.csv)" "numeric" "kilogramsCarbonPerSquareMeter" "NA" "missing value"
13+
"va_mean_annual_npp" "mean annual watershed-median terrestrial net primary production over the entire record (see attribution_and_intellectual_rights_ws_attr.csv)" "numeric" "kilogramsCarbonPerSquareMeter" "NA" "missing value"
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"te_slope_mean" "mean watershed slope (see Methods and Protocols, attribution_and_intellectual_rights_ws_attr.csv)" "numeric" "percent" "NA" "missing value" "Watershed slope is calculated based on DEM downloaded with the R function elevatr::get_elev_raster() (from Amazon Web Services and Open Topography Global Datasets API) and the watershed shapefile with the R function whitebox::wbt_slope() "
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"te_elev_mean" "mean watershed elevation (see Methods and Protocols, attribution_and_intellectual_rights_ws_attr.csv)" "numeric" "meter" "NA" "missing value" "Watershed elevation is calculated based on DEM downloaded with the R function elevatr::get_elev_raster() (from Amazon Web Services and Open Topography Global Datasets API)"
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"te_elev_min" "minimum watershed elevation (see Methods and Protocols, attribution_and_intellectual_rights_ws_attr.csv)" "numeric" "meter" "NA" "missing value" "Watershed elevation is calculated based on DEM downloaded with the R function elevatr::get_elev_raster() (from Amazon Web Services and Open Topography Global Datasets API)"
@@ -42,19 +43,19 @@
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"pf_soil_clay" "watershed soil clay content (see Methods and Protocols, attribution_and_intellectual_rights_ws_attr.csv)" "numeric" "percent" "NA" "missing value" "Data from gSSURGO is summarized by taking a weighted mean of the particular parameter for the full depth of the soil column for all data available in the watershed boundary. Because SSURGO has gaps in some areas, if data was not available for more than 15 percent of the watershed no data is reported for this variable. Soil clay definition from NRCS: Mineral particles less than 0.002mm in equivalent diameter as a weight percentage of the less than 2.0mm fraction"
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"pf_soil_ph" "mean watershed soil pH (see Methods and Protocols, attribution_and_intellectual_rights_ws_attr.csv)" "numeric" "dimensionless" "NA" "missing value" "Data from gSSURGO is summarized by taking a weighted mean of the particular parameter for the full depth of the soil column for all data available in the watershed boundary. Because SSURGO has gaps in some areas, if data was not available for more than 15 percent of the watershed no data is reported for this variable. Soil pH definition from NRCS: The negative logarithm to the base 10, of the hydrogen ion activity in the soil using the 1:1 soil-water ratio method. A numerical expression of the relative acidity or alkalinity of a soil sample"
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"pi_soil_thickness" "mean watershed soil thickness" "numeric" "meter" "NA" "missing value"
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"ck_mean_annual_et" "mean daily watershed-mean evapotranspiration (grass reference) averaged again by mean per year over the entire record" "numeric" "millimetersPerDay" "NA" "missing value"
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"pd_geo_Al2O3_mean" "watershed mean Lithological aluminum oxide in surface or near surface geology" "numeric" "percent" "NA" "missing value"
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"pd_geo_CaO_mean" "watershed mean Lithological calcium oxide in surface or near surface geology" "numeric" "percent" "NA" "missing value"
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"pd_geo_CompressStrength_mean" "watershed mean Lithological uniaxial compressive strength in surface or near surface geology" "numeric" "megapascal" "NA" "missing value"
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"pd_geo_Fe2O3_mean" "watershed mean Lithological ferric oxide in surface or near surface geology" "numeric" "percent" "NA" "missing value"
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"pd_geo_HydaulicCond_mean" "watershed mean Lithological hydraulic conductivity in surface or near surface geology" "numeric" "micrometerPerSecond" "NA" "missing value"
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"pd_geo_K2O_mean" "watershed mean Lithological potassium oxide in surface or near surface geology" "numeric" "percent" "NA" "missing value"
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"pd_geo_MgO_mean" "watershed mean Lithological magnesium oxide in surface or near surface geology" "numeric" "percent" "NA" "missing value"
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"pd_geo_N_mean" "watershed mean Lithological nitrogen in surface or near surface geology" "numeric" "percent" "NA" "missing value"
54-
"pd_geo_Na2O_mean" "watershed mean Lithological sodium oxide in surface or near surface geology" "numeric" "percent" "NA" "missing value"
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"pd_geo_P2O5_mean" "watershed mean Lithological phosphorus pentoxide in surface or near surface geology" "numeric" "percent" "NA" "missing value"
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"pd_geo_S_mean" "watershed mean Lithological sulfur in surface or near surface geology" "numeric" "percent" "NA" "missing value"
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"pd_geo_SiO2_mean" "watershed mean Lithological silicon dioxide in surface or near surface geology" "numeric" "percent" "NA" "missing value"
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"ck_mean_annual_et" "mean daily watershed-median evapotranspiration (grass reference) over the entire record" "numeric" "millimetersPerDay" "NA" "missing value"
47+
"pd_geo_Al2O3_mean" "watershed mean aluminum oxide in surface or near surface geology" "numeric" "percent" "NA" "missing value"
48+
"pd_geo_CaO_mean" "watershed mean calcium oxide in surface or near surface geology" "numeric" "percent" "NA" "missing value"
49+
"pd_geo_CompressStrength_mean" "watershed mean uniaxial compressive strength in surface or near surface geology" "numeric" "megapascal" "NA" "missing value"
50+
"pd_geo_Fe2O3_mean" "watershed mean ferric oxide in surface or near surface geology" "numeric" "percent" "NA" "missing value"
51+
"pd_geo_HydaulicCond_mean" "watershed mean hydraulic conductivity in surface or near surface geology" "numeric" "micrometerPerSecond" "NA" "missing value"
52+
"pd_geo_K2O_mean" "watershed mean potassium oxide in surface or near surface geology" "numeric" "percent" "NA" "missing value"
53+
"pd_geo_MgO_mean" "watershed mean magnesium oxide in surface or near surface geology" "numeric" "percent" "NA" "missing value"
54+
"pd_geo_N_mean" "watershed mean nitrogen in surface or near surface geology" "numeric" "percent" "NA" "missing value"
55+
"pd_geo_Na2O_mean" "watershed mean sodium oxide in surface or near surface geology" "numeric" "percent" "NA" "missing value"
56+
"pd_geo_P2O5_mean" "watershed mean phosphorus pentoxide in surface or near surface geology" "numeric" "percent" "NA" "missing value"
57+
"pd_geo_S_mean" "watershed mean sulfur in surface or near surface geology" "numeric" "percent" "NA" "missing value"
58+
"pd_geo_SiO2_mean" "watershed mean silicon dioxide in surface or near surface geology" "numeric" "percent" "NA" "missing value"
5859
"ch_annual_Ca_flux_mean" "watershed mean annual atmospheric calcium flux" "numeric" "kilogramPerHectarePerYear" "NA" "missing value"
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"ch_annual_Cl_flux_mean" "watershed mean annual atmospheric chlorine flux" "numeric" "kilogramPerHectarePerYear" "NA" "missing value"
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"ch_annual_H_flux_mean" "watershed mean annual atmospheric hydrogen ion flux" "numeric" "kilogramPerHectarePerYear" "NA" "missing value"
@@ -89,7 +90,23 @@
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"pm_sub_surf_porosity_mean" "watershed mean subsurface porosity" "numeric" "percent" "NA" "missing value"
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"cl_snow_depth_ann_mean" "watershed mean annual snow depth" "numeric" "millimeter" "NA" "missing value"
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"cl_swe_ann_mean" "watershed mean annual snow water equivalent" "numeric" "millimeter" "NA" "missing value"
92-
"vb_mean_annual_fpar" "watershed mean annual FPAR (fraction of absorbed photosynthetically active radiation)" "numeric" "percent" "NA" "missing value"
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"vb_mean_annual_lai" "watershed mean annual LAI (leaf area index)" "numeric" "dimensionless" "NA" "missing value"
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"vj_mean_annual_tcw" "watershed mean annual TCW (tesselated cap wetness)" "numeric" "dimensionless" "NA" "missing value"
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"vb_mean_annual_ndvi" "watershed mean annual NDVI (normalized difference vegetation index)" "numeric" "dimensionless" "NA" "missing value"
93+
"vb_mean_annual_fpar" "mean annual watershed-median FPAR (fraction of absorbed photosynthetically active radiation)" "numeric" "percent" "NA" "missing value"
94+
"vb_mean_annual_lai" "mean annual watershed-median LAI (leaf area index)" "numeric" "dimensionless" "NA" "missing value"
95+
"vj_mean_annual_tcw" "mean annual watershed-median TCW (tesselated cap wetness)" "numeric" "dimensionless" "NA" "missing value"
96+
"vb_mean_annual_ndvi" "mean annual watershed-median NDVI (normalized difference vegetation index)" "numeric" "dimensionless" "NA" "missing value"
97+
"pn_geol_class_EV" "watershed underlying geologic class: evaporites" "numeric" "percent" "NA" "missing value"
98+
"pn_geol_class_IG" "watershed underlying geologic class: ice and glaciers" "numeric" "percent" "NA" "missing value"
99+
"pn_geol_class_MT" "watershed underlying geologic class: metamorphic rocks" "numeric" "percent" "NA" "missing value"
100+
"pn_geol_class_ND" "watershed underlying geologic class: no data" "numeric" "percent" "NA" "missing value"
101+
"pn_geol_class_PA" "watershed underlying geologic class: acid plutonic rocks" "numeric" "percent" "NA" "missing value"
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"pn_geol_class_PB" "watershed underlying geologic class: basic plutonic rocks" "numeric" "percent" "NA" "missing value"
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"pn_geol_class_PI" "watershed underlying geologic class: intermediate plutonic rock" "numeric" "percent" "NA" "missing value"
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"pn_geol_class_PY" "watershed underlying geologic class: pyroclastics" "numeric" "percent" "NA" "missing value"
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"pn_geol_class_SC" "watershed underlying geologic class: carbonate sedimentary rocks" "numeric" "percent" "NA" "missing value"
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"pn_geol_class_SM" "watershed underlying geologic class: mixed sedimentary rocks" "numeric" "percent" "NA" "missing value"
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"pn_geol_class_SS" "watershed underlying geologic class: siliciclastic sedimentary rock" "numeric" "percent" "NA" "missing value"
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"pn_geol_class_SU" "watershed underlying geologic class: unconsolidated sediments" "numeric" "percent" "NA" "missing value"
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"pn_geol_class_VA" "watershed underlying geologic class: acid volcanic rocks" "numeric" "percent" "NA" "missing value"
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"pn_geol_class_VB" "watershed underlying geologic class: basic volcanic rocks" "numeric" "percent" "NA" "missing value"
111+
"pn_geol_class_VI" "watershed underlying geologic class: intermediate volcanic rock" "numeric" "percent" "NA" "missing value"
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"pn_geol_class_WB" "watershed underlying geologic class: water bodies" "numeric" "percent" "NA" "missing value"

‎src/global/general.R‎

Lines changed: 15 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -35,13 +35,25 @@ boundaries <- try(read_combine_shapefiles(network = network,
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prodname_ms = ws_prodname))
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3737
#tiny watersheds can't be summarized by gee for some products.
38-
#if < 10 ha, replace with 10 ha circle on centroid
39-
too_small_wb <- boundaries$area < 10
38+
#if < 15 ha, replace with 15 ha circle on centroid
39+
ws_areas <- site_data %>%
40+
filter(in_workflow == 1,
41+
site_type != 'rain_gauge',
42+
domain == !!domain) %>%
43+
right_join(select(boundaries, site_code)) %>%
44+
select(site_code, ws_area_ha)
45+
46+
boundaries <- boundaries %>%
47+
select(-area) %>%
48+
left_join(ws_areas) %>%
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rename(area = ws_area_ha)
50+
51+
too_small_wb <- boundaries$area < 15
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reupload <- FALSE
4153
if(any(too_small_wb)) reupload <- TRUE
4254
boundaries[too_small_wb, ] <- boundaries[too_small_wb, ] %>%
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mutate(geometry = st_buffer(st_centroid(geometry),
44-
dist = sqrt(10000 * 10 / pi)))
56+
dist = sqrt(10000 * 15 / pi)))
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4658
if(any(!sf::st_is_valid(boundaries))){
4759
log_with_indent(generate_ms_err('All watershed boundaries must be s2 valid'),

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