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msorlienmsorlien
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updated lookup tables
* Removed "County" from wqdashboard columns * Moved raw variable lookup tables to data-raw, final lookup tables to inst/extdata
1 parent 106d05b commit 10a2106

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-880
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‎R/sysdata.rda‎

19 Bytes
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‎data-raw/sysdata.R‎

Lines changed: 40 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -16,15 +16,21 @@ colnames_results <- readr::read_csv(
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# Import variable lookup tables ----
1818
varnames_activity <- readr::read_csv(
19-
"inst/extdata/varnames_activity.csv",
19+
"data-raw/varnames_activity.csv",
2020
show_col_types = FALSE
2121
) %>%
2222
dplyr::select_if(function(x) !(all(is.na(x)))) %>%
2323
dplyr::mutate("wqdashboard" = .data$wqx) %>%
2424
dplyr::mutate("ri_ww" = .data$ri_dem)
2525

26+
readr::write_csv(
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varnames_activity,
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"inst/extdata/varnames_activity.csv",
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na = ""
30+
)
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2632
varnames_parameters <- readr::read_csv(
27-
"inst/extdata/varnames_parameters.csv",
33+
"data-raw/varnames_parameters.csv",
2834
show_col_types = FALSE
2935
) %>%
3036
dplyr::select_if(function(x) !(all(is.na(x)))) %>%
@@ -37,24 +43,51 @@ varnames_parameters <- readr::read_csv(
3743
)
3844
)
3945

46+
readr::write_csv(
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varnames_parameters,
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"inst/extdata/varnames_parameters.csv",
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na = ""
50+
)
51+
4052
varnames_qualifiers <- readr::read_csv(
41-
"inst/extdata/varnames_qualifiers.csv",
53+
"data-raw/varnames_qualifiers.csv",
4254
show_col_types = FALSE
4355
) %>%
4456
dplyr::select_if(function(x) !(all(is.na(x)))) %>%
45-
dplyr::select(!dplyr::any_of(c("Flag", "Description"))) %>%
46-
dplyr::mutate("masswater" = .data$wqx) %>%
57+
dplyr::mutate(
58+
"masswater" = dplyr::if_else(
59+
is.na(.data$masswater),
60+
.data$wqx,
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.data$masswater
62+
)
63+
) %>%
4764
dplyr::mutate("wqdashboard" = .data$wqx) %>%
48-
dplyr::mutate("ri_ww" = .data$ri_dem)
65+
dplyr::mutate("ri_ww" = .data$ri_dem) %>%
66+
dplyr::relocate("Description", .after = "ri_ww")
67+
68+
readr::write_csv(
69+
varnames_qualifiers,
70+
"inst/extdata/varnames_qualifiers.csv",
71+
na = ""
72+
)
73+
74+
varnames_qualifiers <- varnames_qualifiers %>%
75+
dplyr::select(!"Description")
4976

5077
varnames_units <- readr::read_csv(
51-
"inst/extdata/varnames_units.csv",
78+
"data-raw/varnames_units.csv",
5279
show_col_types = FALSE
5380
) %>%
5481
dplyr::select_if(function(x) !(all(is.na(x)))) %>%
5582
dplyr::mutate("wqdashboard" = .data$wqx) %>%
5683
dplyr::mutate("ri_ww" = .data$ri_dem)
5784

85+
readr::write_csv(
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varnames_units,
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"inst/extdata/varnames_units.csv",
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na = ""
89+
)
90+
5891
# Save data ----
5992
usethis::use_data(
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colnames_results, colnames_sites, varnames_activity, varnames_parameters,

‎data-raw/varnames_activity.csv‎

Lines changed: 76 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,76 @@
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wqx,masswater,ri_dem,ma_brc,me_dep,me_focb
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Field Msr/Obs,Field Msr/Obs,Grab,Grab,NA|NOT APPLICABLE (NORMAL ENVIRONMENTAL SAMPLE),Field Measurement|NA|NOT APPLICABLE (NORMAL ENVIRONMENTAL SAMPLE)
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Quality Control Field Replicate Msr/Obs,Quality Control Field Replicate Msr/Obs,Replicate,Replicate,D|FIELD DUPLICATE,D|FIELD DUPLICATE
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Quality Control Sample-Field Blank,Quality Control Sample-Field Blank,,Field Blank,FB|FIELD BLANK,FB|FIELD BLANK
5+
Quality Control Sample-Field Replicate,Quality Control Sample-Field Replicate,,,,
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Quality Control Sample-Lab Blank,Quality Control Sample-Lab Blank,Blank,Lab Blank,LB|LAB BLANK,LB|LAB BLANK
7+
Quality Control Sample-Lab Duplicate,Quality Control Sample-Lab Duplicate,Duplicate,,L|LAB DUPLICATE,L|LAB DUPLICATE
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Quality Control Sample-Lab Duplicate 2,Quality Control Sample-Lab Duplicate 2,,,,
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Quality Control Sample-Lab Spike,Quality Control Sample-Lab Spike,,,,
10+
Quality Control Sample-Lab Spike Target,Quality Control Sample-Lab Spike Target,,,,
11+
Quality Control-Calibration Check,Quality Control-Calibration Check,,,,
12+
Quality Control-Calibration Check Buffer,Quality Control-Calibration Check Buffer,,,,
13+
Quality Control-Meter Lab Blank,Quality Control-Meter Lab Blank,,,,
14+
Quality Control-Meter Lab Duplicate,Quality Control-Meter Lab Duplicate,,,,
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Quality Control-Meter Lab Duplicate 2,Quality Control-Meter Lab Duplicate 2,,,,
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Sample-Routine,Sample-Routine,,,,
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Quality Control Field Replicate Sample-Composite,,Composite,,,
18+
Quality Contorl Sample-Lab Control Sample/Blank Spike,,,,LCS|LAB CONTROL SAMPLE,LCS|LAB CONTROL SAMPLE
19+
Quality Control Sample-Lab Control Sample/Blank Spike Duplicate,,,,LCSD|LAB CONTROL SAMPLE DUPLICATE,LCSD|LAB CONTROL SAMPLE DUPLICATE
20+
Quality Control Sample-Lab Matrix Spike,,,,MS|MATRIX SPIKE,MS|MATRIX SPIKE
21+
Quality Control Sample-Lab Matrix Spike Duplicate,,,,MSD|MATRIX SPIKE DUPLICATE,MSD|MATRIX SPIKE DUPLICATE
22+
Sample-Other,,,,UNK|UNKNOWN,UNK|UNKNOWN
23+
Field Msr/Obs-Continuous Time Series,,,,,
24+
Field Msr/Obs-Habitat Assessment,,,,,
25+
Field Msr/Obs-Incidental,,,,,
26+
Field Msr/Obs-Portable Data Logger,,,,,
27+
Quality Control Alternative Measurement Sensitivity,,,,,
28+
Quality Control Alternative Measurement Sensitivity Plus,,,,,
29+
Quality Control Field Calibration Check,,,,,
30+
Quality Control Field Msr/Obs Post-Calibration,,,,,
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Quality Control Field Msr/Obs Pre-Calibration,,,,,
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Quality Control Field Replicate Habitat Assessment,,,,,
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Quality Control Field Replicate Portable Data Logger,,,,,
34+
Quality Control Field Replicate Sample-Field Subsample,,,,,
35+
Quality Control Field Sample Equipment Rinsate Blank,,,,,
36+
Quality Control Lab Sample Equipment Rinsate Blank,,,,,
37+
Quality Control Sample-Blind Duplicate,,,,,
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Quality Control Sample-Equipment Blank,,,,,
39+
Quality Control Sample-Field Ambient Conditions Blank,,,,,
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Quality Control Sample-Field Spike,,,,,
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Quality Control Sample-Field Surrogate Spike,,,,,
42+
Quality Control Sample-Inter-lab Split,,,,,
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Quality Control Sample-Lab Continuing Calibration Verification,,,,,
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Quality Control Sample-Lab Control Standard,,,,,
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Quality Control Sample-Lab Control Standard Duplicate,,,,,
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Quality Control Sample-Lab Initial Calib Certified Reference Material,,,,,
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Quality Control Sample-Lab Initial Calibration Verification,,,,,
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Quality Control Sample-Lab Re-Analysis,,,,,
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Quality Control Sample-Lab Spike Duplicate,,,,,
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Quality Control Sample-Lab Spike of a Lab Blank,,,,,
51+
Quality Control Sample-Lab Split,,,,,
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Quality Control Sample-Lab Surrogate Control Standard,,,,,
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Quality Control Sample-Lab Surrogate Control Standard Duplicate,,,,,
54+
Quality Control Sample-Lab Surrogate Method Blank,,,,,
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Quality Control Sample-Measurement Precision Sample,,,,,
56+
Quality Control Sample-Other,,,,,
57+
Quality Control Sample-Post-preservative Blank,,,,,
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Quality Control Sample-Pre-preservative Blank,,,,,
59+
Quality Control Sample-Reagent Blank,,,,,
60+
Quality Control Sample-Reference Sample,,,,,
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Quality Control Sample-Trip Blank,,,,,
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Quality Control-Negative Control,,,,,
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Sample-Composite With Parents,,,,,
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Sample-Composite Without Parents,,,,,
65+
Sample-Depletion Replicate,,,,,
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Sample-Field Split,,,,,
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Sample-Field Subsample,,,,,
68+
Sample-Integrated Cross-Sectional Profile,,,,,
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Sample-Integrated Flow Proportioned,,,,,
70+
Sample-Integrated Horizontal and Vertical Composite Profile,,,,,
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Sample-Integrated Horizontal Profile,,,,,
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Sample-Integrated Time Series,,,,,
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Sample-Integrated Vertical Profile,,,,,
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Sample-Negative Control,,,,,
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Sample-Positive Control,,,,,
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Sample-Routine Resample,,,,,

‎data-raw/varnames_parameters.csv‎

Lines changed: 67 additions & 0 deletions
Original file line numberDiff line numberDiff line change
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wqx,masswater,wqdashboard,ri_dem,ma_brc,me_dep,me_focb
2+
"Temperature, air","Air Temp|Temperature, air",,,Air Temperature,,
3+
Ammonia|Ammonia-nitrogen,Ammonia,,"Nitrogen, Ammonia Dissolved as N - 00608",,NH3 AS N|AMMONIA AS NITROGEN,NH3 AS N|AMMONIA AS NITROGEN
4+
Ammonium,Ammonium,,,,NH4 AS N|AMMONIUM AS NITROGEN,NH4 AS N|AMMONIUM AS NITROGEN
5+
Chlorophyll a (probe)|Chlorophyll a (probe relative fluorescence),Chl a (probe)|Chlorophyll a (probe),,,,,
6+
Chlorophyll a,Chl a|Chlorophyll a,,,,CHLOROPHYLL,Chlorophyll|CHLOROPHYLL
7+
Chloride,Chloride,,Chloride - 00940,,,
8+
Conductivity|Conductance,Conductivity,,,Conductivity,,
9+
"Algae, blue-green (phylum cyanophyta) density","Cyanobacteria (lab)|Algae, blue-green (phylum cyanophyta) density",,,,,
10+
"Chlorophyll a (probe) concentration, Cyanobacteria (bluegreen)","Cyanobacteria (probe)|Chlorophyll a (probe) concentration, Cyanobacteria (bluegreen)",,,,,
11+
Depth,Depth,,"Depth to bottom from water surface at sampling location, meters - 82903",Water Depth,DEPTH,Water Depth|DEPTH
12+
Dissolved oxygen saturation,DO saturation|Dissolved oxygen saturation,,Dissolved Oxygen Percent Saturation - 00301,Dissolved Oxy Saturation,DO SAT|DISSOLVED OXYGEN SATURATION,DO Saturation|DO SAT|DISSOLVED OXYGEN SATURATION
13+
Dissolved oxygen (DO),DO|Dissolved oxygen (DO),,Dissolved Oxygen - 00300,Dissolved Oxygen,DO|DISSOLVED OXYGEN,Dissolved Oxygen|DO|DISSOLVED OXYGEN
14+
Escherichia coli,E.coli|Escherichia coli,E. coli|Escherichia coli,E.coli - 31633,E. coli,,
15+
Enterococcus,Enterococcus,,Enterococci - 31639,,,
16+
Fecal Coliform,Fecal Coliform,,Fecal Coliform - 74055,,,
17+
Flow,Flow,,Flow - 50050,,,
18+
"Height, gage","Gage|Height, gage",,,,,
19+
Metals,Metals,,,,,
20+
Microcystins,Microcystins,,,,,
21+
Nitrate,Nitrate,,,Nitrate,,
22+
Nitrate + Nitrite|Neon-21/neon-22,Nitrate + Nitrite,,"Nitrate + Nitrite, Dissolved - 00631",,NO3 + NO2 AS N|NITRATE + NITRITE AS NITROGEN,NO3 + NO2 AS N|NITRATE + NITRITE AS NITROGEN
23+
Nitrite,Nitrite,,,,,
24+
Orthophosphate|Inorganic phosphorus|Non-apatite inorganic phosphorus|Particulate Inorganic Phosphorus|Phosphate-phosphorus,Ortho P|Orthophosphate,,"Orthophosphate, Dissolved - 00671",Orthophosphate,,
25+
pH,pH,,pH - 00400,,PH,pH|PH
26+
Pheophytin a,Pheophytin|Pheophytin a,,,,PHAEOPHYTIN,PHAEOPHYTIN
27+
Phycocyanin,Phycocyanin,,,,,
28+
Phycocyanin (probe),Phycocyanin (probe),,,,,
29+
Particulate organic carbon,POC|Particulate organic carbon,,,,,
30+
"Organic phosphorus|Phosphorus, Particulate Organic","POP|Phosphorus, Particulate Organic",,,,,
31+
Salinity,Salinity,,"Salinity, (ppt) - 00480",,SALINITY|SALINITY (FROM SODIUM),Salinity|SALINITY|SALINITY (FROM SODIUM)
32+
"Depth, Secchi disk depth|Depth, Secchi disk depth disappears|Depth, Secchi disk depth reappears","Secchi Depth|Depth, Secchi disk depth",,Secchi Depth - 00069,,SECCHI,Secchi|SECCHI
33+
Silicate,Silicate,,,,,
34+
Specific conductance,Sp Conductance|Specific conductance,,"Specific Conductance, water, unfiltered, microsiemens per centimeter at 25° C - 00095",,,
35+
Sulfate,Sulfate,,Sulfate as SO4 - 00945,,,
36+
Surfactants,Surfactants,,Surfactants - 38260,,,
37+
Total dissolved solids,TDS|Total dissolved solids,,"Solids, Total Dissolved (Electrical Conductivity), mg/l - 47004|Solids, Total Dissolved (Electrical Conductivity) - 47004",,,
38+
Total Kjeldahl nitrogen|Total Kjeldahl nitrogen (Organic N & NH3)|Kjeldahl nitrogen,TKN|Total Kjeldahl nitrogen,,,,,
39+
"Total Nitrogen, mixed forms|Nitrogen|Nitrogen, mixed forms (NH3), (NH4), organic, (NO2) and (NO3)|Total Nitrogen, mixed forms (NH3), (NH4), organic, (NO2) and (NO3)","TN|PON|TDN|Total Nitrogen, mixed forms",,"Nitrogen, Total (unfiltered) - 00600",,"TN AS N|TOTAL NITROGEN MIXED FORMS (NH3, NH4, ORGANIC, NO2, AND NO3) AS NITROGEN","TN as N|TN AS N|TOTAL NITROGEN MIXED FORMS (NH3, NH4, ORGANIC, NO2, AND NO3) AS NITROGEN"
40+
"Total Phosphorus, mixed forms|Phosphates (orthophosphate plus condensed and polyphosphates)|Phosphorus|Total Particulate Phosphorus","TP|TDP|Total Phosphorus, mixed forms",,"Phosphorus, Total - 00665",,,
41+
Total suspended solids,TSS|Total suspended solids,,TSS - 00530,,,
42+
Turbidity,Turbidity,,Turbidity - 00070,Turbidity,TUR|TURBIDITY,Turbidity|TUR|TURBIDITY
43+
"Temperature, water","Water Temp|Temperature, water",,Temperature - 00011,Water Temperature,TEMP|TEMPERATURE,Temperature|TEMP|TEMPERATURE
44+
"1,1,1-Trichloroethane",,,"1,1,1 Trichloroethane - 34506",,,
45+
"1,2-Dichlorobenzene-d4",,,"1,2 Dichlorobenzene - 34536",,,
46+
"1,4-Dichlorobenzene-d4",,,"1,4 Dichlorobenzene - 34571",,,
47+
Alkalinity,,,Alkalinity - 00410,,,
48+
Benzene,,,Benzene - 34030,,,
49+
Calcium,,,"Calcium, Dissolved - 00915",,,
50+
Chloroform,,,Chloroform - 32106,,,
51+
"Chlorophyll a, corrected for pheophytin",,,"Chlorophyll a, water, fluorometric method, corrected for pheophytin - 32209",,CHL-A-PH|CHLOROPHYLL A - PHAEOPHYTIN,CHL-A-PH|CHLOROPHYLL A - PHAEOPHYTIN
52+
Cloud cover,,,,,CLOUD COVER,Cloud Cover|CLOUD COVER
53+
Ethylbenzene,,,Ethylbenzene - 34371,,,
54+
Ethylene glycol,,,"Ethylene Glycol, water, unfiltered, recoverable, mg/l - 91075|Ethylene Glycol, water, unfiltered, recoverable - 91075",,,
55+
Magnesium,,,Magnesium - 00927,,,
56+
Methylene Chloride,,,Methylene Chloride - 34423,,,
57+
Propylene glycol,,,"Propylene Glycol, water, unfiltered, recoverable, mg/l - 91080|Propylene Glycol, water, unfiltered, recoverable - 91080",,,
58+
Sodium,,,"Sodium, Dissolved as NA - 00930",,,
59+
Tetrachloroethylene,,,Tetrachloroethylene - 34475,,,
60+
Toluene,,,Toluene - 34010,,,
61+
Total Coliform,,,Total Coliform - 31502,,,
62+
Trichloroethylene,,,Trichloroethylene - 39180,,,
63+
"Wind direction, horizontal",,,,,WDIR|WIND DIRECTION,Wind Direction|WDIR|WIND DIRECTION
64+
"Wind force, Beaufort scale",,,,,WSPD|WIND SPEED,Wind Speed|WSPD|WIND SPEED
65+
,,,"Phosphorus, Dissolved - 00666",,,
66+
Nitrogen/Phosphorus molar ratio|Dissolved Inorganic Nitrogen/Total Phosphorus ratio|Dissolved inorganic nitrogen/soluble reactive phosphorus ratio|Molar ratio of nitrate (plus nitrite) and orthophosphate|Total Nitrogen/Total Phosphorus Ratio (TN:TP),,,,,,
67+
Oxidation reduction potential (ORP),,,,,,

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