Organization of chemistry scripts - USEPA/SuRGE GitHub Wiki
We have chemistry data from several different labs and years. We need to develop separate scripts to read in chunks of data that are formatted similarly. See table below for a list of all scripts needed to read in chemistry.
| Lab | Sample_year | Script | Analytes | Notes | Status |
|---|---|---|---|---|---|
| R10 | 2018 | readChlorophyllR10_2018.R | chlorophyll | Samples collect by Region 10 in 2018. | complete |
| R10 | 2018 | readNutrientsR10_2018.R | Orthophosphate (op) Nitrite (no2) Nitrite+nitrate (no2_3) Ammonium (nh4) Total organic carbon (toc) Total nitrogen (tn) Total phosphorus (tp) |
Samples collected by Region 10 in 2018. | complete |
| CIN RTP NAR USGS |
2021 2022 2023 |
readNutrientsAwberc.R | oP no2 no2.3 tp tn |
Not all years for all labs (e.g., USGS only in 2021) |
complete |
| R10 CIN RTP ADA |
2020 for R10, CIN, and RTP 2021-2023 for ADA |
readNutrientsAda.R | Orthophosphate (op) Total nitrogen (tn) total phosphorus (tp) Nitrate + nitrite (no2.3) ammonium (nh4) |
Excel file name contains: oP TN,TP NO3+NO2NH4 |
complete |
| ADA | 2021, 2022, 2023 | readAnionsAda.R | Fluoride Chloride (cl) Bromide (br) Sulfate (so4) |
Excel file name contains ClSO4BrF,NO3,NO2,oP |
complete |
| CIN RTP USGS |
2021 | readAnionsDaniels.R | -Fluoride -Chloride (cl) -Bromide (br) -Sulfate (so4) |
Script complete, but waiting for database update | |
| ADA | 2021 2022 2023 |
readOcAda.R | -Non-purgeable organic carbon (NPOC) -Non-purgeable dissolved organic carbon (NPDOC) |
-NPOC is unflitered (TN) -NPDOC is filtered (DN) |
complete |
| R10 CIN RTP |
2020 | readOcMasi.R | TOC (no doc in 2020) | EPA labs shutdown. MASI is external contract lab. | complete |
| CIN RTP NAR GB USGS DOE R10 |
2018 2020 2021 2022 2023 |
readTteb.R | -toc -doc (>=2021) -metals -toc |
-need analytical run date to calculate holding times -Need database update |
script complete, waiting for database update |
| CIN RTP NAR GB USGS DOE R10 |
2020 2021 2022 2023 |
readPigmentsMicrocystin.R | -chlorophyll a (chla) -phycocyanin (phyco) -microcystin |
-chla and phyco analyzed on material captured on filter -microcystin in unfiltered water sample |
Script file exists, but no code written and no data available as of 1/13/2022. |
| CIN RTP NAR GB USGS DOE R10 |
2020 2021 2022 2023 |
readTaxonomy.R | algal taxonomy | No script or data. | |
| CIN RTP NAR GB USGS DOE R10 |
2020 2021 2022 2023 |
readPhysiology.R | algal physiology | No script or data. |