Information about the data we have

• old repo, previous analysis done by Erin

• some issues with data used; some issues with not filtering out bad data

• Google drive for final environmental data by thais

• Filtered, clean environment data SiteEnviDataQC202011Thais

• List of populations and data source for each population

  • Entered by Thais in Dec 2020
  • Skip the selection line populations - populations whose name ends in an "S"

• List of datasources and what filters were applied, data cleaning

Data we need

TO DO: MAKE A LIST

• List of range-wide bouys we assessed for salinity data
• MVP Google Drive

Map

• NEW MAP WITH COMBINED INFO

  • One color for salinity only data NONE
  • One color for temperature only data BLUE
  • One color for both salinity and temp data GREEN
  • "P" for whole-genome samples we have ORANGE "P"
  • "C" for sites to collect from based on collaborator info RED "C"
  • See if we can add information on:
  • general salinity (<15ppt, 15-25, or >25) for the bouy THIS INFO IS IN THE 'TITLE' OF EACH P LOCATION AND UNDER 'SALINITY INFO' FOR EACH C LOCATION (note that data have not been cleaned up for the C locations).
  • website link for buoy DONE
  • use "datasource" as name in map - DONE

• OLD Map of bouy sites that have salinity data

• OLD Map of all Wild Populations and their respective environmental data locations FIX THIS LINK

What we want to calculate for each dataset

Apply filters

1. USGS: Flags are:
   A Approved for publication, Processing and review completed or
   P Provisional data subject to revision.

2. NERR data: multiple flags, QC Flags and QC codes are combined; QC may be combined with 1 or more QC codes.

3. We focused on the QC Flags & Codes below - exclude and include flags/codes are listed below; NA were flags/codes not encountered in the datasets that we looked at so far.

QC Flags

Each parameter in the exported data file contains a flag column. The flag column, Fparam, contains a quality control (QC) flag and may contain additional QC codes. In a chart mouse-over, the QAQC flag and any codes are displayed behind the Fparam: designation. Refer to the list below for the available QC flags and their descriptions.

| QC Flag | criteria | |---------|----------| |-5 Outside high sensor range |exclude |
|-4 Outside low sensor range |exclude |
|-3 Data rejected due to QAQC |exclude |
|-2 Missing data |exclude | |-1 Optional parameter not collected | NA| |0 Passed initial QAQC checks |include
|1 Suspect data |include
|2 Reserved for future use | NA| |3 Calculated data: non-vented depth/level sensor correction for changes in barometric pressure | NA| |4 Historical: Pre-auto QAQC |include |
|5 Corrected data |include |

QC Codes by Dataset
- Water Quality:

| QC Code | criteria | |---------|----------| |General Errors||
||| |GIC No instrument deployed due to ice| NA| |GIM Instrument malfunction| exclude | | GIT Instrument recording error; recovered telemetry data| exclude | |GMC No instrument deployed due to maintenance/calibration| NA| |GNF Deployment tube clogged / no flow | NA| |GOW Out of water event |NA| |GPF Power failure / low battery | NA| |GQR Data rejected due to QAQC checks |NA| |GSM See metadata| include | |Corrected Depth/Level Data Codes | NA| ||| |GCC Calculated with data that were corrected during QAQC | NA| |GCM Calculated value could not be determined due to missing data | NA| |GCR Calculated value could not be determined due to rejected data| NA|NA| |GCS Calculated value suspect due to questionable data |NA| |GCU Calculated value could not be determined due to unavailable data |NA| |Sensor Errors || ||| |SBO Blocked optic | NA| |SCF Conductivity sensor failure | NA| |SCS Chlorophyll spike | NA| |SDF Depth port frozen | NA| |SDG Suspect due to sensor diagnostics| NA| |SDO DO suspect |NA| |SDP DO membrane puncture |NA| |SIC Incorrect calibration / contaminated standard |exclude | |SNV Negative value |include for temp, exclude for sal | |SOW Sensor out of water |NA| |SPC Post calibration out of range |exclude | |SQR Data rejected due to QAQC checks |NA| |SSD Sensor drift |exclude | | SSM Sensor malfunction |exclude | |SSR Sensor removed / not deployed | NA| |STF Catastrophic temperature sensor failure |exclude | |STS Turbidity spike | NA| |SWM Wiper malfunction / loss| NA| |Comments || ||| |CAB* Algal bloom |NA| |CAF Acceptable calibration/accuracy error of sensor |NA| |CAP Depth sensor in water, affected by atmospheric pressure |NA| |CBF Biofouling | exclude | |CCU Cause unknown | exclude | |CDA* DO hypoxia (<3 mg/L) |NA| |CDB* Disturbed bottom |NA| |CDF Data appear to fit conditions |include | |CFK* Fish kill |NA| |CIP* Surface ice present at sample station | NA| |CLT* Low tide |NA| |CMC* In field maintenance/cleaning | exclude | |CMD* Mud in probe guard |NA| |CND New deployment begins | include | |CRE* Significant rain event | include | |CSM* See metadata |exclude | |CTS Turbidity spike |NA| |CVT* Possible vandalism/tampering | NA| |CWD* Data collected at wrong depth | exclude | |CWE* Significant weather event |NA|

*Indicates comments that can be applied to an entire record in the F_Record column.

Temperature

• MeanAnnualTemperature_C : average of all available data
• Meanmaxtemperature_C : average of (maximums for each year)
• Meanmintemperature_C : average of (minimums for each year)
• Temperaturestdev: SD of all available data (if only daily averages are reported separately from mean/max daily this SD could be biased)
• Temperature_n: number of datapoints
• Temperature_years: number of years
  no longer including the following 3:
• dd_0: number of days where temp fell below 0
• dd_15: number of days where temp above 15C
• dd_30: number of days where temp above 30C

Salinity

• MeanAnnualSalinity_ppt : average of all available data
• Salinitystdev : SD of all available data (if only daily averages are reported separately from mean/max daily this SD could be biased)
• MeanminSalinity_ppt : average of (minimums for each year)
• MeanmaxSalinity_ppt : average of (maximums for each year)
• Salinity_n: number of datapoints
• Salinity_years: number of years

The following populations from the resequencing project do not have salinity data:

• NJDBCSMedW
• MESRSMLowW
• NYLILHHighW
• NYLICMHighW