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Mount-Hood-Environmental / DASH

R Package Companion to the Drone Assisted Stream Habitat (DASH) Protocol
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Update Ocular Estimate and Pebble Count QCs and Protocol #37

Open mackerman44 opened 3 years ago

mackerman44 commented 3 years ago

Beginning in 2019, the desire is that ocular substrate estimates are recorded for ALL channel units (both slow and fast), and in addition, pebble counts are taken in the first 10 fast water channel units.

  1. Currently, the QC only checks for missing ocular substrate estimates in slow channel units and needs to be updated to reflect the above.
  2. The DASH protocol needs to be updated to reflect this.
  3. We should consider whether still missing ocular estimates can be imputed in the rollup_cu() function. These would be the remaining CU records where field staff forgot to estimate in the field AND we can't reliably estimate from drone imagery

@rcarmichael3 did, we believe, fill in all of the missing values he could in the 2018 data using drone imagery. Perhaps the same needs to be done to the 2019 and 2020 data?

Also, this brought up the idea of moving the master DASH document over to the repo to put in under versioning control. Can we move the .docx and .pdf versions over to the repo and delete from SharePoint? And we'll consider moving to a .Rmd file in the future.

mackerman44 commented 3 years ago

Okay, for starters, I've moved the DASH protocol from the MRA Teams site and into this repo at /inst/DASH_Protocol/. I've also copied the protocol and initiated a Word version with today's date as a suffix (_20210119) to begin edits. Is now a good time to move this to an .Rmd doc to track changes to the protocol?

  1. The qc_cu() function now checks for missing ocular substrate estimates in all channel units except rapid+ (oc_cus = c("Pool", "Run", "Riffle", "OCA", "SSC")
  2. The substrate composition in the DASH protocol now begins "Substrate composition will be measured or estimated for all channel unit types except rapid+. Substrate is difficult to reliable estimate in rapid+ channel units due to safely reasons (in the case of pebble counts) and difficulty seeing the substrate (in the case of ocular estimates). Beginning in 2019, ocular substrate estimates will be recorded in all channel unit types except rapid+, including pool, run, riffle, small side channel, and off-channel following methods defined by CHaMP (2016). In addition to ocular estimates, pebble counts will be collected in the first 10 riffles of each DASH survey location following CHaMP (2016)."

We do still need to determine whether we want to impute missing ocular estimates in the rollup_cu() function, and how, in the case that a CU is missing ocular estimates AND we can't obtain from imagery.