nwfsc-math-bio / nwctrends

This is an R package that runs the standardized trends metrics used in the 5-year Viability Reports for listed PNW salmonids.

nwfsc-math-bio

Some info.

nwctrends's Issues

test

test

html versus latex tables when no fracwild

html table when no frac wild the () are missing.

Clarify the table legend for raw geomeans

• Need to clarify that when there are only 2 data points, say, that the geomean is sqrt(N_1 * N_2) not (N_1 * N_2)^(1/5)
• Need to clarify 0s behavior (changed to NA)

Change where the files are saved

not in doc/files/ESU_figures

data header and documentation changes

Compiled by: instead of author

Contributor:
WA Department of F & W

Citation:
available at https://fortress.wa.gov/dfw/score/score/; http://odfwrecoverytracker.org/metadata/; https://www.monitoringmethods.org

East Fork South Fork Salmon River summer Chinook, Secesh River summer Chinook, and Snake River Lower Mainstem fall Chinook Natural Origin Spawner Abundance Dataset (1949-2018). Spawner abundance data.

Nez Perce Tribe. Protocol and methods available at https://www.cbfish.org/Document.mvc/Viewer/P165414; https://www.cbfish.org/Document.mvc/Viewer/P164600. Personal communication with Mari Williams, NOAAF NWFSC/OAI Dec 2019.

Description (what is this a data set of)
contributor,
Citation
methods,
download date
data source(s)
compiler,

Format add info if number
ESU/DPS (constrained field)
Fracwild (decimal number between 0 and 1).
Year. Integer. See details for ESU/DPS comments.
NUMBER_OF_SPAWNERS Total spawners or escapement.

Reports

spawners on same plot
y-scaling

Review State of the Salmon

• Print off emails. Add here.
• Summarize differences
• Probably add a doc about that.

fix links to nwfsc-timeseries

should be nwfsc-math-bio. Look in the pkgdown material.

check any links to github anywhere

Make plan for cleaning up the code base

• Review files one by one and make notes on changes
• Write notes here

Revamp the NWCTrends code

• Clean out all the old stuff from 2015 hacks

check all the demo file ESUs

Check that all the ESUs can be run in the demofiles.

test

the summary fig w 5-year geomean for wild spawners has all red points

Lower Columbia chinook example. points above 0 should be black

add magrittr to dependencies

clarify how zeros are dealt with for the geomeans

The documentation is unclear.

from email with Mari: "Ok well forget everything I wrote before. For the raw geomeans, 0s are replaced with NA, not quite on purpose but because all the code works on the log-scale and log(0) = NA. I say not quite on purpose because in the modeling all work is done on the log-scale, so 0s do become NAs. I'd forgotten that when computing the raw geomeans that I also work with the log data so 0s become NAs. Well, again add that to the things to revisit for next go round."

test2

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