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Color changes to Status Summary plots, and added notes to color definitions.#5

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tjtreska wants to merge 24 commits intoJVAdams:masterfrom
Great-Lakes-Fishery-Commission:mainTT
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Color changes to Status Summary plots, and added notes to color definitions.#5
tjtreska wants to merge 24 commits intoJVAdams:masterfrom
Great-Lakes-Fishery-Commission:mainTT

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tjtreska and others added 24 commits September 15, 2023 10:35
changed color of lakes to dark blue and filled in the lakes
Changed to deepskyblue to make black lines stand out
Edits made to Table 1,2,3
and Figure 1,2,3
Added comments to figs and tables in code, standardized "Index w/o mark-recap" to "Modeled - Index w/o mark-recap"
Added code to color definitions on lines ~120 and adjusted not to use yellow as it hard to see.
second try to commit
Changed from 0.6 to 0.8 in cbind(0.8, bayerkg....
Changed index[sel]/1000, lwd=1 to lwd=2 in plots of lamprey abundance and other metrics
…ng RGB values

Changed Vermillion which was too dark to Salmon in blindcolz definition, with RGB of 250,128,114
forgot to change the lwd=2 on the combined plots.
Edited language for plots to make them clearer. deleted some whitespace in code.
Change NA language from original to "NA indicates that a minimum of two successful mark-recapture estimates were not achieved."
Changed from "The Status of whether a lake is above target is based on the mean adult index over the last 3 years." to "The Status of a lake is based on the mean adult index over the last 3 years relative to Target."
Adjusted LM target values in variables years (to 2015-2019) and adjust (1).
Replaced old version that used 5/8.9 conversion of widely varying marking rates with more accurate and recent data time series. Commented out previous time series along with 5/8.9 conversion. See Treska et al 2021
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