Extracting numeric (key) quantities #29
Conversation
…iomass and landings plots
…ecruitment, recruitment devs, spawning recruitment, and spawning biomass plots
…tment names to sr
sbreitbart-NOAA
force-pushed
the
key-quantities
branch
from
1dd6a51 to
6b591d1
Compare
…iomass and landings plots
…ecruitment, recruitment devs, spawning recruitment, and spawning biomass plots
…tment names to sr
…o key-quantities
-replaced placeholder quantities with real values -updated workflow to improve how quantities are inserted into caps/alt text df -updated file.path() --> fs:::path()
…d .Rd files -included replacing export_rda param with make_rda param
…caption/alt text to figure
-removed Fend and added R0 as vars -removed old notes/code
removed make_rda param from exp_all_figs_tables.R
…lative biomass & relative spawning biomass caption/alt text to figures
… whole number -added quantites incl. Btarg, ssbtarg, and relative B, relative SSB, and relative recruitment max and mins -updated alt text/caps csv with relative quantities
Change plot_biomass and spawning_biomass plots to work through errors from reference line
R/write_captions.R
Outdated
| ## relative B | ||
| # relative B min | ||
| rel_B_min <- (B_min / Btarg) |> | ||
| round(digits = 0) |
There was a problem hiding this comment.
I changed my mind - can we round to 2 digits with the exception of abundance since those are in terms of number of fish
| # start year of ssb plot | ||
| ssb_start_year <- dat |> | ||
| dplyr::filter( | ||
| label == "spawning_biomass", |
There was a problem hiding this comment.
does this work for all examples?
There was a problem hiding this comment.
It works for two of my example dat files. Is it failing with yours? Or are there specific files that I should make sure to test it with?
| # 'catchability_fleet' = catchability_fleet | ||
| ) | ||
|
|
||
| caps_alttext_subbed <- caps_alttext |> |
There was a problem hiding this comment.
Can you add a note explaining what this pipeline is doing? I also haven't see the ", ~{" notation before in the below line
There was a problem hiding this comment.
Sure, added the note. The internet helped me with chunk, so here's what I believe is going on: the ~ is present because an anonymous function is passed to another function (dplyr::mutate). The { is separating the for loop from the output of the for loop, which is acted upon by dplyr::mutate.
…iomass and landings plots
…ecruitment, recruitment devs, spawning recruitment, and spawning biomass plots
…tment names to sr
-replaced placeholder quantities with real values -updated workflow to improve how quantities are inserted into caps/alt text df -updated file.path() --> fs:::path()
…d .Rd files -included replacing export_rda param with make_rda param
…caption/alt text to figure
-removed Fend and added R0 as vars -removed old notes/code
…lative biomass & relative spawning biomass caption/alt text to figures
… whole number -added quantites incl. Btarg, ssbtarg, and relative B, relative SSB, and relative recruitment max and mins -updated alt text/caps csv with relative quantities
…o key-quantities
| @@ -53,6 +52,8 @@ exp_all_figs_tables <- function( | |||
|
|
|||
| ) { | |||
|
|
|||
| make_rda = TRUE | |||
There was a problem hiding this comment.
Why did you take this out of the arguments?
There was a problem hiding this comment.
Because if the user is using this function (to export all figs/tables), that implies that all figures and tables will be exported as rda files. So, make_rda would always be true.
-change rounding to 2 digits -add comment describing how caps_alttext_subbed is created
… underscores being recognized as special characters in latex script
Wrote code to extract numeric quantities for values associated with biomass and landings plots