More plot ideas - Githubissues

[x] Add Fmsy to F plots
[x] CPUE fit plot with all series - CR too. Translate them all into same scale using q's
[x] add LF data to data_extent plot
[x] CR residual plot
[x] error bars on sexr plots
[x] LF residuals by season and sex (with size on x-axis)
[x] Add a surplus production plot
[x] posterior plot of spawning stock biomass (SSB)
[x] Add signal decomposition of recruitment plot
[x] Add SSB vs. recruitment plot (will need to add SSB to model outputs first) and overlay best fit SR curve
[ ] Add total panel to multi-area biomass plots
[x] Plot that shows the extent of each data set (i.e. Year along x-axis, data source up y-axis, thick line to show data extent)
[ ] panels of trace plots showing initial value, prior, posterior, MLE for each parameter
[ ] panels of histograms showing initial value, prior, posterior, MLE for each parameter
[ ] Plots of posterior density, histograms, and traces showing priors, bounds, initial values, and MAP where available/applicable. Bounds and priors will be easy to extract from the data input as they always begin with bnd and pri, they could stay in the data slot or go in their own bound and prior slots and get removed from data slot in s4 object. Initial values can be read in from lsd.ini file and go in their slot. You'll also notice I added a sim slot, this is for later when we get to it. Could set the plots up as ggplot2 facet_wraps, with some set number of panels per plot (like I did with the LF plots).
[x] observed, posterior and MLE of catch by fishing year, season, and SL, NSL
[x] observed, posterior and MLE of CPUE by fishing year and season
[x] observed, posterior and MLE of catch rate (CR)
[x] observed (but not fitted), posterior and MLE of maturity by length
[x] posterior plot of total biomass
[x] posterior plot of vulnerable biomass
[x] posterior plot of recruitment
[x] posterior plot of recruitment deviations
[x] panel plot of selectivity showing posterior and MLE by sex and tail width
[x] plot of posterior fishing mortality (F)
[ ] some step-by-step plots showing, for example, selectivity, vulnerability, the combination of the two, then how this turns in to F and then catch
[x] posterior plot of LFs
[x] LF plots add N and eff. N, xlim using bin limits
[ ] Components of the catch (i.e. the SL and NSL as data points with the components of each that are coming out like male female etc)
[x] Generate standardised residuals
[ ] Do mean width output/plot (I need to add code to produce this)
[x] Growth matrix plot
[ ] add a returned to water panel on catch plot
[ ] add a total catch row/column to catch plot
[x] either add 1944 to recruitment plot, or add line at R0
[ ] want to think about the LF plots more, I'm not actually plotting the LF data but instead the observations after doing tail compression, would be good to see the data beyond the bin limits though!
[x] ggjoy LF plot of data only
[x] Add posterior exploitation rate plot(s) (need to calculate this in code)
[x] Retrospective plots
[x] Add a rule plot, with CPUE on it
[ ] Length-weight plot
[ ] Swap out selectivity for vuln_selectivity (or make an extra plot)
[ ] Add alpha and beta to growth increment plots
[ ] New tag plot. Take slices of time and plot tw vs gi
[ ] Plot of length weight.
[ ] Add plot that cf proj and non proj numbers.
[ ] Do patchwork plots of catch, cpue etc.

quantifish / rlsd

More plot ideas #2