ices-tools-dev / bluebridge Goto Github PK

A web interface is needed to display most recent stock status according to ecoregion, guild, spp., etc. Software is extant but needs to be cleaned up. It could be streamlined with code from fisheryO, which interfaces with the most recent version of icesSAG and icesSD.

To clean and prepare the scripts used to produce seabed pressure (5) and impact (2) indicators, as well as standard indexes and outputs contained in the ICES advice and annex demonstration advice (sr.2017.13 and sr.2017.13 annex). End products (cleaned scripts) in line with the guiding principles of TAF, facilitate the making of a technical guideline document, and be end user friendly (managers and benthic ecologists) for future assessments/benchmarking processes (i.e. shiny app).

Link: http://www.ices.dk/sites/pub/Publication%20Reports/Advice/2017/Special_requests/eu.2017.13.pdf

WKFooWI, WGECO, and others have provided indicators and we need to make these into operational products from SA, survey, etc.

DLMTools and FLR (and others?) are key packages for ICES stock assessments. It will be useful to be able to translate objects from FLR to DLMtool and vice versa. This might end up being a beast.

ICES InterCatch is the current system for raising landings and discards data to the level of catch data. Software is extant to summarize intercatch output - but could benefit from a thorough clean-up/modernization. Further, it might be useful to convert to a shiny (proxy) app to be hosted on ICES to allow deeper exploration of the data.

Assessment working groups have many diagnostics used to evaluate data quality, model assumptions, and model fit. It will be useful to pare these down into a common group of functions. I suggest we migrate towards "tidy data principles" to encourage best practices and to simplify input. Many of these plots may be extant with FL* models, so maybe if we figure out #1.

Suggestions:

• Standardized plots of catch-by-square by month by species (possibly produced from VMS datacall)
  suggested by @nielshintzen
• Weight-at-age in stock, landings, discards
• Maturity-at-age, M-at-age (in case of time-varying)
• N/biomass/F in surveys, catch over time + age
• Internal consistency of datasets
• Fitted vs observed for all datasets
• Residuals over time + age
• Correlation among parameters
• Estimated total catch vs observed catch
• SSB, F, R with uncertainty
• Retrospective + mohns rho
• Catchabilities of surveys & selectivity of fleets
• Software package + version used