In kshtzgupta1/ramlegacy: Download And Read RAM Legacy Stock Assessment Database

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
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Description of the dataframes present in the database:

metadata: Table with summarized metadata (only available in newer versions 4.40, 4.41, 4.44)
stock: This stores the stock database table
assessment: This stores the assessment database table
taxonomy: This stores the taxonomy database table
management: This stores the management database table
assessor: This stores the assessor database table
assessmetod: This stores the assessmetod database table
area: This stores the area database table
biometrics: This stores the biometrics database table
tsmetrics: This stores the tsmetrics database table
timeseries: The time series data is a matrix object with the following headers/columns: (1) assessid (2) stockid (3) stocklong (4) tsid (5) tsyear (6) tsvalue
bioparams: The parameter data is a matrix object with the following headers/columns: (1) assessid (2) stockid (3) stocklong (4) bioid (5) biovalue (6) bioyear (7) bionotes
timeseries_values_views: This stores the timeseries values with timeseries type along the columns and stocks along the rows
timeseries_units_views: This stores the timeseries values with timeseries type along the columns and stocks along the rows
timeseries_ids_views: This stores the timeseries IDs with timeseries type along the columns and stocks along the rows
timeseries_assessments_views: This stores the timeseries assessments with timeseries type along the columns and stocks along the rows
timeseries_notes_views: This stores the timeseries notes with timeseries type along the columns and stocks along the rows
timeseries_sources_views: This stores the timeseries sources with timeseries type along the columns and stocks along the rows
timeseries_years_views: This stores the timeseries years with timeseries type along the columns and stocks along the rows
bioparams_values_views: This stores the reference point values, with reference point type along the columns and stocks along the rows
bioparams_units_views: This stores the reference point units, with reference point type along the columns and stocks along the rows
bioparams_ids_views: This stores the reference point IDs, with reference point type along the columns and stocks along the rows
bioparams_assessments_views: This stores the reference point assessments, with reference point type along the columns and stocks along the rows
bioparams_sources_views: This stores the reference point sources, with reference point type along the columns and stocks along the rows
bioparams_notes_views: This stores the reference point notes, with reference point type along the columns and stocks along the rows

Newer Versions (4.40, 4.41, 4.44) also contain tables for individual most-used time series:

tb.data: Total Biomass
ssb.data: Spawning Stock Biomass
tn.data: Total Abundance
r.data: Recruits
tc.data: Total Catch
tl.data: Total Landings
recc.data: Recreational Catch
f.data: Fishing Mortality
er.data: Exploitation Rate
divtb.data: TB/TBmsy
divssb.data: SSB/SSBmsy
ivf.data: F/Fmsy
diver.data: ER/ERmsy
divbpref.data: B/Bmsypref
divupref.data: U/Umsypref
tbbest.data: TBbest
tcbest.data: TCbest
erbest.data: ERbest
divtb.mgt.data: TB/TBmgt
divssb.mgt.data: SSB/SSBmgt
divf.mgt.data: F/Fmgt
diver.mgt.data: ER/ERmgt
divbpref.mgt.data: B/Bmgtpref
divupref.mgt.data: U/Umgtpref
cpair.data: Cpair
tac.data: TAC
cadv.data: Cadvised
survb.data: survB
cpue.data: CPUE
effort.data: EFFORT

Stock Summary Description

Information Contained in the Stock Summary Documents

A list of all stocks present in the region
- specifies whether the stock includes B/Bmsy, U/Umsy, B/Bmgt, and U/Umgt time series data
- specifies whether TB or SSB is preferred, and whether ER or F is preferred, if both types are present

Information available for each stock:

Metadata (scientific name, area, management authority, assessor, assessment years)
Reference points available for stock
Time series available for stock
Plots – based on available data, may include:
- Kobe plot (MSYpref) – Plots U/Umsy vs. B/Bmsy if available, filling in gaps with U/Umgt and B/Bmgt if available
- Kobe plot (MGTpref) – Plots U/Umgt vs. B/Bmgt if available, filling in gaps with U/Umsy and B/Bmsy if available
- Spawner Recruitment – Plots recruits vs. spawning-stock biomass
- Surplus Production – Plots annual surplus production vs. total biomass
- Total Biomass – Preferably plots the most recent TB time series from an assessment with a MSY, management target, or limit reference point available, otherwise plots most recent TB time series.
- Spawning stock biomass – Preferably plots the most recent SSB time series from an assessment with a MSY, management target, or limit reference point available, otherwise plots most recent SSB time series.
- Total abundance (in numbers) – Preferably plots the most recent TN time series from an assessment with a MSY, management target, or limit reference point available, otherwise plots most recent TN time series.
- Fishing mortality (instantaneous rate) – Preferably plots the most recent F time series from an assessment with a MSY, management target, or limit reference point available, otherwise plots most recent F time series.
- Exploitation rate (annual proportion) – Preferably plots the most recent ER time series from an assessment with a MSY, management target, or limit reference point available, otherwise plots most recent ER time series.
- Recruits – Plots the most recent recruitment time series. If known, the year range during which recruitment deviates were estimated in the assessment model is shaded grey.
- TC, TL, RecC – Plots most recent catch and/or landings as well as recreational catch and MSY if they are also available from that assessment. (The year range of moratoriums are shaded grey if available.)
- TAC, Cpair, Cadv – Plots most recent total allowable catch or landings (or other measures of total quota), the corresponding catch or landings, and the corresponding scientifically advised catch if available from the same assessment.
- survB – Plots the most recent fishery-independent survey biomass time series.
- CPUE – Plots the most recent fishery-independent catch-per-unit-effort time series.
- EFFORT – Plots the most recent fishing effort time series.
- CdivMSY – Plots the ratio of the most recent catch time series to MSY. MSY is drawn from the assessment directly if available, or else is calculated from Bmsy and Umsy reference points (including proxies) if available.