In casaultb/azmpdata: A data package to share derived metrics from AZMP research documents

Discussion of Maritimes environmental data access, April 7, 2020

B. Casault, E. Chisholm, C. Johnson, M. McMahon

Review of metadata names

• review document in grouup chat: azmpmetrics_csv_organizer.doc
• Linking look up tables with odf filename may be more difficult than sample ID or event ID
• should first standardize names and make sure they are consistent

Regional look up table

• Emily's csv version is a sheet in azmpmetrics_v2.xlsx
• single table combining all types of coordinate data (stations, polygons), lots of repetition
• Benoit's examples are csv files in group chat (eg. AZMP_sections_names.csv), with RData (sf objects) options as well (eg. AZMP_Sections.RData)
• seperate sections, stations, polygons into individual csv tables
• needs more discussion and examples to see how each type would interact with code in multivaR/ azmpdata
• NAFO polygons full or cut at 200m isobath?
• sf objects?
• sf files are based on row IDs, possible to get mixed up?
• concern for multiple files when searching for a region to plot/ visualize, will be more difficult to code if need to chack in multiple files
• concern for single table being overwhelmingly large with excess repetition
• compromise by adding type in ss_names?
• create a look up table for regional look up tables, columns: name of region, csv filename
• Emily and Benoit will discuss further
• EC will work on plotting functionality and see how each format would interact
• assemble all polygon data would be a good solid step forward
• trawl survey strat data may also be included in polygon tables (very large)
• can sf handle this? holes in polygons?
• BC will investigate
• Scallop people in PED may have experience
• Mike shared Oracle example of all 'types' of coordinate data in a single table

Occupations look up table

• Benoit sent examples in group chat (eg. DIS_Occupations_HL2.csv )
• currently have HL2, will be created for other stations
• connect to data frames with sample ID or Event ID
• some differences in event ID format in BioChem may be of concern (keep an eye out)
• make sure there is consistency between data frames

Anomalies

• Emily shared an RMD example (available at rpubs.com/e_chisholm/anomaly_example)
• Benoit's method was not implemented correctly
• may be issue about section grouping
• Benoit will clarify his method and help EC properly implement the code provided
• Use GLM method (AZMP standard)
• need to decide on particular model
• differences based on type of data (stations, sections, time series, etc)
• set up to use with azmpdata and other data
• present resdoc anomalies (annual sections, trawl surveys, seasonal anomalies, monthly - Chantelle?)

Next meeting

• update on regional look up table
• plotting code for polygons
• anomalies update
• occupations tables from other stations

casaultb/azmpdata documentation built on July 4, 2025, 11:04 a.m.