README.md

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Living Data Rescue: Harvey Janszen Legacy Project

This repository contains data entry templates, digitization protocols, processing scripts, and digitized data outputs for the field notes of Harvey Janszen

The three types of data entered & processed by these scripts and protocols:

1. Observation-only occurrence data (in field journals)

2. Field notes of collected specimens (in field journals)

3. Digitized herbarium label data (on specimen photographs)

Data Sources

1. Field Journals

   • HJ5 = Flora of Saturna (1973-1981)

   • HJ7 = Journal ca. 1981-1996

   • HJ8 = Journal ca. 1996-2000

   • HJ9 = Unbound field notes ca. 1999-2003

   • HJ27 = Field notes ca. 2003-2017

2. Collected specimens

   • Royal British Columbia Museum (RBCM) Herbarium (~1263 specimens)

     • Specimens labels

     • Digitized collection label data in database

   • University of British Columbia (UBC) Herbarium (~ 50 specimens)

   • ~ 65 specimens from later in Harvey's life to be accesseioned at the UBC Herbarium

General workflow

DwC = Darwin Core occurrence data standards

GBIF = Global Biodiversity Information Facility

Ultimate goals for this project

1. To publish observation-only (occurrence) data to GBIF (potentially via Canadensys)

2. Clean/ review berbarium records for Harvey's collections housed at the RBCM (ultimately published to GBIF by the RBCM Herbarium)

3. Deposit & accession ~ 65 new specimens at the UBC Herbarium (ultimately published to GBIF by the UBC Herbarium)

Grouped Components

1. Observation-only occurrence data

   Data entry

   • occ-data-entry-template (template to enter data)

   • 1_raw_data folder (houses the data entry files for respective journals)

   • occ-data-entry-protocol (follow this protocol to enter data)

   Data processing

   • post-entry-processing (follow this protocol to process entered data)

   Output

   • CSV files of Darwin Core formatted occurrences found here

2. Collection data

   Data entry

   • coll-data-entry-template (template to enter data)

   • 1_raw_data folder (houses the data entry files for respective journals)

   • coll-data-entry-protocol (follow this protocol to enter data)

   Data processing

   • post-entry-processing (follow this protocol to process entered data)

   Output

   • CSV files of Darwin Core formatted collection data found here

3. RBCM data checking ||||| [under construction] ||||

   Label data entry ||||| [under construction] ||||

   • RBCM-label-entry.xlsx

   • label-data-entry-protocol.Rmd

   Processing & comparing labels to database ||||| [under construction] ||||

   • part-1_label-processing.R

   • part-2_label-to-database-comparison.R

   Processing & reviewing field notes to database ||||| [under construction] ||||

   • part-1_field-note-processing.R

   • part-2_field-note-database-comparison.R

4. Observation-only & Collection data aggregation

   • total-occurrence-aggregation.R

Recommended workflows

For observation-only (occurrence) data

For collection data

• To further use this data to review RBCM herbarium data, follow the protocols here