createSummaryReport: Create a Summary Report for a List of Stations

In EricArcher/PAMsbuoy: Manipulation and filtering for PAM (Passive Acoustic Monitoring) data collected from sonobuoys

Description

Creates a summary report to be used for cruise reports or as a starting point for publications. Saves the report as a word document, and saves all associated figures and tables as images in a Report folder. Automatically fills in summary information (number of sonobuoys deployed, detections, etc.), and prompts user for some information not contained in the databases. The created report should not be considered a final document, some information will need to be added / edited.

Usage

createSummaryReport(
  stationList,
  outDir = ".",
  fileName = "summaryReport",
  format = "word",
  test = FALSE,
  wincruz = NULL,
  specFile = NULL
)

Arguments

stationList	list of stations to create the summary report for
outDir	directory to write the report to. Will create subfolders Report, Report/Tables, and Report/Figures within this directory
fileName	name of the report file
format	output format of report, either word or html
test	temporary logical flag for testing
wincruz	an optional wincruz file for matching species to opportunistic sightings
specFile	an optional species code file to match with wincruz species IDs

Author(s)

Taiki Sakai [e-mail]

EricArcher/PAMsbuoy documentation built on March 3, 2021, 5:56 a.m.