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Stitch all deployments for a site and year

Source: R/stitch_site.R
stitch_site.Rd

Merges all QC'd deployments for the specified site and year and writes result files. Missing dates and times are interpolated, with a warning for gaps that are suspiciously large. Data that are out range for their sensor are flagged. Writes three versions of the data file for the complete season, and hash files for use by check_site.

Usage

stitch_site(site_dir, max_gap = 1, report = FALSE, baywatchers = TRUE)

Arguments

site_dir

Full path to site data (i.e., <base>/<year>/<site>). The path must include QC'd results

max_gap

Maximum gap to quietly accept between deployments (hours); a message will be printed if this gap is exceeded

report

Run report_site if TRUE

baywatchers

If TRUE, do 2 additional comparison plots with Baywatchers data (only if report = TRUE; see report_site)

Details

Three versions of the data file are written to <site_dir>/combined/:

  1. archive_<site>_<year>.csv - contains all columns, for complete archival.

  2. WPP_<site>_<year>.csv - contains only columns required by MassDEP (a.k.a. the "WPP" file).

  3. core_<site>_<year> - just the good stuff. This is the file used for producing summaries and reports.

An additional file is written for internal use by check_site:

  1. hash.txt - a tab-delimited file lists paths to deployment files and md5 hashes.