Skip to contents

Produce stats and a report for a site and year

Source: R/report_site.R
report_site.Rd

Produces daily stats and a report with seasonal stats and a number of graphs for a specified site and year.

Usage

report_site(
  site_dir,
  check = TRUE,
  baywatchers = TRUE,
  salinity = TRUE,
  clip = NULL
)

Arguments

site_dir

Full path to site data (i.e., <base>/<year>/<site>)

check

If TRUE, runs check_site to make sure source files haven't been changed

baywatchers

If TRUE, do 2 additional comparison plots with Baywatchers data

salinity

If TRUE, include an additional time series plot of salinity

clip

Optionally supply a pair of dates (in yyyy-mm-dd format) to clip seasonal statistics

Details

Two files are written:

  1. daily_stats_<site>_<year>.csv - a file with a row for each day of the season with several summary statistics

  2. report_<site>_<year>.pdf - a PDF report with a table of seasonal stats and a number of graphs

stitch_site must be run first to create the necessary data. If stitch_site was run at some point in the past, it is highly advisable to run check_site to make sure deployment files haven't changed since the last stitch_site run.

Including plots based on Baywatchers data requires a file within the site baywatchers/<site>.csv. This file must include the date and time (a column that includes Date_Time in the name) and dissolved oxygen in mg/L (DO in the name, but not percent, pct, or %). Column names are case-insensitive. If this file is missing or the necessary columns are not present, an error will be reported. You can use baywatchers = FALSE for datasets that don't have Baywatchers data to exclude these plots.

You may clip the seasonal statistics to a date range, for example, clip = c("2024-08-10", "2024-08-25"). This will affect the seasonal statistics table in the report and CSV file, but not graphs.