Package index • BuzzardsBay

Quality Control Module

Run automated QC and support interactive QC on individual deployments

qc_deployment(): Run automatic quality control on a deployment

make_deployment_report(): Make QAQC report for a deployment

Analysis Module

Stitch and report on all the deployments at a site

report_site(): Produce stats and a report for a site and year

check_site(): Check to be sure that result files from stitch_site are up to date

stitch_site(): Stitch all deployments for a site and year

Secondary functions

Secondary functions that are primarily used internally but might be useful to users

bb_options(): Set and retrieve BuzzardsBay package options

bb_plot(): Make static plot of logger data

create_parameter_file(): Create a BuzzardsBay parameter file

extract_baywatchers(): Extract relevant Baywatchers data from ginormous Excel file

get_tide_height(): Get the tide height at a particular station corresponding to a series of date, times. Note due to limitations in the rtide package this only works for about a third of the Buzzards Bay NOAA tide stations.

import_calibrated_data(): Import Calibrated Deployment Data

is_daylight(): Determine if observation correspond to daylight hours or not

lookup_paths(): Lookup paths for data and parameter files

plot_tide_sun(): Plot tide height and daylight hours

tide_station_info: Locations of NOAA tide stations within Buzzards Bay

setup_example_dir(): Set up an example directory

Internal functions

Internal functions, not intended for package users

aggreg(): Improved version of aggregate

apply_timezone(): Apply at timezone to a date time string or object

bb_interactive_plot(): Interactive logger data plot

check_placement(): Check SN, site, deployment date, and logger type against placements table

clean_csv_import_names(): Clean up column names for basic CSV input

combine_flags(): Combine the flags from individual "_Flags" columns into a single flags vector.

cut_path_items(): cut items off the end of a path

daily_stats(): Produce daily stats for a site

format_csv_date(): Format CSV date that might have been corrupted by excel

format_csv_date_time(): Format CSV date that might have been corrupted by excel

format_date_time(): Internal function to reformat the date time date from Details.txt

get_cond_details(): Retrieve information from a conductivity calibration details file

get_do_details(): Retrieve information stored a Dissolved Oxygen calibration details file

get_expected_columns(): Look up expected column names and order

get_file_hashes(): Get md5 hashes for a vector of files

get_site_name(): Get the full site name for a site

longest_duration(): Give duration of the longest run of low DO for each day

lookup_devices(): Lookup the DO and conductivity logger device models

lookup_site_paths(): Look up paths for a specified site

make_facet_plot(): Produce a paired time series plot of DO and Temperature for the final report

make_plot(): Produce a time series plot for the final report

make_plot_2var(): Produce a time series plot with two datasets for the final report

mean_daily_durations(): Give mean duration of low-DO runs in hours

parse_hoboware_details(): Read HOBOware details file

parse_mx801_details(): Extract specific metadata items from the MX801 details sheet

read_and_format_placements(): Read and format placements

read_deployment_yaml(): Read deployment metadata from a yaml file

read_mx801_data(): Import data from MX801 logger

replace_na_runs(): Replace short runs of NA in logical vector

rle2(): A drop-in replacement for base::rle() that treats all NAs as identical

seasonal_stats(): Produce seasonal stats for a site

suppress_specific_warnings(): Suppress some specific warnings

update_bb_parameters(): Update Buzzards Bay parameters