Set and retrieve BuzzardsBay package options — bb

With no arguments all the Buzzards Bay parameters will be returned as a list. Use a single character value to retrieve the value of a single option. Use one or more named arguments to set options.

Usage

bb_options(...)

Arguments

...

One of:

one or more named arguments where the name is a an option and the value its new setting e.g. sal_max_jump = 0.75;
a single unnamed argument stating an option to retrieve e.g. "sal_max_jump".
No arguments, indicating that all options and their current settings should be returned in a list; or
a single list argument with named items and their new values.

Value

If no arguments are used than all options will be returned as a list. If there is a single, unnamed argument with a character value indicating an option than the value of that option will be returned. Otherwise, the arguments should indicate new option settings and nothing will be returned.

Details

The options:

do_lv_duration, do_lv_range

For Low Variation in Dissolved Oxygen (Dlv) flag. do_lv_range is the maximum difference between the maximum and the minimum values in a streak longer than do_lv_duration minutes before the the low variation in dissolved oxygen (Dlv) flag is set

do_max_jump

The maximum difference between consecutive DO readings before the jump in dissolved oxygen (Dj) flag is is set.

do_streak_duration, do_streak_min

If DO remains below do_streak_min for more than do_streak_duration than the Dissolved Oxygen low streak (Dls) flag is set.

logger_error_values

One or more values that indicate a logger error. If setting multiple values in a YAML file use indented lines with a dash for each value:

logger_error_values:
  - -888.88
  - 9999

Temperature (from both loggers), High Range, and Raw DO are all checked for this value. Flags: TDe, TCe, He, and Re.

max_hr, min_hr

Thresholds for the high high range (Hh) and low high range (Hl) flags.

max_raw_do

Threshold for the high raw DO (Rh) flag.

max_temp, min_temp

Thresholds for the high temperature (TDh, TCh) and low temperature (TDl, TCl)

plot_min_do, plot_max_do, plot_min_sal, plot_max_sal, plot_min_temp, plot_max_temp

These constrain the Y range in the QC Report plots when plotting Dissolved Oxygen (DO), Salinity (sal), and temperature (temp)

sal_lv_duration, sal_lv_range

If the difference between the maximum and minimum salinity remains below sal_lc_range for more than sal_lv_duration minutes than the low variation in salinity (Slv) flag is set.

sal_max_jump

The maximum difference between successive salinity records before the salinity jump (Sj) flag is set for both involved records.

min_depth, max_depth

The minimum and maximum water depth. If the Depth column is present and falls outside of this range either the Wl (water depth low) or Wh (water depth high) flags will be thrown. Additionally 7 will be written to Depth_QC and either 9999 or 7 will be written to Gen_QC depending on if it's high or low respectively

Examples

 o <- bb_options()
 cat(yaml::as.yaml(o))
#> do_lv_duration: 60.0
#> do_lv_range: 0.01
#> do_max_jump: 2.0
#> do_streak_duration: 60.0
#> do_streak_min: 0.5
#> logger_error_values: -888.88
#> max_depth: 9.0
#> max_hr: 55000.0
#> max_raw_do: 20.0
#> max_temp: 35.0
#> min_depth: 0.0
#> min_hr: 1000.0
#> min_temp: 5.0
#> plot_max_do: 20.0
#> plot_max_sal: 36.0
#> plot_max_temp: 31.0
#> plot_min_do: -0.5
#> plot_min_sal: 0.0
#> plot_min_temp: 0.0
#> sal_lv_duration: 60.0
#> sal_lv_range: 0.01
#> sal_max_jump: 0.75
 bb_options(sal_max_jump = 0.5)
 bb_options("sal_max_jump")
#> [1] 0.5
 bb_options(o)  # Reset original options
 bb_options("sal_max_jump")
#> [1] 0.75