Run full quality-control check on feeder and drinker data

This function performs comprehensive quality control checks on feeder and drinker data, identifying and handling various data quality issues.

Usage

qc(
  feed = NULL,
  water = NULL,
  cfg = qc_config(),
  id_col = id_col2(),
  start_col = start_col2(),
  end_col = end_col2(),
  bin_col = bin_col2(),
  dur_col = duration_col2(),
  intake_col = intake_col2(),
  start_weight_col = start_weight_col2(),
  end_weight_col = end_weight_col2(),
  tz = tz2(),
  bins_feed = bins_feed2(),
  bins_wat = bins_wat2(),
  bin_offset = bin_offset2(),
  verbose = TRUE,
  fix_double_detections = TRUE
)

Arguments

feed: A list of daily feed data frames named by date, or NULL if you don't have feeder data
water: A list of daily water data frames named by date, or NULL if you don't have water data
cfg: A configuration list created by qc_config().
id_col: Animal ID column name (default current global value from id_col2())
start_col: Start time column name (default current global value from start_col2())
end_col: End time column name (default current global value from end_col2())
bin_col: Bin ID column name (default current global value from bin_col2())
dur_col: Duration column name (default current global value from duration_col2())
intake_col: Intake column name (default current global value from intake_col2())
start_weight_col: Start weight column name (default current global value from start_weight_col2())
end_weight_col: End weight column name (default current global value from end_weight_col2())
tz: Time zone string for date-time operations
bins_feed: Integer vector of feed bins (default current global value from bins_feed2())
bins_wat: Integer vector of water bins (default current global value from bins_wat2())
bin_offset: Numeric bin offset (default current global value from bin_offset2())
verbose: Logical. If TRUE, print details of data where errors were detected
fix_double_detections: Logical. If TRUE, applies corrections to double detection issues by adjusting end times of overlapping bouts. Default is TRUE.

Value

A list with four elements:

warnings: a tidy data frame with one row per day and one column per warning code.
feed: cleaned feed list (or NULL).
water: cleaned water list (or NULL).
combined: merged feed + water list (after all fixes).

Details

Combines feed and water data (if both are provided)
Checks for expected number of cows and reports missing animals
Detects and optionally fixes double detections (when the same cow is detected at different bins at the same time)
Flags negative values in duration, intake, or weight measurements
Removes records with negative durations or intakes
Identifies abnormally large feed/water intakes based on thresholds
Flags cows that did not feed or drink after noon (potentially lost ear tag or due to illness)
Flgas bins with very low traffic or no visits at all

Use this function after initial data processing with process_all_feed() and process_all_water() to clean your data and prepare it for analysis. Customize thresholds using qc_config() to match your specific study parameters.

Examples

cfg <- qc_config(high_dur_feed = 2500, low_visit_threshold = 5, total_cows_expected=48)
out <- qc(feed = all_fed, water = all_wat, cfg = cfg, verbose = FALSE)
out$warnings
#> # A tibble: 2 × 16
#>   date       total_cows missing_cow double_detection_bins negative_visit_bins
#>   <chr>           <int> <chr>       <chr>                 <chr>              
#> 1 2020-10-31         47 Yes         30                    6; 12; 13          
#> 2 2020-11-01         47 Yes         3; 5; 6; 18           6; 12; 13; 30      
#> # ℹ 11 more variables: cows_disappeared_after_noon <chr>,
#> #   bins_never_visited <chr>, bins_low_traffic <chr>, long_dur_feeder <chr>,
#> #   large_intake_feed_visit <chr>, low_daily_feed_intake_cows <chr>,
#> #   high_daily_feed_intake_cows <chr>, long_dur_drinker <chr>,
#> #   large_intake_water_visit <chr>, low_daily_water_intake_cows <chr>,
#> #   high_daily_water_intake_cows <chr>