Package index • moo4feed

Getting Started

Core functions for reading and processing data.

read_data_safely(): Safely Read Data from a File

process_all_feed(): Process a batch of feeder files

process_all_water(): Process a batch of water files

process_feeder(): Process 1 feeder data file

process_water(): Process 1 water data file

Data Cleaning and Preparation

Data Quality Checks

Check and validate feeding and drinking visits.

qc_config(): Build a configuration list for data quality-control

qc(): Run full quality-control check on feeder and drinker data

knn_outlier_detection(): Detect outliers using k-nearest neighbors (KNN) method

knn_clean_feed(): Process multiple days of feeding data and remove outliers using KNN

knn_clean_water(): Process multiple days of water data and remove outliers using KNN

viz_outliers(): Visualize outliers from KNN outlier detection

Data Filtering

Filter data relevant to animals and sensors in your study.

delete_rows(): Remove rows by matching values in a specified column

keep_bins(): Keep only rows for specified bins

rename_bins(): Shift specified bin IDs by an offset

Time Adjustments

Handle Daylight Saving Time changes for North America.

daylight_saving_adjust(): Adjust Time Stamp for Daylight Saving Time (DST) Transitions in North America

get_dst_switch_info(): Get Daylight Saving Time (DST) Switch Dates and Exact Transition Times

dst_switch_day(): Detect Daylight Saving Time (DST) Change Dates

dst_switch_hm(): Detect the Exact Time (hour and minute; hm) of Daylight Saving Time (DST) Change

File Management

Extract date information from file names and compare files.

file_name_processing(): Process file names and extract date tokens

compare_files(): Compare feed and water file names by shared dates

get_date_range(): Get the overall date range for a set of files

cap_first(): Capitalize the First Letter of a String

lower_first(): De-capitalize the First Letter of a String to Lower Case

Data Integration

Merge and unmerge feeding and drinking data

combine_feed_water(): Combine Feeder and Water Data by Date

merge_list_df(): Merge a List of Data Frames

unmerge_data(): Un-merge a combined data frame into a list of data frames by date

Story of Every Cow

Feed and Water Summary

Summarize daily feed/water intake, duration, and visit counts.

feed_water_summary(): Summarize and check for abnormal feed & water intake

Bin visit summary

Analyze bin visit patterns.

unique_bin_visits(): Analyze Bin Visit Patterns For Each Cow

Non-nutritive Visit Analysis

Functions for analyzing non-nutritive and no-feed visits per animal per day.

calculate_non_nutritive_visits(): Calculate non-nutritive visits per animal per day

calculate_no_feed_visits(): Calculate visits with no feed available per animal per day

Replacement Behavior Analysis

Functions to identify replacement behavior across multiple days, and validate those events by checking whether the actor cow was already present at another bin.

record_replacement_days(): Identify and validate replacement events across multiple days

Meal clustering

Cluster feeding visits into meals.

meal_interval(): Calculate optimal interval between feeding visits for meal clustering

viz_eps_percentile(): Visualize gap distribution and percentile-based optimal interval (eps) selection

viz_eps_gmm(): Visualize gap distribution with GMM fit and optimal interval (eps)

cluster_meals(): Cluster feeding visits into meals using DBSCAN

meal_label_visits(): Cluster feeding visits into meals and label each visit

merge_cluster_results(): Merge meal clustering results with original visit data

viz_meal_clusters(): Visualize meal clustering results as timeline plots

combine_animal_plots(): Combine multiple days for one animal with pagination

combine_date_plots(): Combine multiple animals for one date with pagination

extract_plots(): Extract subset of plots by animal and/or date

Configuration and Customization

Global Variables

Configure global variables to customize for your data structure.

set_global_cols(): Set multiple global variables at once

tz2(): Get the timezone currently set as global variable

set_tz2(): Set a new timezone which will be used as a global variable governing the processing of timestamp data

id_col2(): Get the name of the column recording animal ID

set_id_col2(): Set the name of the column recording animal ID as global variable

trans_col2(): Get the name of the column recording transponder ID for each visit

set_trans_col2(): Set the name of the column recording transponder ID as global variable

start_col2(): Get the name of the column recording the start time of an event

set_start_col2(): Set the name of the column recording the start time of an event as global variable

end_col2(): Get the name of the column recording the end time of an event

set_end_col2(): Set the name of the column recording the end time of an event as a global variable

bin_col2(): Get the name of the column recording the ID of the bin for each visit

set_bin_col2(): Set the name of the column recording bin ID as global variable

bin_offset2(): Get the numeric bin offset which was set as global variable bin_offset

set_bin_offset2(): Set the numeric bin offset

bins_feed2(): Get the vector of all feed bins included in your study

set_bins_feed2(): Set the vector of all feed bins included in your study as global variable

bins_wat2(): Get the vector of all water bins included in your study

set_bins_wat2(): Set the vector of all water bins included in your study as global variable

duration_col2(): Get the name of the column recording visit duration

set_duration_col2(): Set the name of the duration column as global variable

intake_col2(): Get the name of the column recording feed/water intake

set_intake_col2(): Set the name of the intake column as global variable

start_weight_col2(): Get the name of the column recording start weight

set_start_weight_col2(): Set the name of the start weight column as global variable

end_weight_col2(): Get the name of the column recording end weight

set_end_weight_col2(): Set the name of the end weight column as global variable

Example Data

Example datasets and functions for demonstration.

all_fed: Cattle feeding behavior and visit record data

all_wat: Cattle water drinking behavior and visit record data

clean_feed: Cattle feeding behavior data after quality check and outlier removal

clean_water: Cattle drinking behavior data after quality check and outlier removal

clean_comb: Combined feeding and drinking behavior data with outliers removed

moo4feed_example(): Access Example Data Files Shipped with moo4feed