# Animal Tracker

## Documentation for package ‘animaltracker’ version 0.1.0

- DESCRIPTION file.

## Help Pages

app_server | Defines logic for updating the app based on user interaction in the ui
app_ui | Defines a user interface for the 'shiny' app
boxplot_altitude | Generates a boxplot to visualize the distribution of altitude by GPS.
boxplot_time_unit | Generates a boxplot to visualize the distribution of time between GPS measurements by GPS unit.
calc_bearing | Helper function for cleaning Columbus P-1 datasets. Given lat and long coords in degree decimal, convert to radians and compute bearing.
clean_batch_df | Cleans a directory of animal data files
clean_export_files | Cleans all animal GPS datasets (in .csv format) in a chosen directory. Optionally exports the clean data as spreadsheets, a single .rds data file, or as a list of data frames
clean_location_data | Cleans a raw animal GPS dataset, implementing a standardized procedure to remove impossible values
clean_store_batch | Cleans a directory of animal data files and stores them locally in rds format
compare_flags | Joins and reformats two animal data frames for the purpose of flag comparison
compare_summarise_daily | Compares two animal datasets and calculates daily summary statistics by GPS GPS, date, lat, long, course, distance, rate, elevation column names should match.
compare_summarise_data | Compares two animal data frames and calculates summary statistics. GPS, date, lat, long, course, distance, rate, elevation column names should match.
deg_to_dec | Helper function for cleaning Columbus P-1 datasets. Given lat or long coords in degrees and a direction, convert to decimal.
demo | Demo animal GPS data from cows
demo_comparison | Demo comparison of two animal datasets
demo_filtered | Filtered demo animal GPS data from cows
demo_filtered_elev | Filtered demo animal GPS data from cows with elevation appended at zoom 1
demo_info | Raw demo animal GPS data from cows with information
demo_meta | Metadata for demo animal GPS data from cows
demo_unfiltered | Unfiltered demo animal GPS data from cows
demo_unfiltered_elev | Unfiltered demo animal GPS data from cows with elevation appended at zoom 1
detect_peak_modz | Alternative implementation of the robust peak detection algorithm by van Brakel 2016
dev_add_to_gitignore | Add big files to a .gitignore file
get_data_from_meta | Get animal data set from specified meta. If date range is invalid, automatically returns all animal data specified by meta_df.
get_file_meta | Generate metadata for a directory of animal data files
get_meta | Generate metadata for an animal data frame - filename, site, date min/max, animals, min/max lat/longitude, storage location
histogram_animal_elevation | Generate a histogram of the distribution of modeled elevation - measured altitude
histogram_time | Generates a histogram to visualize the distribution of time between GPS measurements.
histogram_time_unit | Generates a histogram to visualize the distribution of time between GPS measurements by GPS unit.
join_summaries | Joins two animal data frame summaries by a column and appends differences
line_compare | Compares moving averages of a variable for two datasets over time, grouped by GPS GPS, Date, and col columns should match
lookup_elevation_aws | Add elevation data from public AWS terrain tiles to long/lat coordinates of animal gps data
lookup_elevation_file | Add elevation data from terrain tiles to long/lat coordinates of animal gps data
process_elevation | Process and optionally export modeled elevation data from existing animal data file
qqplot_time | Generates a QQ plot to show the distribution of time between GPS measurements.
quantile_time | Determines the GPS measurement time value difference values roughly corresponding to quantiles with .05 intervals.
read_columbus | Read and process a Columbus P-1 data file containing NMEA records into a data frame
read_gps | Reads a GPS dataset of unknown format at location filename
read_zip_to_rasters | Read an archive of altitude mask files and convert the first file into a raster object
run_shiny_animaltracker | Run the animaltracker 'shiny' app by calling this function. Depending on the size of input files, it may be advisable to increase the maximum request size.
run_validation_app | Run the 'shiny' validation app. Depending on the size of input files, it may be advisable to increase the maximum request size.
save_meta | Save metadata to a data frame and return it
store_batch_list | Generates basic metadata about a directory of animal data files and stores the files as data frames as a list with the meta
summarise_anidf | Calculates summary statistics for an animal data frame
summarise_col | Get summary statistics for a single column in an animal data frame
summarise_unit | Summarise a number of animal datasets by GPS unit
violin_compare | Compares summary statistics from two datasets as side-by-side violin plots