Animal Tracker


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Documentation for package ‘animaltracker’ version 0.2.0

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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.
datePicker 'shiny' module server-side UI generator for the animaltracker app's date picker.
datePickerOutput 'shiny' module UI output for the animaltracker app's date picker.
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
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
detect_peak_modz Alternative implementation of the robust peak detection algorithm by van Brakel 2014 Classifies data points with modified z-scores greater than max_score as outliers ccording to Iglewicz and Hoaglin 1993
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.
reactivePicker 'shiny' module server-side UI generator for the animaltracker app's dynamic dropdown selections.
reactivePickerOutput 'shiny' module UI output for the animaltracker app's dynamic dropdown selections.
reactivePlot 'shiny' module server-side UI generator for the animaltracker app's summary statistics tables.
reactivePlotOutput 'shiny' module UI output for the animaltracker app's plots tab.
reactiveRange 'shiny' module server-side UI generator for the animaltracker app's coordinate range input.
reactiveRangeOutput 'shiny' module UI output for the animaltracker app's coordinate range input.
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 You can run the animaltracker 'shiny' app by calling this function.
run_validation_app Run the 'shiny' validation app
save_meta Save metadata to a data frame and return it
staticPicker 'shiny' module server-side UI generator for the animaltracker app's basic dropdown selections.
staticPickerOutput Shiny Module UI output for the animaltracker app's basic dropdown selections.
stats 'shiny' module server-side UI generator for the animaltracker app's summary statistics tables.
statsLabel 'shiny' module server-side UI generator for the animaltracker app's summary statistics labels.
statsLabelOutput 'shiny' Module UI output for the animaltracker app's summary statistics labels.
statsOutput 'shiny' module UI output for the animaltracker app's summary statistics tables.
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
time 'shiny' module server-side UI generator for the animaltracker app's time input.
timeOutput 'shiny' module UI output for the animaltracker app's time input
violin_compare Compares summary statistics from two datasets as side-by-side violin plots