Getting started

This is an overview of how to use functions in the feedr package to transform and visual your RFID data. Note that while we’ve tried to explain the code in detail, if you are new to R, you may benefit from an introduction to coding in R before tackling your data with the feedr package

Order of operations

This package contains functions to perform three broad services:

Loading/Importing Data
Raw data directly from the loggers, already amalgamated, or from the animal__nexus__ website
Housekeeping
Functions for checking and correcting errors before you transform the data
Transformations
Transforming raw data into visits, presence, activity, etc
Visualizations
Static or interactive maps produced by the mapping functions which visualize movements between and presence around the RFID loggers.

There are also three ‘user-interface’ (UI) functions that can be used to simplify the use of these functions (see below).

In the normal order of operations, several functions depend on the output of other functions.

For example, to get daily activity patterns, you could get your data from the animalnexus database with dl_data(), turn this raw data to visits data with visits(), turn visits data to activity data with activity() and finally, turn activity data into daily activity patterns with daily().

Tutorial Data

Two data frames, finches and chickadees are included in the feedr package for the purpose of demonstration.

head(finches)

##    animal_id       date                time logger_id     species age sex    site_name       lon      lat
## 1 0620000514 2016-01-28 2016-01-28 12:34:25      2200 House Finch AHY   F Kamloops, BC -120.3612 50.66778
## 2 0620000514 2016-01-28 2016-01-28 12:34:28      2200 House Finch AHY   F Kamloops, BC -120.3612 50.66778
## 3 041868D861 2016-01-28 2016-01-28 12:35:41      2200 House Finch AHY   M Kamloops, BC -120.3612 50.66778
## 4 06200004F8 2016-01-28 2016-01-28 12:35:52      2200 House Finch AHY   F Kamloops, BC -120.3612 50.66778
## 5 06200004F8 2016-01-28 2016-01-28 12:35:59      2200 House Finch AHY   F Kamloops, BC -120.3612 50.66778
## 6 06200004F8 2016-01-28 2016-01-28 12:36:02      2200 House Finch AHY   F Kamloops, BC -120.3612 50.66778

head(chickadees)

##    animal_id       date                time     logger_id experiment      lat       lon
## 1 06200004BF 2016-01-11 2016-01-11 10:48:49 exp2-GR10DATA       exp2 53.89086 -122.8193
## 2 062000038F 2016-01-11 2016-01-11 10:48:50 exp2-GR10DATA       exp2 53.89086 -122.8193
## 3 06200004E4 2016-01-11 2016-01-11 10:48:55 exp2-GR10DATA       exp2 53.89086 -122.8193
## 4 06200004BF 2016-01-11 2016-01-11 10:50:02 exp2-GR10DATA       exp2 53.89086 -122.8193
## 5 06200004E4 2016-01-11 2016-01-11 10:51:07 exp2-GR10DATA       exp2 53.89086 -122.8193
## 6 06200004BE 2016-01-11 2016-01-11 10:51:51 exp2-GR10DATA       exp2 53.89086 -122.8193

Function Index

Loading/Importing Data

ui_import(): Launch an interactive user-interface to import/load local data files
load_raw(): Load in a single file of raw logger data
load_raw_all(): Load in and combine multiple files of raw logger data
dl_data(): Download and load data directly from the animal__nexus__ website

Housekeeping

check_ids(): Remove known bad ids (i.e. errors, wands, etc.)
check_problems(): Fix known id problems

Transformations

ui_trans(): Launch an interactive user-interface to transform data
visits(): Transform raw data into visits data
move(): Transform visits data into movements between loggers
presence(): Transform visits data into presence around loggers
disp(): Transform visits data into displacements
dom(): Transform displacements into dominance matrices and hierarchies
activity(): Transform visits data into activity data
daily(): Transform activity data into daily activity patterns

Visualizations

ui_animate(): Launch an interactive user-interface to create animations
map_ggmap(): Visualize movements and/or presence with ggmap (static)
map_leaflet(): Visualize movements and/or presence with leaflet (interactive)