map_leaflet: Map data using leaflet

In steffilazerte/feedr: Transforming Raw RFID Data

Map data using leaflet

Description

A visual summary of presence at and movements between loggers using leaflet for R. This produces an interactive html map. This function can take invidiual data as well as grand summaries (see Details and Examples).

Usage

map_leaflet(
  p = NULL,
  m = NULL,
  locs = NULL,
  summary = "none",
  p_scale = 1,
  m_scale = 1,
  p_title = "Time",
  m_title = "Path use",
  p_pal = c("yellow", "red"),
  m_pal = c("yellow", "red"),
  controls = TRUE,
  u.scale,
  p.scale,
  u.title,
  p.title,
  u.pal,
  p.pal
)

Arguments

p	Dataframe. Regular or summarized presence data with columns logger_id and, if already summarized, amount. It can also contain animal_id for individual-based data, and lat/lon columns.
m	Dataframe. Regular or summarized movement data with columns logger_id, move_path, and, if already summarized, path_use. It can also contain animal_id for individual-based data, and lat/lon columns.
locs	Dataframe. Lat and lon for each logger_id, required if lat and lon not provided in either p or m.
summary	Character. How the data should be summarized. If providing summarized data, use "none" (default). "sum" calculates total movements and total amount of time spent at a logger, "sum_indiv", averages the totals by the number of individuals in the data, "indiv" calculates totals for each individual.
p_scale, m_scale	Numerical. Scaling constants to increase (> 1) or decrease (< 1) the relative size of presence (p) and movements (m) data.
p_title, m_title	Character. Titles for the legends of presence (p) and movements (m) data.
p_pal, m_pal	Character vectors. Colours used to construct gradients for presence (p) and path (m) data.
controls	Logical. Add controls to map (allows showing/hiding of different layers)
u.scale, p.scale, u.title, p.title, u.pal, p.pal	Depreciated.

Details

The type of summary visualized is defined by the summary argument: summary = "sum" calculates the total amount of time spent at each logger (presence) or total number of movements between loggers (movements). summary = "sum_indiv" averages these totals by the number of individuals in the data set, resulting in an average total amount of time per individual and an average amount of movements per individual for, or between, each logger. summary = "indiv" calculates individual totals. If the data is already summarized, use summary = "none".

Value

An interactive leaflet map with layers for presence, movement paths and logger positions.

Examples

v <- visits(finches)
p <- presence(v, bw = 15)
m <- move(v)

# Built in summaries
map_leaflet(p = p, m = m, summary = "sum")
map_leaflet(p = p, m = m, summary = "sum_indiv")
map_leaflet(p = p, m = m, summary = "indiv")

# Custom summaries
# Here, we average by the number of loggers (using dplyr)

library(dplyr)

p2 <- p %>%
  group_by(logger_id, lat, lon) %>%
  summarize(amount = sum(length) / logger_n[1])

m2 <- m %>%
  group_by(logger_id, move_path, lat, lon) %>%
  summarize(path_use = length(move_path) / logger_n[1])

map_leaflet(p = p2, m = m2)

steffilazerte/feedr documentation built on Jan. 27, 2023, 3:46 a.m.