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Visualize deployments features

Source: R/map_dep.R
map_dep.Rd

This function visualizes deployments features such as number of detected species, number of observations and RAI on a dynamic map. The circle size and colour are proportional to the mapped feature. Deployments without observations are shown as gray circles and a message is returned.

Usage

map_dep(
  package = NULL,
  feature,
  ...,
  species = NULL,
  sex = NULL,
  life_stage = NULL,
  effort_unit = NULL,
  cluster = TRUE,
  hover_columns = c("n", "species", "deploymentID", "locationID", "locationName",
    "latitude", "longitude", "start", "end"),
  palette = "inferno",
  zero_values_show = TRUE,
  zero_values_icon_url = "https://img.icons8.com/ios-glyphs/30/000000/multiply.png",
  zero_values_icon_size = 10,
  na_values_show = TRUE,
  na_values_icon_url = "https://img.icons8.com/ios-glyphs/30/FA5252/multiply.png",
  na_values_icon_size = 10,
  relative_scale = TRUE,
  max_scale = NULL,
  radius_range = c(10, 50),
  datapkg = lifecycle::deprecated()
)

Arguments

package

Camera trap data package object, as returned by read_camtrap_dp().

feature

Deployment feature to visualize. One of:

  • n_species: Number of identified species.

  • n_obs: Number of observations.

  • n_individuals: Number of individuals.

  • rai: Relative Abundance Index.

  • rai_individuals: Relative Abundance Index based on number of individuals.

  • effort: Effort (duration) of the deployment.

...

Filter predicates for subsetting deployments.

species

Character with a scientific name. Required for rai, optional for n_obs. Default: NULL.

sex

Character defining the sex class to filter on, e.g. "female". If NULL (default) all observations of all sex classes are taken into account. Optional parameter for n_obs and n_individuals.

life_stage

Character vector defining the life stage class to filter on, e.g. "adult" or c("subadult", "adult"). If NULL (default) all observations of all life stage classes are taken into account. Optional parameter for n_obs and n_individuals.

effort_unit

Time unit to use while visualizing deployment effort (duration). One of:

  • second

  • minute

  • hour

  • day

  • month

  • year If NULL (default), the effort is returned in hours.

cluster

Logical value indicating whether using the cluster option while visualizing maps. Default: TRUE.

hover_columns

Character vector with the name of the columns to use for showing location deployment information on mouse hover. One or more from deployment columns. Use NULL to disable hovering. Default information:

  • n: Number of species, number of observations, RAI or effort (column created internally by a get_*() function).

  • species: Species name(s).

  • start: Start deployment.

  • end: End deployment.

  • deploymentID: Deployment unique identifier.

  • locationID: Location unique identifier.

  • locationName: Location name.

  • latitude

  • longitude

See the Deployment section of Camtrap DP for the full list of columns you can use.

palette

The palette name or the colour function that values will be mapped to. Typically one of the following:

  • A character vector of RGB or named colours. Examples: c("#000000", "#0000FF", "#FFFFFF")),topo.colors(10)).

  • The full name of a RColorBrewer palette, e.g. "BuPu" or "Greens", or viridis palette: "viridis", "magma", "inferno" or "plasma". For more options, see parameter palette of leaflet::colorNumeric().

zero_values_show

Logical indicating whether to show deployments with zero values. Default: TRUE.

zero_values_icon_url

Character with URL to icon for showing deployments with zero values. Default: a cross (multiply symbol) "https://img.icons8.com/ios-glyphs/30/000000/multiply.png".

zero_values_icon_size

A number to set the size of the icon to show deployments with zero values. Default: 10.

na_values_show

Logical indicating whether to show deployments with zero values. Notice that only feature "n_species" generates NA values. Default: TRUE.

na_values_icon_url

Character with URL to icon for showing deployments with NA values. Notice that only feature "n_species" generates NA values. Default: a red cross (multiply symbol) "https://img.icons8.com/ios-glyphs/30/FA5252/multiply.png".

na_values_icon_size

A number to set the size of the icon to show deployments with NA values. Notice that only feature "n_species" generates NA values. Default: 10.

relative_scale

Logical indicating whether to use a relative colour and radius scale (TRUE) or an absolute scale (FALSE). If absolute scale is used, specify a valid max_scale.

max_scale

Number indicating the max value used to map colour and radius.

radius_range

Vector of length 2 containing the lower and upper limit of the circle radius. The lower value is used for deployments with zero feature value, i.e. no observations, no identified species, zero RAI or zero effort. The upper value is used for the deployment(s) with the highest feature value (relative_scale = TRUE) or max_scale (relative_scale = FALSE). Default: c(10, 50).

datapkg

Deprecated. Use package instead.

Value

Leaflet map.

See also

Check documentation about filter predicates: pred(), pred_in(), pred_and(), ...

Examples

if (FALSE) {
# Show number of species
map_dep(
  mica,
  "n_species"
)

# Show number of observations (observations of unidentified species included
# if any)
map_dep(
  mica,
  "n_obs"
)

# Show number of observations of Anas platyrhynchos
map_dep(
  mica,
  "n_obs",
  species = "Anas platyrhynchos"
)

# Show number of observations of subadult individuals of Anas strepera
map_dep(
  mica,
  "n_obs",
  species = "Anas strepera",
  life_stage = "subadult"
)

# Show number of observations of female or unknown individuals of gadwall
map_dep(
  mica,
  "n_obs",
  species = "gadwall",
  sex = c("female", "unknown")
)

# Show number of individuals (individuals of unidentified species included if
# any)
map_dep(
  mica,
  "n_individuals"
)

# Same filters by life stage and sex as for number of observations apply
map_dep(
  mica,
  "n_individuals",
  species = "Anas strepera",
  sex = "female",
  life_stage = "adult"
)

# Show RAI
map_dep(
  mica,
  "rai",
  species = "Anas strepera"
)

# Same filters by life_stage and sex as for number of observations apply
map_dep(
  mica,
  "rai",
  species = "Anas strepera",
  sex = "female",
  life_stage = "adult"
)

# Show RAI calculated by using number of detected individuals
map_dep(
  mica,
  "rai_individuals",
  species = "Anas strepera"
)

# Same filters by life stage and sex as for basic RAI apply
map_dep(
  mica,
  "rai_individuals",
  species = "Anas strepera",
  sex = "female",
  life_stage = "adult"
)

# Show effort (hours)
map_dep(
  mica,
  "effort"
)
# Show effort (days)
map_dep(
  mica,
  "effort",
  effort_unit = "day"
)

# Use viridis palette (viridis palettes)
map_dep(
  mica,
  "n_obs",
  palette = "viridis"
)

# Use "BuPu" colour palette (RColorBrewer palettes)
map_dep(
  mica,
  "n_obs",
  palette = "BuPu"
)

# Use a palette defined by colour names
map_dep(
  mica,
  "n_obs",
  palette = c("black", "blue", "white")
)

# Use a palette defined by hex colours
map_dep(
  mica,
  "n_obs",
  palette = c("#000000", "#0000FF", "#FFFFFF")
)

# Do not show deployments with zero values
map_dep(
  mica,
  "n_obs",
  life_stage = "subadult",
  zero_values_show = FALSE
)

# Use same icon but but a non default colour for zero values deployments,
# e.g. red (hex: E74C3C)
map_dep(
  mica,
  "n_obs",
  life_stage = "subadult",
  zero_values_icon_url = "https://img.icons8.com/ios-glyphs/30/E74C3C/multiply.png"
)

# ... or yellow (F1C40F)
map_dep(
  mica,
  "n_obs",
  life_stage = "subadult",
  zero_values_icon_url = "https://img.icons8.com/ios-glyphs/30/F1C40F/multiply.png"
)

# Use another icon via a different URL, e.g. the character Fry from Futurama
# in green (2ECC71)
map_dep(
  mica,
  "n_obs",
  life_stage = "subadult",
  zero_values_icon_url = "https://img.icons8.com/ios-glyphs/30/2ECC71/futurama-fry.png"
)

# Same behavior for the icon visualizing NA values (`"n_species"` feature)
unknown_species_vs_no_obs <- mica
unknown_species_vs_no_obs$data$observations <- 
  unknown_species_vs_no_obs$data$observations %>% 
  # a deployment has detected only unknown species
  filter(is.na(.data$scientificName) | 
           .data$scientificName != "Homo sapiens") %>%
  # a deployment has no observations
  filter(deploymentID != "62c200a9-0e03-4495-bcd8-032944f6f5a1")
# create new map
map_dep(
  unknown_species_vs_no_obs,
  feature = "n_species",
  zero_values_icon_url = "https://img.icons8.com/ios-glyphs/30/2ECC71/futurama-fry.png",
  zero_values_icon_size = 60,
  na_values_icon_url = "https://img.icons8.com/ios-glyphs/30/E74C3C/futurama-fry.png",
  na_values_icon_size = 60
)

# Set size of the icon for zero values deployments
map_dep(
  mica,
  "n_obs",
  life_stage = "subadult",
  zero_values_icon_size = 30
)

# Disable cluster
map_dep(
  mica,
  "n_species",
  cluster = FALSE
)

# Show only number of observations and location name while hovering
map_dep(
  mica,
  "n_obs",
  hover_columns = c("locationName", "n")
)

# Use absolute scale for colours and radius
map_dep(mica,
  "n_species",
  relative_scale = FALSE,
  max_scale = 4
)

# Change max and min size circles
map_dep(
  mica,
  "n_obs",
  radius_range = c(40, 150)
)
}