Occurrence R6 Class

An R6 class representing acoustic / vocal occurrence data from Passive Acoustic Monitoring (PAM).

Super class

PAMvieweR::Makara -> Occurrence

Public fields

species_id

A vector of species IDs, see data table PAGROUP.S_SPECIES.

pam_data

The data.

Methods

Public methods

• Occurrence$new()

• Occurrence$get_data()

• Occurrence$set_data()

• Occurrence$where_species()

• Occurrence$order()

• Occurrence$filter()

• Occurrence$mutate()

• Occurrence$select()

• Occurrence$group()

• Occurrence$aggregate()

• Occurrence$reset()

• Occurrence$print()

• Occurrence$finalize()

• Occurrence$clone()

---

Method new()

Initializes the Makara R6 object.

Usage

Occurrence$new(connection, table, data = NULL)

Arguments

connection

DB connection

table

Table or view name

data

tibble or data.frame object

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Method get_data()

Queries the DB using an SQL statement and fetches the data into R.

Usage

Occurrence$get_data()

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Method set_data()

Manually set data in an Occurrence R6 class.

Usage

Occurrence$set_data(new_data)

Arguments

new_data

tibble or data.frame

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Method where_species()

Modifies the where clause of the SQL statement used by get_data() to include species IDs.

Usage

Occurrence$where_species(species_id)

Arguments

species_id

Vector of species IDs (see data table PAGROUP.S_SPECIES)

Details

This method modifies the SQL statement used to query the DB. If changed, you must re-execute Occurrence$get_data().

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Method order()

Order rows using column values.

Usage

Occurrence$order(...)

Arguments

...

See arrange

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Method filter()

Keep rows that match a condition.

Usage

Occurrence$filter(...)

Arguments

...

See filter

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Method mutate()

Create, modify, and delete columns.

Usage

Occurrence$mutate(...)

Arguments

...

See mutate

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Method select()

Select variables in a data frame.

Usage

Occurrence$select(...)

Arguments

...

See select

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Method group()

Group by one or more variables.

Usage

Occurrence$group(...)

Arguments

...

See group_by

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Method aggregate()

Summarise each group down to one row.

Usage

Occurrence$aggregate(...)

Arguments

...

See summarize

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Method reset()

Resets the data.

Usage

Occurrence$reset()

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Method print()

Prints the Occurrence R6 Object

Usage

Occurrence$print()

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Method finalize()

What to do when you remove the Occurrence R6 object.

Usage

Occurrence$finalize()

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Method clone()

The objects of this class are cloneable with this method.

Usage

Occurrence$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.