taxon_state: Keep track of queries in get_* functions

In taxize: Taxonomic Information from Around the Web

Keep track of queries in ⁠get_*⁠ functions

Description

Keep track of queries in ⁠get_*⁠ functions

Keep track of queries in ⁠get_*⁠ functions

Details

This object lives inside each ⁠get_*⁠ function call, maintaining results as they are accumulated.

Public fields

initialized

(time) time job started

finalized

(time) time job finished

class

(character) a class name (e.g., "gbif")

names

(character) one or more taxon names

Active bindings

count

(integer) count number of records

exit

record date/time function exited

Methods

Public methods

• taxon_state$new()

• taxon_state$print()

• taxon_state$add()

• taxon_state$get()

• taxon_state$remove()

• taxon_state$purge()

• taxon_state$taxa_remaining()

• taxon_state$taxa_completed()

• taxon_state$clone()

---

Method new()

Create a new taxon_state object

Usage

taxon_state$new(class, names)

Arguments

class

(character) a class name (e.g., "gbif")

names

(character) one or more taxon names

Returns

A new taxon_state object

---

Method print()

print method for the taxon_state class

Usage

taxon_state$print(x, ...)

Arguments

x

self

...

ignored

---

Method add()

add a record with it's result; duplicates allowed

Usage

taxon_state$add(query, result)

Arguments

query

(character), a taxon name

result

(list) a named list

Returns

nothing returned; sets only

---

Method get()

get all records matching 'query'

Usage

taxon_state$get(query = NULL)

Arguments

query

(character), a taxon name

Returns

a named list, with slots for the taxon id, and other attributes, named by the taxon name

---

Method remove()

remove's all records matching 'query'

Usage

taxon_state$remove(query)

Arguments

query

(character), a taxon name

Returns

nothing, removes records matching query

---

Method purge()

removes all records

Usage

taxon_state$purge()

Returns

nothing returned; sets only

---

Method taxa_remaining()

get remaining taxa

Usage

taxon_state$taxa_remaining()

Returns

sorted taxon names

---

Method taxa_completed()

get completed taxa

Usage

taxon_state$taxa_completed()

Returns

sorted taxon names

---

Method clone()

The objects of this class are cloneable with this method.

Usage

taxon_state$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

## Not run: 
if (interactive()) {
ts <- taxon_state$new()
taxon_last()
ts
res <- list(
  id = 123456,
  att = "found",
  multiple = FALSE,
  direct = FALSE,
  class = "tsn"
)
ts$add(query = "Quercus robur", result = res)
ts
ts$get(query = "Quercus robur")
ts$count
ts$remove(query = "Quercus robur")
ts
ts$count

res2 <- list(
  id = 3430834535,
  att = "found",
  multiple = FALSE,
  direct = FALSE,
  class = "gbifid"
)
ts$add(query = "Poa annua", result = res2)
res3 <- list(
  id = 1223424,
  att = "found",
  multiple = FALSE,
  direct = FALSE,
  class = "uid"
)
ts$add(query = "Puma concolor", result = res3)
ts
ts$count
ts$get("Puma concolor")
ts$get()

# cleanup
ts$purge()
ts$count
}

## End(Not run)

taxize documentation built on April 4, 2025, 2:12 a.m.