qcTagHistory: Quality Check Complete Tag Histories

In KevinSee/PITcleanr: Cleans up PIT tag capture histories

Quality Check Complete Tag Histories

Description

The function takes complete capture histories downloaded from PTAGIS and performs several QA/QC checks on them. It returns the results in the form of a list.

Usage

qcTagHistory(
  cth_file = NULL,
  file_type = c("PTAGIS", "Biologic_csv", "raw"),
  ignore_event_vs_release = F
)

Arguments

cth_file	is the path to the complete tag history file
file_type	describes the source of the complete tag history file. If PTAGIS, then cth_file should be a PTAGIS observation file downloaded as a csv from PTAGIS. This must be the output from a Complete Tag History query (part of the Advanced Reporting). This query should contain: Tag, Mark Species, Mark Rear Type, Event Type, Event Site Type, Event Site Code, Event Date Time, Antenna, Antenna Group Configuration, Event Release Site Code, and Event Release Date Time. If Biologic_csv, that implies the data was downloaded from Biologic software in a .csv format. If raw, that implies the data was downloaded directly from the reader, in either a .log or .xlsx format. In this case, the largest string containing alphabetic characters in the file name will be assigned as the site code.
ignore_event_vs_release	Should the function attempt to choose whether to use the event time value or the event release time value for different release batches? Default is 'FALSE'. If set to 'TRUE', the event time value will be used

Value

a list consisting of a vector of tag codes that are listed as "Disown" in PTAGIS ('disown_tags'), a vector of tag codes that are listed as "Orphan" in PTAGIS ('orphan_tags'), and, if 'ignore_event_vs_release' is 'TRUE', a tibble containing information about sites with release information to help the user determine with event time or release time should be used for those sites.

Author(s)

Kevin See

Examples

cth_file = system.file("extdata", "PRO_Steelhead_2019.csv", package = "PITcleanr")
qcTagHistory(cth_file)

KevinSee/PITcleanr documentation built on Feb. 27, 2024, 11:03 p.m.