In KevinSee/PITcleanr: Cleans up PIT tag capture histories

# knitr options
knitr::opts_chunk$set(
  collapse = TRUE,
  warning = FALSE,
  message = FALSE,
  echo = TRUE,
  comment = "#>"
)

library(knitr)
library(here)

Introduction

Raw PIT tag detections contain a record of every detection of a tag code on an individual antenna, with the associate time-stamp. This data may be queried in primarily two different ways: 1) all of the tag codes detected at a site or antenna, or 2) all the detections of a particular tag code at a variety of sites or antennas. Regardless of what type of query is used, the user is generally dealing with a row of data for every single detection, identified by tag code, site, antenna and date/time (and detections may contain additional data as well).

This data may be stored in a variety of formats or databases. Often these can be broken out into data stored in PTAGIS (The Columbia Basin PIT Tag Information System), and data stored in non-PTAGIS databases (e.g. BioLogic) or local formats (e.g. .xlsx, .txt, .log). One of the first steps in analyzing this data is to read it into R and standardize the format. PITcleanr contains a workhorse function, readCTH() (for "read complete tag history"), that can accomplish this across many data formats.