mmmTags: Prepare Tag Data

In luke-a-rogers/mmmTMB: Fit Markov Movement Models (MMM) via Template Model Builder

Description

Prepare tag release and recovery data prior to fitting a Markov movement model via mmmFit().

Usage

mmmTags(
  x,
  y,
  cols = NULL,
  groups = NULL,
  step = NULL,
  limits = NULL,
  days_liberty = NULL
)

Arguments

x	data.frame() Tag release data. See details.
y	data.frame() Tag recovery data. See details.
cols	list() Named list of character strings. See details.
groups	list() Named list of atomic vectors. See details.
step	character() One of year, month, or day.
limits	character() Start and end dates as "%Y-%M-%D" character strings.
days_liberty	integer() Minimum number of days at liberty.

Details

The x & y arguments must be data frames that contain certain columns that have the same column name in both data frames. Both x & y must include:

• character() column giving unique individual tag IDs.

• Date() column giving individual tag release dates.

• integer() column giving release areas indexed from one.

In addition, y must include:

• Date() column giving individual tag recovery dates.

• integer() column giving recovery areas indexed from one.

Optionally, both x & y can include:

• atomic() column giving values grouped by groups.

Note that character() columns in "%Y-%M-%D" format may be substituted for Date() columns.

The cols argument is a list() of named elements. The elements must be character() string names of columns in x or y. There must be one element for each of the required element names (except as noted):

• id: x & y Individual tag identification

• release_date: x & y Release date

• release_area: x & y Release area

• recover_date: y Recovery date

• recover_area: y Recovery area

• group: (Optional) Grouping variable

The groups argument is a list() of named elements. The elements must be atomic vectors that include all values included in each named group. All element vectors must be of the same type. The names of the element vectors must be unique. For groups to have any effect, the element group in argument cols must name a column in both x & y that has values include in the element vectors in groups.

Value

A list object of class mmmTags.

Examples

x <- data.frame(
  Release_Date = c("2010-06-01", "2015-04-01", "2018-06-01", "2019-06-01"),
  Release_Area = c(1,1,1,1),
  Release_Group = c("F", "F", "F", "M"),
  ID = c("TAG001", "TAG002", "TAG003", "TAG004"))
y <- data.frame(
  Release_Date = c("2010-06-01", "2018-06-01", "2019-06-01"),
  Release_Area = c(1,1,1),
  Release_Group = c("F", "F", "M"),
  Recover_Date = c("2013-08-01", "2020-01-01", "2020-08-01"),
  Recover_Area = c(1,2,1),
  ID = c("TAG001", "TAG003", "TAG004"))
cols <- list(
  release_date = "Release_Date",
  release_area = "Release_Area",
  recover_date = "Recover_Date",
  recover_area = "Recover_Area",
  group = "Release_Group",
  id = "ID")
groups <- list(m = "M", f = "F")
step <- "year"
limits <- c("2010-01-01", "2020-12-31")
days_liberty <- 0L

tags <- mmmTags(x, y, cols, groups, step, limits, days_liberty)

luke-a-rogers/mmmTMB documentation built on Jan. 16, 2021, 3:53 p.m.