RunPartModel: RunPartModel

In khuggler/Ovis: Tools to Manipulate, Collate, and Analyze BHS Data from Idaho and Wyoming

RunPartModel

Description

Calculate movement statistics including movement rate, first passage time, bivariate gaussian bridge, and machine learning predictions to identify parturition events of ungulates.

Usage

RunPartModel(
  gpsdat,
  lookup,
  gpsproj,
  projectedproj,
  tempdir,
  subsetmonth,
  ncpus,
  markdownpath,
  user,
  pass,
  from = NA,
  to = NA,
  attach = NA
)

Arguments

gpsdat	data.frame of gps data to run model that includes the following columns (in this order): 'IdCol', 'SerialNumber', 'TelemDate', 'x', 'y'. Optional columns include: 'dop', 'X2D.3D', but recommended if available to help improve data cleaning process. IdCol = column that represents unique identifier, TelemDate = as.POSIXct format. Fix time and date, x = x coordinate, y = y coordinate. See data(sheep.gps) for example of expected format.
lookup	data.frame of lookup table. This table should include the following columns: 'Frequency', 'Serial', 'IdCol'. Frequency = collar frequency in XXX.XXX format, Serial = Serial number of collar, IdCol = Unique identifier column. MUST match the IdCol in the gpsdat, BirthDate (optional), used to fill in birth dates as they occur and add to plots. Other columns such as VitFrequency, TagNumber are allowed. See data(lookup) for example of expected format.
gpsproj	proj4 of gps data
projectedproj	proj4 of projected coordinate system to use for data cleaning (UTM or Albers Equal Area recommended)
tempdir	path of directory for products to be saved
subsetmonth	character of month to subset data
ncpus	number of CPUs for parallel processing. Recommend 1-2 less than max.
markdownpath	complete path to location of markdown file for parturition report
user	character of email username
pass	character of email password
from	character vector of email sender
to	character vector of email recipients
attach	character vector of paths to email attachments

Value

Resulting object is a pdf with movement metrics for each unique animal, and a data.frame with machine learning predictions

Examples

RunPartModel(data=gps, lookup = lookup, gpsproj = +proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs", projectedproj = +proj=utm +zone=11 +ellps=GRS80 +datum=NAD83 +units=m +no_defs", tempdir = "C:/Users/khuggler/Desktop/", ncpus = 5, markdownpath = "C:/Users/Desktop/PartPlots2.Rmd")

khuggler/Ovis documentation built on Nov. 30, 2023, 7:41 p.m.