standardize_tunnel.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utility_functions.R
\name{standardize_tunnel}
\alias{standardize_tunnel}
\title{Rotate and center a tunnel based on landmarks}
\usage{
standardize_tunnel(
  obj_name,
  landmark_one = "perch1",
  landmark_two = "perch2",
  ...
)
}
\arguments{
\item{obj_name}{The input viewr object; a tibble or data.frame with attribute
\code{pathviewR_steps} that includes \code{"viewr"} that has been passed
through \code{relabel_viewr_axes()} and \code{gather_tunnel_data()} (or is
structured as though it has been passed through those functions).}

\item{landmark_one}{Subject name of the first landmark}

\item{landmark_two}{Subject name of the second landmark}

\item{...}{Additional arguments passed to/from other pathviewR functions}
}
\value{
A viewr object (tibble or data.frame with attribute
\code{pathviewR_steps} that includes \code{"viewr"}) in which data have
been rotated according to the positions of the landmarks in the data.
}
\description{
Similar to \code{rotate_tunnel()}; rotate and center tunnel data based on
landmarks (specific subjects in the data).
}
\details{
The center point of the tunnel is estimated as the point between the
two landmarks. The angle between landmark_one, tunnel_center_point, and
arbitrary point along the length axis (tunnel_center_point - 1 on length)
is estimated. That angle is then used to rotate the data, again only in the
length and width dimensions. Height is standardized by average landmark
height; values greater than 0 are above the landmarks and values less than
0 are below the landmark level.
}
\section{Warning}{

The \code{position_length} values of landmark_one MUST be less than
the \code{position_length} values of landmark_two; otherwise,
the rotation will apply to a mirror-image of the tunnel
}

\examples{
## Example data that would work with this function are
## not included in this version of pathviewR. Please
## contact the package authors for further guidance
## should you need it.
}
\seealso{
Other data cleaning functions: 
\code{\link{gather_tunnel_data}()},
\code{\link{get_full_trajectories}()},
\code{\link{quick_separate_trajectories}()},
\code{\link{redefine_tunnel_center}()},
\code{\link{relabel_viewr_axes}()},
\code{\link{rename_viewr_characters}()},
\code{\link{rotate_tunnel}()},
\code{\link{select_x_percent}()},
\code{\link{separate_trajectories}()},
\code{\link{trim_tunnel_outliers}()},
\code{\link{visualize_frame_gap_choice}()}

Other tunnel standardization functions: 
\code{\link{redefine_tunnel_center}()},
\code{\link{rotate_tunnel}()}
}
\author{
Vikram B. Baliga
}
\concept{data cleaning functions}
\concept{tunnel standardization functions}