This is a companion package to the manuscript:
Wong, J. Y., Chan, B. K. K., Chan, K. Y. K. (2020). Evolution of feeding shapes swimming kinematics of barnacle naupliar larvae: a comparison between trophic modes. Integrative Organismal Biology, obaa011. doi:10.1093/iob/obaa011
Functions included in the package were developed for analyses of data generated
from TPSDig2 and
DaVis softwares for
kinematics and hydrodynamics analyses, respectively. TPSDig2 is a landmark
registration tool and was used for digitization of body and appendages
positions. DaVis is a software used for particle image velocimetry, and
outputs velocity and vorticity fields. There is no utility tools for direct data
import from other softwares but all underlying calculations use R's matrix
or array classes of data.
Most of the functions were written specifically for the manuscript. However, some functions such as
calc_flux and calc_r, are suitable for
general use with any velocity field data.
Data are not bundled with the package due to the large file size and are stored in OSF repository.
These data can also be downloaded directly inside R:
# download path
tps_url <- 'https://files.osf.io/v1/resources/r9abn/providers/googledrive/kinematics/?zip='
vf_url <- 'https://files.osf.io/v1/resources/r9abn/providers/googledrive/vf_pxscale/?zip='
vort_url <- 'https://files.osf.io/v1/resources/r9abn/providers/googledrive/Vorticity/?zip='
# create local temporary saving paths
# (or change to any path you want to save, temporary files are.. temporary)
tps_temp <- tempfile(fileext = ".zip")
vf_temp <- tempfile(fileext = ".zip")
vort_temp <- tempfile(fileext = ".zip")
# download and unzip the downloaded data
# it takes time for osf to zip the files, so expect waiting time before download
# commence (and download for vector/vorticity fields may fail sometimes due to
# long response time resulted from large file sizes).
tps_zip <- download.file(tps_url, tps_temp, mode = 'wb')
vf_zip <- download.file(vf_url, vf_temp, mode = 'wb')
vort_zip <- download.file(vort_url, vort_temp, mode = 'wb')
tps_dir <- unzip(tps_temp, exdir = tempdir())
vf_dir <- unzip(vf_temp, exdir = tempdir())
vort_dir <- unzip(vort_temp, exdir = tempdir())
# now you can read the downloaded files, for example: 'tps_dir' is now a list
# of file paths of all the .TPS files downloaded, to read the first .TPS file
# using the 'readtps' function:
npiv::kt$readtps(tps_dir[1])Notes on using python module from the package
Functions for kinematics analysis was written in python and is located in
kinematics.py module. The module is imported into
R when the package is loaded via
reticulate package as kt
object*, and the functions can be called with kt$<function name>. Help file
can be accessed with reticulate::py_help function, e.g.
reticulate::py_help(kt) will show the help messages for all functions in the
module**.
* Please refrain from naming R object as kt.
** May not work inside RStudio. Terminal (Ubuntu)/ cmd (Windows) are ok.