routine1: Process shape descriptor files

Description Usage Arguments Value See Also

View source: R/routine1.r

Description

A wrapper function to do the routine of reading the files from imagej output (from runmacro) and combine the descriptor files into a single file.

Usage

1
2
routine1(imagejdir, write = TRUE, plot = FALSE, label = TRUE,
  extract = c(1, 6))

Arguments

imagejdir

path of the folder containing the shape descriptor files. if not given, a GUI folder selector will prompt user to select (if run in Windows)

write

logical. whether to save a new file of combined descriptor.

plot

logical. whether to plot PCA for preliminary assessment of descriptor data. Only graphical output of first 3 PCs.

label

logical. Whether to extract label from the image file name.

extract

a numeric vector of two number telling which characters to extract from the file name to become the species name, if label=TRUE. The first is the starting position, second is the last position of character to extract.

Value

A dataframe of combined shape descriptor data

See Also

runmacro


jinyung/otolith documentation built on May 19, 2019, 10:36 a.m.