imageprof: Identifies significant changes for each column of a matrix...

In jbrabazon13/profilr: Identifies significant changes in a changing data set with time

Description

imageprof identifies the most significant statistical change in mean, variance, or both mean and variance in the data (often pixel data) as specified by user on changing datasets

Usage

imageprof(basepath = NULL, savepath = NULL, samplename = NULL,
  L_per_pix = 1, stats = FALSE, type = "meanvar", filetail = NULL)

Arguments

basepath	a file directory to a folder containing matrix images (e.g. TIFF or text images)
savepath	a file directory to a desired save folder
samplename	desired name of the sample, enter in quotes (e.g. "sample-x"), if left as NULL then the folder name will be used
L_per_pix	a unit conversion of length per pixel, or desired unit per data unit; default = 1 which implies no conversion
stats	indicates if a dataframe of statistics should be saved in place of changepoint dataframe. This stats dataframe includes the mean, median, variance, and sdev of all the changepoints taken within each column in the matrix, default =FALSE
type	type of changepoint desired. Choose between "meanvar" (mean and variance), "mean", and "variance"(changepoints for meanvar, mean, and variance); note the default is "meanvar" see Killick et al., 2013 for more details
filetail	to add a desired save file tail after the samplename, default includes "samplename"_"meanvar(or other type)".csv for stats = FALSE and "samplename"_"meanvar(or other type)"_"stats".csv; change filetail by inputing a character string = "yourfiletail"

Value

two possible return options. 1)results in a dataframe where changepoints are the rows and the columns are the matrix image filename; changepoints are potentially converted to unit of choice as indicated by user. 2) stats of each image in stack (e.g. mean, median, variance, stdev, of all changepoints in each image)

Examples

changepoint_df <- imageprof(basepath = "./../file/directory/foldercontainingmatriximages/", savepath = "./../file/directory/desiredsavefolder/", samplename = NULL, L_per_pix = 1, stats = FALSE, type = "meanvar", filetail = NULL)

stats_df <- imageprof(basepath = "./../file/directory/foldercontainingmatriximages/", savepath = "./../file/directory/desiredsavefolder/", samplename = "samplenumber123", L_per_pix = 1, stats = TRUE, type = "meanvar", filetail = NULL)

variation_change_df <- imageprof(basepath = "./../../University/Research/rockimages/", savepath = "./../../University/Research/save/", samplename = "samplenumber", L_per_pix = 0.123, stats = FALSE, type = "variance", filetail = "conversion0.123")

change_mean_df <- imageprof(basepath = "./../../University/Research/rockimages/", savepath = "./../../University/Research/save/", samplename = "rock-CO-1", L_per_pix = 0.5, stats = FALSE, type = "mean", filetail = "2018-5-14-changepoints")

stats_df <- imageprof(basepath = "./../../University/Research/rockimages/", savepath = "./../../University/Research/save/", samplename = "rock-CO-1", L_per_pix = 0.5, stats = TRUE, type = "meanvar", filetail = "2018-5-14-stats")

jbrabazon13/profilr documentation built on May 20, 2019, 2:58 p.m.