Copyright 2004 Center for Biofilm Engineering, Montana State University - Bozeman, USA

Citation: 
Suzanne Wilson, Martin Hamilton, Gordon Hamilton, Margo Schumann, and Paul Stoodley
(2004) "Statistical quantification of the detachment rates and size distribution of 
cell clumps from wild type (PAO1) and cell signaling mutant (JP1) Pseudomonas aeruginosa 
biofilms." Applied and Environmental Microbiology

The computer programs and this readme file are in the self-extracting zip file (80 KB):  
              CBE_BiofilmDetachmentPrograms.exe

The programs are functions written in the R programming language.
R is free software.  The homepage for acquiring and installing  R is http://www.r-project.org

These functions output their results in text files.  The output is tab
delimited, and can be opened by a spreadsheet program.
Unless told otherwise, R will place the text files in its default directory.
To change the directory:
	1.  Start R
	2.  Click the 'File' menu
	3.  Select 'Change directory' (may appear as 'Change dir...')

To use these functions:
	1.  Open the R function in a text editor
	2.  Select and copy all the text
	3.  Start R
	4.  Paste function text into R at the command prompt
	5.  Type the function command (the name of the function followed by
	    the fuction parameters in parentheses).

The text of each function contains comments which explain the purpose of the
function, descriptions of the parameters, and the name of the outputted text file.

andarcalc_R_function.txt
	Used by paretocalc and paretopool.  Copy into R and run before using
	paretocalc and paretopool.

curveone_R_function.txt
	Calculates the the cdf values of a Pareto distribution corresponding to an
	inputted set of numbers.
	Example command:  curveone("Numbers.txt", 6.633512, 1.037689, -6.418221, 1.214)
	
curvemany_R_function.txt
	Calculates the the cdf values of multiple Pareto distribution corresponding to
	an inputted set of numbers.
	Example command:  curvemany("Numbers.txt", "Th1.txt", "Th2.txt", "Th3.txt", 1.214)

goodfitcalc_R_function.txt
	Creates an estimated set of detachment events based on an inputted Pareto distribution.
	Calculates the percentage of estimated detachment events, and estimated detached cells,
	corresponding to detachment event size classes.
	Example command:  goodfitcalc("PA01#1Day3.txt", 26.34526, 0.7949384, 1.812325, 1.214)

paretocalc_R_function.txt
	Truncates an inputted set of observations, removing detachment events smaller than an
	inputted number of cells.  Uses Anderson-Darling discrepancy function to find the Pareto
	distribution which best fits the truncated set of observations.  Uses the andarcalc function.
	Copy andarcalc into R before using paretocalc.
	Example command:  paretocalc("PA01#1Day3.txt", 1.214, 2.5, 30, 0.8, 2)
		
paretopool_R_function.txt
	Creates estimated sets of detachment events based on multiple inputted Pareto distributions.
	Uses Anderson-Darling discrepancy function to find Pareto distribution which best fits an
	inputted set of observations.  Uses the andarcalc function.  Copy andarcalc into R before
	using paretopool.
	Example command:  paretopool(2638, 1649, 1103, 4884, 3086, 5416, 2013, 1502, 2496, "tp1.txt",
			    "tp2.txt", "tp3.txt", "tp4.txt", "tp5.txt", "tp6.txt", "tp7.txt", "tp8.txt",
			    "tp9.txt", 1.214, 7, 1, 0.1)
	
percentscalc_R_function.txt
	Calculates the percentage of detachment events, and detached cells, corresponding
	to detachment event size classes.
	Example command:  percentscalc("PA01#1Day3.txt", 1.214)