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#  README   #
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# July 2022
# N. Abad

This code is supplementary to the paper "Kinetic modulation of bacterial hydrolases by microbial community structure in coastal waters" by Abad et al.  
It contains the following files: 

0) README.txt: 
	- This README file.

1) Complex saturation kinetics modelling.R: 
	- It contains the code developed for the determination of the kinetic parameters of the extracellular enzymatic activities by fitting the 
	  hydrolysis rates to four different kinetic models of increasing complexity using a non-linear least squares regression


2) LSA functions.R: 	
	- It contains the functions implemented in R to perform the Local Similarity analysis.
	- Our specific modifications related to the function LocalSimilarity3 are indicated by the comment "#New: modified function".

3) LSA script.R: 	
	- It is an updated version of the code developed by Ruan et al (2006) that has been used to perform the Local Similarity analysis in our study. 
	- The comment "#New: modified function” indicates our specific modifications within the original code.
	- The following modifications were added to the original code: 
		- The calculation of the linear interpolation of missing values (NA’s) using the R package zoo (Zeleis et al 2021) 
		- The calculation of the q-values by using the R package qvalue (Storey et al 2022)

## NOTE: it is important to set the working directory in the same folder where all the provided files are stored.
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