Data for LSA analysis

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.