The code description is as follows:

   1. Code for extracting parameters for an investigation:
          * extractparams4inv.R: controls loop & can be called from the command prompt
                o splineDBcon3.R (main)
                o splineDBcon3Queries.R: all SQL queries used to obtain readings from the database and insert parameter values
                o splogod14.R: code for extracting parameters from the readings corresponding to one well
                      + gapfill.R
                      + DumpNegGrowth?.R
                      + growthparams10.R
                      + regspline5.R
                      + slidespline5.R
                      + rawsploutlier2.R
                      + aux.R 
   2. Code for performing statistical tests on each of the extracted growth parameters. The tests are: signtest, t-test, Wilcoxon signed rank test, Kolmogorov-Smirnoff test
          * dostats4inv.R: controls loop & can be called from the command prompt
                o statsfromparamsplate4.R (main)
                      + applysignttest2.R: applies the tests. Assumes the input is a dataframe where each columns stands for a template.
                      + process_wellsp.R
                      + process_wellsg.R: The latter two files are essentially the same, for pre-growth and growth respectively. The result is the dataframe on which the statistical tests should be performed, based on the plate layout. 
                o splineDBcon4Queries.R: all SQL queries for obtaining parameter information from the database 
   3. * splogod14.R:generates parameters with graphs for individual well
          * splinePrologcsvtest.R: auxiliary file for testing the splogod process
          * testsplines.R: auxiliary file for testing the splogod process 
   4. Code for generating median+mean files as well as plots for each individual investigation
          * doplots4inv.R: controls the loop and can be called from the command prompt
                o plotparams.R (main): also contains functions for the generation of histograms for each parameter
                o The following to be used interchangeably:
                      + plotMedians.R : calculation of knockout-wildtype medians
                      + plotWMedians.R : calculation of wildtype medians
                      + plotKMedians.R : calculation of knockout medians
                      + plotparamMedians.R: plots graphs on a per-trial basis 
   5. * plot3histograms.R: Produce histograms of miy_lag_time, double_time, global_max_od significant at 5%. To run source the file from within R.
          * remove_dupl_medians.R: merge together 'duplicate' cases of investigations by taking the means or medians 

    * plot3histogramsNoDupl.R: The same as above only values of xlim and ylim have changed according to whether duplicate instances have been removed using means or medians.
          o remove_dupl_medians.R 

   6. * gen_art_data.R: generate artificial data for the signtest
          * gen_art_dataT.R: generate artificial data for the t-test