Upload ReadmeGetMDK.txt

ReadmeGetMDK.txt

+The GetMDK function is a simple tool to calculate the minimum duration for killing (MDK) from time killing assays.
+
+It takes an excel file as input with the sampling time points in the first column (header set to time (Days) as default)
+folowed by survival data for each strain with each column labelled by strain name.
+
+Example input:
+
+time (Days)	Strain A	Strain B	Strain C	Strain C
+0	1	1	1	1
+2	0.024630542	0.017617925	7.69073E-06	0.027384615
+4	0.000525452	0.004351415	4.61444E-11	0.002030769
+6	9.85222E-05	0.000141509	0	0.000615385
+
+
+Antibiotic action is generalized to presume an exponential decal model, tolerance is measured
+during the exponential portion so typically log survival is considered to extrapolate a linear function.
+If you do not want to assume a decay model you can toggle log to = FALSE
+
+This script considers each pair of adjacent timepoints and assesses whether survival within that interval
+crosses the set threshold for MDK. By default a threshold of 0.01 is set to assess 99% killing or 1% survival
+Once the interval is found, it solves for x (time) where y (survival) is at 0.01 or the input threshold
+
+The output is a csv file containing MDK values for all strains in the input file
+
+This script was written for experiments with Mycobacterium tuberculosis as such all labels specify "Days" but 
+this can be changed.
+
+Developed by Dr. Michaela Zwyer
+