Pooling strategies for SARS-CoV-2 -- web calculator v2.0
Implementation of code adapted from:
Westreich D, Hudgens M, Fiscus S, Pilcher C. Optimizing screening for acute HIV infection
with pooled nucleic acid amplification tests. Journal of Clinical Microbiology, 2008 May;
and published in:
Pilcher CD, Westreich D, Hudgens MG.
Group Testing for Severe Acute Respiratory Syndrome
Coronavirus 2 to Enable Rapid Scale-up of Testing and Real-Time Surveillance of Incidence.
The Journal of Infectious Diseases, 2020 Aug 17;222(6):903-909.
This code has been validated in
THIS INFORMATION IS PROVIDED PROVIDED "AS IS". THERE ARE NO
WARRANTIES, EXPRESSED OR IMPLIED, AS TO MERCHANTABILITY OR
FITNESS FOR A PARTICULAR PURPOSE REGARDING THE ACCURACY OF
THE MATERIALS OR CODE CONTAINED HEREIN.
THIS SOFTWARE IS RELEASED UNDER A CREATIVE COMMONS LICENSE.
Questions and comments to:
- Daniel Westreich (djw at unc dot edu)
- Michael Hudgens (mhudgens at bios dot unc dot edu)
I accept these terms and conditions. Take me to the calculator.
Changes from version 1 (last update 15 April 2020):
- NOTE: all lines numbers refer to within the code on the linked calculator.
- Addition of ttrd2 and ttrd3 functions (lines 167-182 in code), for calculating time to results for d2 and d3 pooling strategies.
- Addition of dilmodel function (lines 202-205) for adjusting underlying viral dynamic model if contradicting information comes out later
- optDN function (lines 260-334) changed to loop through pool sizes, updating sensitivity when calculating efficiency at each step and selecting the pool size with the lowest value for efficiency
- opt function now generates errors for incompatible MAD/MAPS values
- Addition of calcMAPS and calcMAD functions (lines 377-396), for calculating MAPS based on an entered MAD value and vice versa
- MAPS value at MAD of 0.4 is now listed as 630 instead of 631 for consistency on using a floor function for MAPS (Line 456)
- Text updated to say that MAPS and MAD can be calculated by hand or using the buttons on the form (lines 460-462)
- Addition of buttons for calculating MAPS and MAD (lines 506 and 515)
- Time to results added to table (lines 556-577)
- Explanation of time to results from JID paper added (line 584)
- Legacy code from April 15 is linked here for reference.