compute the prophylactic efficacy of DTG using different methods
usage: ./prophylaxisEstimator.py <command> [options]
command:
Choose one method for computing
{extrande,ntm,ctsm,pgs}
extrande run method extrande
ntm run next transition method
ctsm run constant time step method
pgs run probability generating system
Run './prophylaxisEstimator.py COMMAND --help' for more information on a command
(Default setup may take hour to run)
usage: ./prophylaxisEstimator.py extrande [options]
optional arguments:
-h, --help show this help message and exit
--mdose float mass of DTG dose [mg] (default: 50)
--adh float adherence of drug taken (default: 1)
--cdose int count of doses in a regimen (default: 3)
--inputfile str specify the inputfile that contains the pharmacokinetic
parameters. For deterministic methods please input only
one set of pk parameters (default: PK_default.csv)
--outputfile str specify the name of output csv file (default:
extrande.csv)
--ifpdf bool if output the graphic of results in pdf (default: False)
--csimul int count of simulations (default: 5000)
--tps list time points to begin simulation, i.e. time of viral
exposure relative to timing of first dose [hr] (default:
[1,6,18,23])
--vload str int or str {"homo", "hetero"}, initial viral load, can be
fixed number or generated randomly according to the
transition mode (default: 1)
(Default setup may take several minutes to run)
usage: ./prophylaxisEstimator.py ntm [<options>]
optional arguments:
-h, --help show this help message and exit
--mdose float mass of DTG dose [mg] (default: 50)
--adh float adherence of drug taken (default: 1)
--cdose int count of doses in a regimen (default: 3)
--inputfile str specify the inputfile that contains the
pharmacokinetic parameters. For deterministic methods
please input only one set of pk parameters (default:
PK_default.csv)
--outputfile str specify the name of output csv file (default: ntm.csv)
--ifpdf bool if output the graphic of results in pdf (default:
False)
--ts float start time point to run the computation, relative to
timing of first dose [hr] (default: 0)
--te float end time point of the computation, relative to timing
of first dose [hr] (default: 240)
--tspanres float timespan in the output data [hr] should not be shorter
than timesteps (default: 1)
--ifll bool if long-lived and latently infected cells are
considered (default: False)
--timesteps number number number
time steps for V, T1, T2, [min] Fraction like 1/6 is
allowed. For V and T1 the time steps should be same
and cannot be shorter than T2 (default: 10 10 1)
--rate float percentage of the observed next transition (default:
0.999)
usage: ./prophylaxisEstimator.py ctsm [<options>]
optional arguments:
-h, --help show this help message and exit
--mdose float mass of DTG dose [mg] (default: 50)
--adh float adherence of drug taken (default: 1)
--cdose int count of doses in a regimen (default: 3)
--inputfile str specify the inputfile that contains the
pharmacokinetic parameters. For deterministic methods
please input only one set of pk parameters (default:
PK_default.csv)
--outputfile str specify the name of output csv file (default:
ctsm.csv)
--ifpdf bool if output the graphic of results in pdf (default:
False)
--ts float start time point to run the computation, relative to
timing of first dose [hr] (default: 0)
--te float end time point of the computation, relative to timing
of first dose [hr] (default: 240)
--tspanres float timespan in the output data [hr] should not be shorter
than timesteps (default: 1)
--ifll bool if long-lived and latently infected cells are
considered (default: False)
--timesteps number number number
time steps for V, T1, T2, [min] Fraction like 1/6 is
allowed. For V and T1 the time steps should be same
and cannot be shorter than T2 (default: 10 10 1)
usage: ./prophylaxisEstimator.py pgs [<options>]
optional arguments:
-h, --help show this help message and exit
--mdose float mass of DTG dose [mg] (default: 50)
--adh float adherence of drug taken (default: 1)
--cdose int count of doses in a regimen (default: 3)
--inputfile str specify the inputfile that contains the pharmacokinetic
parameters. For deterministic methods please input only
one set of pk parameters (default: PK_default.csv)
--outputfile str specify the name of output csv file (default: pgs.csv)
--ifpdf bool if output the graphic of results in pdf (default: False)
--ts float start time point to run the computation, relative to
timing of first dose [hr] (default: 0)
--te float end time point of the computation, relative to timing of
first dose [hr] (default: 240)
--tspanres float timespan in the output data [hr] should not be shorter
than timesteps (default: 1)
--ifll bool if long-lived and latently infected cells are considered
(default: False)
- compute the prophylactic efficacy with four different methods, including one stochastic simulation (extrande) and three deterministic methods (ntm, ctsm and pgs)
- deterministic methods are very efficient and can be applied in many cased, while extrande can be used to obtain the intermediate state
- return the extinction probabilities and efficacies in csv file
- Uses sane defaults, also provide many possible options
The file config/env.yml can be used to create a (across-platform) conda environment that contains the necessary packages.
$ cd test_dir
$ make test$ make clean
