Extract, curve fit an epidemiological model and transpose CSSE@JHU's Covid-19 cases data per country - Copyright Dr. Rolf Jansen (c) 2020 - Version 1.0.1
Usage: xcssecovid [-a<0-9> value] [-f (0-9)+] [-m model] [-e] [-r] [-s] [-o day#] [-z day#] [-h|-?|?] <Country> <CSV Input file> <TSV Output File>
-a<0..9> value Optionally set initial values for model's parameters the Differential Equation Solver and Curve Fitting.
The models deduce its initial parameters from the boundaries of the imported time series and by common
knowledge/best educated guesses. Example: -a0 0.57 -a1 125000
-f (0-9)+ Overrides the default selection of a model's parameters which take part in curve fitting, and which usually is a0, a1, a2.
Example: -f 1245 would lead to curve fitting against the paramters a1, a2, a4 and a5, while a0 and a would be left untouched.
Different models got different number of parameters, which is currently 3 to 6.
-m model Select the model for curve fitting and simulation:
- LF Logistic Function -- https://en.wikipedia.org/wiki/Logistic_function
- LDE Logistic Differential Equation -- https://en.wikipedia.org/wiki/Logistic_function#Logistic_differential_equation
- SI Epidemiological SI-Model (basically another form of the LDE) -- https://de.wikipedia.org/wiki/SI-Modell
- SIR Epidemiological SIR-Model [default] -- https://en.wikipedia.org/wiki/Mathematical_modelling_of_infectious_disease#The_SIR_model
-e Only export the extracted and transposed time series without curve fitting and simulation of the model.
-r Only report the model description and the values of its parameters with or without fitting, but without exporting any curve data.
-s Simulate the model without curve fitting before.
-o day# The day# of the first data point in the imported time series to be included for curve fitting.
[default: first day with more than 17 cases].
-z day# The day# of the last data point in the imported time series to be included for curve fitting.
[default: last day of the imported eries].
-h|-?|? Show these usage instructions.
<Country> Select the country for which the time series shall be processed.
<CSV Input file> Path to the CSSE@JHU's Covid-19 time series CSV file.
<TSV Output File> Path to the TSV output file containing the extracted and transposed time series for the given <Country>, including
a column for a simulated time series by the given model, using the parameter as resulted from curve fitting.