Changing create_progression_process() rates to probs

[tbreweric]

As raised in the PR #289, the create_progression_process() function (disease_progression.R), which governs the way individuals move between some pairs of states, has an argument rate which is currently passed mean state duration time (e.g. parameters$dd. Within the function, the inverse of this rate argument is used to sample individuals to move between states.

While a fix has been suggested for naming the Bitset$sample() function in the individual package, in the meantime the malariasimulation code has been made clearer by:

• Changing the name of the rate argument to prob in the create_progression_process() and create_asymptomatic_progression_process() functions.
• Changing the inputs to the create_progression_process() and create_asymptomatic_progression_process() function calls in create_processes() from the former average residence time (parameters$dd) to the probability 1 - exp(-1/parameters$dd)

[tbreweric]

I've now fixed (hopefully) the conflicts, so ready for the changes to be reviewed now @giovannic @pwinskill !

[tbreweric]

The CMD checks are failing because the new dt_input method we added for slow parasite clearance, where dt_input is a DoubleVariable when parameters$antimalarial_resistance == TRUE doesn't work with the updated input for create_progression_process(), where the rate input has been converted to prob and passed the mean stage durations (e.g. dt / dt_input in the following way: 1 - exp(-1/dt_input).

I think the easiest solution here it so change the lines assigning dt_input from variables when antimalarial_resistance == TRUE from:

if(parameters$antimalarial_resistance) {
    dt_input <- variables$dt
}

where dt_input is a DoubleVariable, to something like the following, where dt_input becomes a vector:

if(parameters$antimalarial_resistance) {
    dt_input <- variables$dt$get_values()
}

dt_input can then be passed to create_progression_process() via the converted 1 - exp(-1/dt_input).

Within create_progression_process(), which now receives a vector of probs rather than a DoubleVariable of average state residence times (e.g. dt_input <- variables$dt), we can make the following changes:

1. Convert the check from inherits to length() to test whether the function has received a single value of vector of values
2. Use vector subsetting to retrieve the prob values for individuals in the from the inputprobvector which contains the entire populationsprob`

# If function receives a vector transition probabilities rather than a single value:
if (length(prob) > 1) {
  prob <- prob[index$to_vector()]
}

This then allows the sampling of individuals to_move to go ahead using the subsetted prob values:

# Sample the individuals to be moved into a new Bitset using the transition probabilities:
to_move <- index$sample(prob)

[tbreweric]

Have implemented the changes suggested above - seems to have solved the CMD check failures.

[giovannic]

Doesn't dt vary over time?

It appears to me like we have to pass the DoubleVariable so that the disease progression process can calculate probabilities based on dt for that timestep.

[giovannic]

obsolete