change set_rtss_epi to set_pev_epi

[lmhaile]

Quick change per the new malariasimulation version!

[pwinskill]

@lmhaile - we need the checks below to be passing before these changes can be brought in.
You can run devtools::test() and devtools::check() locally to see what errors and warnings are produced.

Given that we have made modifications to the vaccine implementation, it is likely that the associated test will also have to be corrected, that is in this file: https://github.com/mrc-ide/site/blob/main/tests/testthat/test-rtss.R. You can read here (https://r-pkgs.org/testing-basics.html) for more info on unit tests in packages if it is new to you.

[pwinskill]

There are some pieces missing here, if we look at https://mrc-ide.github.io/malariasimulation/articles/Vaccines.html#simulation-2 then we need to:

• additionally specify the booster_profile
• rename the boosters argument to booster_timestep
• seasonal_boosters is by default set to FALSE so we can remove that

[pwinskill]

In addition, it might be nice to add a plot to this PR showing the two site files runs - one with vaccination and one without. That way we can be more cofident that the vaccine implementation if feeding through to the model as expected

[lmhaile]

In addition, it might be nice to add a plot to this PR showing the two site files runs - one with vaccination and one without. That way we can be more cofident that the vaccine implementation if feeding through to the model as expected

Diagnostic of clinical incidence over time (intervention= 100% vaccine coverage for time period, baseline= 0% coverage):

Source code:

install.packages('Q:/site_0.2.2.tar.gz')

# model and plotting functions
run_model <- function(site) {
  
  # pull parameters for this site
  params <- site::site_parameters(
    interventions = site$interventions,
    demography = site$demography,
    vectors = site$vectors,
    seasonality = site$seasonality,
    eir = site$eir$eir[1],
    overrides = list(human_population = 1000),
    burnin = 5 * 365
  )
  
  model <-  malariasimulation::run_simulation(timesteps = 20 * 365,
                                              parameters = params)
  return(model)
}

format_for_plots <- function (baseline, int) {
  baseline <- get_rates(
    baseline,
    time_divisor = 365,
    baseline_t = 0,
    age_divisor = 1,
    scaler = 0.215,
    treatment_scaler = 0.5,
    baseline_treatment = 0
  )
  
  baseline <- baseline |>
    mutate(identifier = 'baseline')
  
  int <- get_rates(
    int,
    time_divisor = 365,
    baseline_t = 0,
    age_divisor = 1,
    scaler = 0.215,
    treatment_scaler = 0.5,
    baseline_treatment = 0
  )
  
  int <- int |>
    mutate(identifier = 'intervention')
  
  
  dt <- rbind(baseline, int, fill = T)
  dt <- dt |>
    rename(year = t) |>
    mutate(age = as.numeric(age_lower)) |>
    mutate(age = round(age / 365)) |>
    mutate(year = year + 1999) |>
    select(identifier, year, age, clinical)
  
  
  dt <- data.table(dt)
  
  dt <- dt[identifier != TRUE]
  return(dt)
}


# run one model with vaccine coverage of 100% and another with 0% coverage
# example site
site_data <- foresite::MWI
site <- site::single_site(site_data, 5)

# run with vaccine coverage
rtss <- copy(site)
rtss$interventions$rtss_cov <- 1

# run without
no_rtss <- copy(site)
no_rtss$interventions$rtss_cov <- 0


intvn <- run_model(rtss)
bl <- run_model(no_rtss)

dt <- format_for_plots(baseline = bl, int = intvn)

# plot
p <-
  ggplot(
    data = dt,
    mapping = aes(
      x = year,
      y = clinical,
      color = identifier,
      fill = identifier
    )
  ) +
  geom_point(alpha = 0.5)  +
  facet_wrap_paginate( ~ round(age), scales = 'free') +
  labs(
    x = 'Time (in years)',
    y = 'Clinical incidence rate',
    title = paste0('Clinical incidence rate over time'),
    color = 'Model Run',
    fill = 'Model Run'
  ) +
  theme_light(base_family = 'Arial') +
  scale_color_manual(values = wes_palette('Royal2', n = 2)) +
  scale_x_continuous(guide = guide_axis(n.dodge = 2)) +
  scale_fill_manual(values = wes_palette('Royal2', n = 2))


print(p)

[codecov]

Codecov Report

Patch coverage: 83.33% and project coverage change: +0.01 🎉

Comparison is base (a031200) 96.55% compared to head (f465303) 96.56%.

❗ Current head f465303 differs from pull request most recent head a399a18. Consider uploading reports for the commit a399a18 to get more accurate results

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #16      +/-   ##
==========================================
+ Coverage   96.55%   96.56%   +0.01%     
==========================================
  Files           9        9              
  Lines         232      233       +1     
==========================================
+ Hits          224      225       +1     
  Misses          8        8              

Impacted Files	Coverage Δ
R/interventions.R	95.39% <83.33%> (+0.03%)	⬆️

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