Package 'denvax' reference manual

Title:	Simple Dengue Test and Vaccinate Cost Thresholds
Description:	Provides the mathematical model described by "Serostatus Testing & Dengue Vaccine Cost-Benefit Thresholds" in <doi:10.1098/rsif.2019.0234>. Using the functions in the package, that analysis can be repeated using sample life histories, either synthesized from local seroprevalence data using other functions in this package (as in the manuscript) or from some other source. The package provides a vignette which walks through the analysis in the publication, a function to generate a project skeleton for such an analysis, and a shiny app to run scenarios.
Authors:	Carl A. B. Pearson [aut, cre] , Kaja M. Abbas [aut] , Samuel Clifford [aut] , Stefan Flasche [aut] , Thomas J. Hladish [aut]
Maintainer:	Carl A. B. Pearson <[email protected]>
License:	MIT + file LICENSE
Version:	0.1.3
Built:	2024-10-07 04:02:41 UTC
Source:	https://gitlab.com/cabp_lshtm/denvax

Creates an ROI estimation project.

Description

Creates an ROI estimation project.

Usage

build.project(targetdir, overwrite = FALSE, copy_pub = TRUE)
build.project(targetdir, overwrite = FALSE, copy_pub = TRUE)

Arguments

`targetdir`	path to enclosing directory. If this directory does not exist, will attempt to create it (recursively)
`overwrite`	overwrite existing files corresponding to the project skeleton elements?
`copy_pub`	copy the 'pub/' folder (which contains the analyses from the publication)

Details

This function sets up the skeleton of an analysis to go from seroprevalence data to the ROI estimation surface. That skeleton uses a series of separate scripts for each analytical step (fitting, simulation, analysis, and application), connected via the command line build tool make (NOTE: this assumes GNU make; if you have a different one, you may need to modify the code). This approach allows clean substitution for various stages (e.g., using a different model to generate life histories). The following files are created:

Makefile: the dependencies for various analysis stages; NOTE: this (and the file in 'pub/') assumes GNU make.
README.md: brief notes about project parts
fit.R: script for fitting seroprevalence data
synthesize.R: script for generating synthetic populations
digest.R: script for converting life histories into probability coefficients for ROI calculation
simple.R: a quick example start-to-finish analysis
pub/*: the precise analysis used in the publication

Value

logical, indicating error free creation of the project skeleton; there may still be other warnings

Examples

require(denvax)
tardir <- tempdir() # replace with desired target
build.project(tardir)
list.files(tardir, recursive = TRUE)

require(denvax)
tardir <- tempdir() # replace with desired target
build.project(tardir)
list.files(tardir, recursive = TRUE)

denvax: Simple Dengue Test and Vaccinate Cost Thresholds

Description

Provides the mathematical model described by "Serostatus Testing & Dengue Vaccine Cost-Benefit Thresholds" in <doi:10.1098/rsif.2019.0234>. Using the functions in the package, that analysis can be repeated using sample life histories, either synthesized from local seroprevalence data using other functions in this package (as in the manuscript) or from some other source. The package provides a vignette which walks through the analysis in the publication, as well as a function to generate a project skeleton for such an analysis.

`denvax` functions

serofit: fits serosurvey data against two-risk model
synthetic.pop: using parameter fit data, generate a sample population
nPxA: estimate dengue infection outcome probabilities based on a synthetic population
ROIcoeffs: using population outcome probabilities, compute ROI equation coefficients
ROI: compute ROIs from setting coefficients and cost scenarios
build.project: create a template project for estimating ROIs

Provide customized ggplot2 continuous scales

Description

These functions provide several standardized wrappers to the scale_continuous functions, simplifying the creation of consistent plots.

Note, these are only functional if 'ggplot2' is installed; otherwise these methods simply issue a warning.

Usage

scale_x_startAge(
  name = "Initial Age for Routine Testing",
  expand = ggplot2::expand_scale(add = 0.5),
  breaks = function(xlim) seq(ceiling(xlim[1]), floor(xlim[2])),
  ...
)

scale_y_endAge(
  name = "Maximum Age for Testing",
  expand = ggplot2::expand_scale(add = 0.5),
  ...
)

scale_y_numTests(
  name = "Maximum # of Tests",
  breaks = function(lims) seq(round(lims[1]), round(lims[2]), by = 1),
  expand = ggplot2::expand_scale(add = 0.5),
  ...
)

scale_x_log10tau(
  name = expression(tau * ", Test Cost Fraction (log scale)"),
  labels = function(b) sprintf("%0.2f", 10^b),
  expand = ggplot2::expand_scale(),
  ...
)

scale_y_nu(
  name = expression(nu * ", Vaccine Cost Fraction"),
  labels = function(b) sprintf("%0.1f", b),
  expand = ggplot2::expand_scale(),
  ...
)

scale_linetype_ROIlvl(
  name = "ROI Limits",
  drop = FALSE,
  values = c(`0` = "dotted", `0.1` = "dotdash", `0.25` = "longdash", `0.5` = "solid"),
  ...
)

scale_color_ROIsign(
  name = "ROI Direction",
  breaks = c(1, 0, -1),
  drop = FALSE,
  labels = c(`-1` = "Negative", `0` = "Neutral", `1` = "Positive"),
  values = c(`-1` = "firebrick", `0` = "black", `1` = "dodgerblue"),
  ...
)

scale_fill_ROI(
  name = "ROI",
  limits = c(-1, 2),
  breaks = seq(-1, 2, by = 0.5),
  na.value = "#3A3A98",
  ...
)

rescale_x_Tcost(
  S,
  name = "Per Test Cost (USD)",
  labels = function(b) b * S,
  ...
)

rescale_y_Vcost(
  S,
  name = "Vaccine Cost (USD)",
  labels = function(b) b * S,
  ...
)
scale_x_startAge(
  name = "Initial Age for Routine Testing",
  expand = ggplot2::expand_scale(add = 0.5),
  breaks = function(xlim) seq(ceiling(xlim[1]), floor(xlim[2])),
  ...
)

scale_y_endAge(
  name = "Maximum Age for Testing",
  expand = ggplot2::expand_scale(add = 0.5),
  ...
)

scale_y_numTests(
  name = "Maximum # of Tests",
  breaks = function(lims) seq(round(lims[1]), round(lims[2]), by = 1),
  expand = ggplot2::expand_scale(add = 0.5),
  ...
)

scale_x_log10tau(
  name = expression(tau * ", Test Cost Fraction (log scale)"),
  labels = function(b) sprintf("%0.2f", 10^b),
  expand = ggplot2::expand_scale(),
  ...
)

scale_y_nu(
  name = expression(nu * ", Vaccine Cost Fraction"),
  labels = function(b) sprintf("%0.1f", b),
  expand = ggplot2::expand_scale(),
  ...
)

scale_linetype_ROIlvl(
  name = "ROI Limits",
  drop = FALSE,
  values = c(`0` = "dotted", `0.1` = "dotdash", `0.25` = "longdash", `0.5` = "solid"),
  ...
)

scale_color_ROIsign(
  name = "ROI Direction",
  breaks = c(1, 0, -1),
  drop = FALSE,
  labels = c(`-1` = "Negative", `0` = "Neutral", `1` = "Positive"),
  values = c(`-1` = "firebrick", `0` = "black", `1` = "dodgerblue"),
  ...
)

scale_fill_ROI(
  name = "ROI",
  limits = c(-1, 2),
  breaks = seq(-1, 2, by = 0.5),
  na.value = "#3A3A98",
  ...
)

rescale_x_Tcost(
  S,
  name = "Per Test Cost (USD)",
  labels = function(b) b * S,
  ...
)

rescale_y_Vcost(
  S,
  name = "Vaccine Cost (USD)",
  labels = function(b) b * S,
  ...
)

Arguments

`name`	the scale name (default value provided)
`expand`	the scale expansion (default value provided)
`breaks`	the tick mark locations (default provided for '...numTests')
`...`	see `scale_continuous` for other arguments
`labels`	the tick mark labels (default provided for '...log10tau')
`drop`	include missing levels in legend? (default value provided for '...ROIlvl' and '...ROIsign')
`values`	key values for levels (default value provided for '...ROIlvl' and '...ROIsign')
`limits`	the ROI range for fill colors (default value provided for '...ROI')
`na.value`	the fill color when outside of the limits (default value provided for '...ROI')
`S`	the scaling factor (cost of a Secondary dengue infection) for test and vaccination cost scales, when x is terms of tau (test cost fraction), and y is in terms of nu (vaccine cost fraction)

Launches shiny apps for denvax analyses.

Description

Provides the shiny app associated with <doi:10.6084/m9.figshare.11695155>. Only works if shiny and ggplot2 packages installed.

Usage

denvaxApp(...)
denvaxApp(...)

Arguments

...

see runApp; all arguments aside from 'appDir'

Value

does not return; interrupt R to stop the shiny app.

Examples

## Not run: 
denvax::denvaxApp()

## End(Not run)

## Not run: 
denvax::denvaxApp()

## End(Not run)

The serosurvey data in L'Azou 2016

Description

From "Symptomatic Dengue in Children in 10 Asian and Latin American Countries", Table 4.

Usage

lazou2016
lazou2016

Format

a data.frame (data.table, if installed) with 20 rows and 4 columns:

Country: character, common country name (all Peru for this data)
Age: character, the bounding ages for the sample; format: lower age '-' upper age
Number: integer, the number of samples
Seropositive: integer, the number of seropositive samples

Source

https://doi.org/10.1056/NEJMoa1503877

Examples

require(denvax); require(ggplot2)
data(lazou2016)
ggplot(lazou2016) + aes(Age, Seropositive/Number*100, color = Country) +
  geom_point() + labs(y="Seropositive %", x="Age Group") + lims(y=c(0,100)) +
  theme_minimal()
require(denvax); require(ggplot2)
data(lazou2016)
ggplot(lazou2016) + aes(Age, Seropositive/Number*100, color = Country) +
  geom_point() + labs(y="Seropositive %", x="Age Group") + lims(y=c(0,100)) +
  theme_minimal()

The serosurvey data in Morrison 2010

Description

From "Epidemiology of Dengue Virus in Iquitos, Peru 1999 to 2005: Interepidemic and Epidemic Patterns of Transmission", combining information from Fig. 2 and Fig. 3. The data from Fig. 3 were extracted using https://automeris.io/WebPlotDigitizer/

Usage

morrison2010
morrison2010

Format

a data.frame (data.table, if installed) with 13 rows and 4 columns:

Country: character, common country name (all Peru for this data)
Age: integer, the age category
Number: integer, the number of samples
Seropositive: integer, the number of seropositive samples

Source

https://doi.org/10.1371/journal.pntd.0000670

Examples

require(denvax)
data(morrison2010)
with(morrison2010,
  plot(Age, Seropositive/Number*100, ylab="% Seropositive", ylim=c(0,100))
)
require(denvax)
data(morrison2010)
with(morrison2010,
  plot(Age, Seropositive/Number*100, ylab="% Seropositive", ylim=c(0,100))
)

Compute the nPx(A), C(A) proportions from a population of life histories

Description

Compute the nPx(A), C(A) proportions from a population of life histories

Usage

nPxA(lifehistory)
nPxA(lifehistory)

Arguments

lifehistory

a matrix with rows (sample individuals) and columns (outcome in year of life); see synthetic.pop return value

Details

computes the relevant nPx(A) and C(A): the probabilities of the various life trajectories, by age. See <doi:10.1098/rsif.2019.0234>, SI section II.A (Cost Benefit Equations: Definitions)

Value

a data.frame (data.table, if available) with columns

A: integer; the reference year of life, from 1 to dim(lifehistory)[2]
p_0: numeric; probability of 0 lifetime infections
p_1p: numeric; probability of 1 or more lifetime infections
p_2p: numeric; probability of 2 or more lifetime infections
p0_1: numeric; probability of 0 infections at age A, and 1 lifetime infection
p0_1p: numeric; probability of 0 infections at age A, and 1 or more lifetime infections
p0_2p: numeric; probability of 0 infections at age A, and 2 or more lifetime infections
p1_A: numeric; probability of 1 infection at age A, and 1 or more lifetime infections
p1_2p: numeric; probability of 1 infection at age A, and 2 or more lifetime infections
p1p_A: numeric; probability of 1 or more infections at age A, and 1 or more lifetime infections
p2p_A: numeric; probability of 2 or more infections at age A, and 2 or more lifetime infections
CA: numeric; probability of converting from seronegative to seropositive between age A and A+1

Examples

require(denvax);
data(morrison2010) # has counts by age
fit <- with(morrison2010, serofit(sero=Seropositive, N=Number, age.min=Age))
m2010pop <- synthetic.pop(fit, runs = 10, popsize = 10) # small sample size for example run time
m2010lh <- nPxA(m2010pop)
m2010lh
with(m2010lh,
  plot(A, p0_2p*100, type="l",
    xlab="Age", ylab="%", ylim = c(0, 100),
    main="Individuals w/ No Infections,\nbut that will have 2"
  )
)

require(denvax);
data(morrison2010) # has counts by age
fit <- with(morrison2010, serofit(sero=Seropositive, N=Number, age.min=Age))
m2010pop <- synthetic.pop(fit, runs = 10, popsize = 10) # small sample size for example run time
m2010lh <- nPxA(m2010pop)
m2010lh
with(m2010lh,
  plot(A, p0_2p*100, type="l",
    xlab="Age", ylab="%", ylim = c(0, 100),
    main="Individuals w/ No Infections,\nbut that will have 2"
  )
)

Compute the ROI surfaces given test and vaccine cost fractions.

Description

Compute the ROI surfaces given test and vaccine cost fractions.

Usage

ROI(
  rcoeffs,
  nus = seq(0.3, 0.9, by = 0.05),
  taus = 10^seq(-2, -0.5, by = 0.05)
)
ROI(
  rcoeffs,
  nus = seq(0.3, 0.9, by = 0.05),
  taus = 10^seq(-2, -0.5, by = 0.05)
)

Arguments

`rcoeffs`	a data.frame with the ROI surface coefficients from ROIcoeffs
`nus`	the series of normalized vaccine costs to use for ROI calcs
`taus`	the series of normalized test costs to use for ROI calcs

Details

tabulates ROI

Value

a 'data.frame' ('data.table', if available) with columns:

nu: numeric, the normalized vaccine cost used
tau: numeric, the normalized test cost used
mechanism: character, either "ordinal" or "binary" corresponding to the type of test
A: integer; the age when routine test-then-vaccinate strategy starts (from As)
L: integer; the maximum number of tests for routine test-then-vaccinate strategy (from Ls)
cost: numeric; the intervention cost (as a fraction of second infection cost)
benefit: numeric; the difference in health outcome cost (as a fraction of second infection cost) minus 'cost'; positive values indicate positive net benefit
roi: numeric; return on investment: 'benefit' over 'cost'

Examples

require(denvax);
data(morrison2010) # has counts by age
fit <- with(morrison2010, serofit(sero=Seropositive, N=Number, age.min=Age))
m2010pop <- synthetic.pop(fit, runs = 10, popsize = 10) # small sample size for example run time
m2010lh <- nPxA(m2010pop)
L <- 5
rc <- ROIcoeffs(m2010lh, As=5:10, Ls=L)
rois <- ROI(rc, nus = 0.5, taus = 0.01)
srois <- subset(rois, mechanism == "binary")
mrois <- matrix(srois$roi, nrow = L)
contour(x=unique(srois$L), y=unique(srois$A), z=mrois,
  xlab = "Max # of Tests", ylab = "Initial Age", main="ROI Contour"
)

require(denvax);
data(morrison2010) # has counts by age
fit <- with(morrison2010, serofit(sero=Seropositive, N=Number, age.min=Age))
m2010pop <- synthetic.pop(fit, runs = 10, popsize = 10) # small sample size for example run time
m2010lh <- nPxA(m2010pop)
L <- 5
rc <- ROIcoeffs(m2010lh, As=5:10, Ls=L)
rois <- ROI(rc, nus = 0.5, taus = 0.01)
srois <- subset(rois, mechanism == "binary")
mrois <- matrix(srois$roi, nrow = L)
contour(x=unique(srois$L), y=unique(srois$A), z=mrois,
  xlab = "Max # of Tests", ylab = "Initial Age", main="ROI Contour"
)

Compute the Return on Investment (ROI) surface coefficients from population probabilities

Description

Compute the Return on Investment (ROI) surface coefficients from population probabilities

Usage

ROIcoeffs(probabilities, As = 5:20, Ls = (diff(range(As)) + 1):1)
ROIcoeffs(probabilities, As = 5:20, Ls = (diff(range(As)) + 1):1)

Arguments

`probabilities`	a `data.frame` (or `data.table`) with the probabilities resulting from nPxA. Rows must correspond to ages, starting with age 1
`As`	the starting age(s) to consider
`Ls`	the maximum number of tests for each age; should either be an integer per age or a single integer for all ages. The default behavior computes the number of tests (for each age) that makes the maximum of 'As' the maximum testing age Note: results will also be provided for shorter testing intervals, as the intermediate coefficients are calculated as part of computing the value at the maximum `L`

Details

computes the coefficients for the economic calculations

Value

a data.frame (data.table, if available) with columns:

A: integer; the age when routine test-then-vaccinate strategy starts (from As)
L: integer; the maximum number of tests for routine test-then-vaccinate strategy (from Ls)
vacfrac: numeric; the fraction of individuals participating in this strategy that get vaccinated
pri.offset: numeric; the (additive) reduction in vacfrac if using the ordinal test
Sfrac: numeric; the proportion experiencing second infection costs
Fresp: numeric; the F/S cost fraction term, when comparing vaccination with and without testing
Sgain: numeric; the S term, when comparing vaccination with and without testing

Examples

require(denvax);
data(morrison2010) # has counts by age
fit <- with(morrison2010, serofit(sero=Seropositive, N=Number, age.min=Age))
m2010pop <- synthetic.pop(fit, runs = 10, popsize = 10) # small sample size for example run time
m2010lh <- nPxA(m2010pop)
rc <- ROIcoeffs(m2010lh, As=5:10, Ls=5)
pp <- par()
par(mfrow=c(1, 2))
rcs <- subset(rc, A==10 & L < 11)
with(rcs, plot(
  L, aveTests, type="l",
  xlab="Max # of Tests Allowed",
  ylab="Ave # of Tests Administered",
  main="Starting @ Age 10",
  ylim=c(1, 3)
))
rcs <- subset(rc, A==5 & L < 11)
with(rcs, plot(
  L, aveTests, type="l",
  xlab="Max # of Tests Allowed",
  ylab="",
  main="Starting @ Age 5",
  ylim=c(1, 3)
))
par(pp)

require(denvax);
data(morrison2010) # has counts by age
fit <- with(morrison2010, serofit(sero=Seropositive, N=Number, age.min=Age))
m2010pop <- synthetic.pop(fit, runs = 10, popsize = 10) # small sample size for example run time
m2010lh <- nPxA(m2010pop)
rc <- ROIcoeffs(m2010lh, As=5:10, Ls=5)
pp <- par()
par(mfrow=c(1, 2))
rcs <- subset(rc, A==10 & L < 11)
with(rcs, plot(
  L, aveTests, type="l",
  xlab="Max # of Tests Allowed",
  ylab="Ave # of Tests Administered",
  main="Starting @ Age 10",
  ylim=c(1, 3)
))
rcs <- subset(rc, A==5 & L < 11)
with(rcs, plot(
  L, aveTests, type="l",
  xlab="Max # of Tests Allowed",
  ylab="",
  main="Starting @ Age 5",
  ylim=c(1, 3)
))
par(pp)

Model fitting for serological data

Description

Model fitting for serological data

Usage

serofit(
  seropositive,
  N,
  age.min = use.default(seq_along(seropositive), "age.min"),
  age.max = use.default(age.min, "age.max")
)
serofit(
  seropositive,
  N,
  age.min = use.default(seq_along(seropositive), "age.min"),
  age.max = use.default(age.min, "age.max")
)

Arguments

`seropositive`	the number of seropositive samples for each age group; length(seropositive) must be at least 3
`N`	the total number of samples for each age group; length(N) must equal length(seropositive)
`age.min`	the low age in age groups; defaults to '1:length(seropositive)', i.e. assumes the seropositive data corresponds to yearly cohorts starting at age 1.
`age.max`	the upper age in age groups; defaults to 'age.min', i.e. assumes each category corresponds to a single year

Details

Fits a constant force of infection, two-risk category model using seroprevalence survey data. i.e.:

$$ P_+(A) = p_H * (1-(1-f_H)^A) + (1-p_H) * (1-(1-f_L)^A) $$

This probability is fit to the seroprevalence by age category data, using maximum likelihood and optim.

Value

a list of best-fit parameters, all numeric values:

f_H: force of infection, for the high risk group
f_L: force of infection, for the low risk group
p_H: the proportion of the population at high risk

Examples

require(denvax);
data(morrison2010) # has counts by age
fit <- with(morrison2010, serofit(sero=Seropositive, N=Number, age.min=Age))
if (requireNamespace("data.table", quietly = TRUE)) {
data(lazou2016) # has counts by age range, instead of counts for every year
# this example uses `data.table`` functions to simplify processing
# several groups at once
  lazou2016[,{
    agerange <- data.table::tstrsplit(Age, "-")
    serofit(
      sero     = Seropositive,
      N        = Number,
      age.min  = as.integer(agerange[[1]]),
      age.max  = as.integer(agerange[[2]])
    )
  }, by = Country]
}
require(denvax);
data(morrison2010) # has counts by age
fit <- with(morrison2010, serofit(sero=Seropositive, N=Number, age.min=Age))
if (requireNamespace("data.table", quietly = TRUE)) {
data(lazou2016) # has counts by age range, instead of counts for every year
# this example uses `data.table`` functions to simplify processing
# several groups at once
  lazou2016[,{
    agerange <- data.table::tstrsplit(Age, "-")
    serofit(
      sero     = Seropositive,
      N        = Number,
      age.min  = as.integer(agerange[[1]]),
      age.max  = as.integer(agerange[[2]])
    )
  }, by = Country]
}

Compute synthetic population trajectories from model parameters

Description

Compute synthetic population trajectories from model parameters

Usage

synthetic.pop(pars, runs = 100, popsize = 1000, maxAge = 70, rngseed = NULL)
synthetic.pop(pars, runs = 100, popsize = 1000, maxAge = 70, rngseed = NULL)

Arguments

`pars`	a list with elements 'f_H', 'f_L', and 'p_H'; see serofit return value
`runs`	the number of different serotype timelines to simulate
`popsize`	the number of individuals to sample for each run
`maxAge`	the length of each lifetime
`rngseed`	an optional seed for the random number generator

Details

Using fitted parameters for a two-risk, constant force of infection model, simulate a dengue annual exposures model for the requested number of serotype series ('runs') and individuals ('popsize'). The resulting matrix is a collection of integers, 0-4. 0 indicates no infection, 1-4 infection by the corresponding serotype.

Value

a matrix of integers 0-4, rows 'runs*popsize' x columns 'maxAge'

Examples

require(denvax);
data(morrison2010) # has counts by age
fit <- with(morrison2010, serofit(sero=Seropositive, N=Number, age.min=Age))
m2010pop <- synthetic.pop(fit, runs = 10, popsize = 10) # small sample size for example run time
head(m2010pop)

require(denvax);
data(morrison2010) # has counts by age
fit <- with(morrison2010, serofit(sero=Seropositive, N=Number, age.min=Age))
m2010pop <- synthetic.pop(fit, runs = 10, popsize = 10) # small sample size for example run time
head(m2010pop)

Package 'denvax'

Help Index

Creates an ROI estimation project.

Description

Usage

Arguments

Details

Value

Examples

denvax: Simple Dengue Test and Vaccinate Cost Thresholds

Description

denvax functions

Provide customized ggplot2 continuous scales

Description

Usage

Arguments

Launches shiny apps for denvax analyses.

Description

Usage

Arguments

Value

Examples

The serosurvey data in L'Azou 2016

Description

Usage

Format

Source

Examples

The serosurvey data in Morrison 2010

Description

Usage

Format

Source

Examples

Compute the nPx(A), C(A) proportions from a population of life histories

Description

Usage

Arguments

Details

Value

Examples

Compute the ROI surfaces given test and vaccine cost fractions.

Description

Usage

Arguments

Details

Value

Examples

Compute the Return on Investment (ROI) surface coefficients from population probabilities

Description

Usage

Arguments

Details

Value

Examples

Model fitting for serological data

Description

Usage

Arguments

Details

Value

Examples

Compute synthetic population trajectories from model parameters

Description

Usage

Arguments

Details

Value

Examples

`denvax` functions