dp.inputs.irr.age: Get Spectrum inputs describing incidence by age and sex

In rlglaubius/SpectrumUtils: Utilities for reading Spectrum files (Title Case)

Get Spectrum inputs describing incidence by age and sex

Description

Get Spectrum inputs describing incidence by age and sex

Usage

dp.inputs.irr.age(
  dp.raw,
  direction = "wide",
  first.year = NULL,
  final.year = NULL
)

dp.inputs.irr.sex(
  dp.raw,
  direction = "wide",
  first.year = NULL,
  final.year = NULL
)

dp.inputs.irr.pattern(dp.raw, direction = "wide")

dp.inputs.irr.custom(dp.raw, direction = "wide")

dp.inputs.irr.sex.from.epp(dp.raw, direction = "wide")

dp.inputs.irr.fitted(dp.raw, direction = "wide")

Arguments

dp.raw	DemProj module data in raw format, as returned by read.raw.dp()
direction	Request "wide" (default) or "long" format data.
first.year	First year of the projection. If first.year=NULL, it will be filled in using dp.inputs.first.year()
final.year	Final year of the projection. If final.year=NULL, it will be filled in using dp.inputs.final.year()

Value

A data frame.

Functions

• dp.inputs.irr.age(): Incidence rate ratios by age relative to ages 25-29 for each sex

• dp.inputs.irr.sex(): Female-to-male incidence rate ratio

• dp.inputs.irr.pattern(): Return the epidemic pattern as a factor value.

• dp.inputs.irr.custom(): Returns TRUE if incidence patterns have been entered manually, FALSE otherwise

• dp.inputs.irr.sex.from.epp(): Returns TRUE if incidence rate ratios by sex were imported from EPP, FALSE otherwise

• dp.inputs.irr.fitted(): Check what options were used to estimate incidence rate ratios.

Details

Spectrum supports several ways of specifying epidemic patterns for determining incidence patterns by sex and age. The choice of pattern can be extracted using dp.inputs.irr.pattern:

1. Generalized - default pattern for generalized epidemics

2. Concentrated non-IDU - default pattern for concentrated epidemics driven by transmission modes other than injection drug use

3. Concentrated IDU - default pattern for concentrated epidemics driven by injection drug use

4. Fitted: fixed over time - deprecated, replaced by "Fitted to HIV prevalence or ART"

5. Fitted: time-varying - deprecated, replaced by "Fitted to HIV prevalence or ART"

6. Fitted to HIV prevalence or ART - pattern estimated from survey data

7. CSAVR - pattern estimated while fitting CSAVR

Spectrum can estimate incidence by age and sex from HIV prevalence by age and sex from household surveys, or from a country's reported numbers of people on ART by age and sex. When fitting to HIV prevalence, countries could choose to use patterns that were fixed or varied over time. In older versions of Spectrum, these choices could be accessed via dp.inputs.irr.pattern. In current Spectrum versions, dp.inputs.irr.pattern just indicates whether a pattern was fitted to HIV prevalence or ART, then dp.inputs.irr.fitted is used to indicate the data source and model type:

1. HIV prevalence, Fixed incidence ratios over time

2. HIV prevalence, Time dependent incidence ratios

3. ART by age

rlglaubius/SpectrumUtils documentation built on Dec. 20, 2024, 7:31 a.m.