SeroData: Create a dataset containing the serological data and other...

In nathoze/Rsero: Estimate the annual force of infection using serological data

Create a dataset containing the serological data and other information

Description

This function contains the definition of the class SeroData. It requires the age and seropositivity of individuals, and accepts more input parameters.

Usage

SeroData(
  age_at_sampling,
  age = NULL,
  Y,
  age_class = 1,
  max_age = NULL,
  sampling_year = NULL,
  location = NULL,
  sex = NULL,
  category = "Category 1",
  reference.category = NULL,
  class1 = NULL,
  class2 = NULL,
  ...
)

compute.age.groups(age, sampling_year)

Arguments

age_at_sampling	A vector of integers containing the age of the sampled individuals at the time of sampling. Must be equal or greater than 1.
Y	A vector containing the seropositivy status of the sampled individuals. It can be in a numeric form (1 or 0) or boolean (TRUE or FALSE). This vector must have the same size as age.
age_class	Integer. The length in years of the age classes. Default = 1.
max_age	Integer. The maximal age considered for the individuals in the sample. Individuals older than max_age are set equal to max_age.
sampling_year	Integer. Defines the sampling year. It can be a single value or a vector of the same size as the number of sampled individuals. If it is a single value, all the sampled individuals have the same sampling year. Default = 2017.
location	An optional character factor defining the sampling location. It can be a single chain of characters or a vector of the same size as the number of sampled individuals. Default = NULL.
sex	An optional character factor defining the sex of the individuals. It can be a single chain of characters or a vector of the same size as the number of sampled individuals. Default = NULL.
category	Character. An optional element containing the name of the categories and defining the category of the individuals. This feature is used when fitting the models assuming different risks of infection for the different categories. It can be a single character element or a matrix of characters with row size equal to the number of individuals and column size equal to the number of different category classes. Default = "Category 1".
reference.category	Character. A vector containing the name of the reference categories. It must have the same length as the number of columns of category. By default, it will take as reference the most common element in each category.
...	Additional arguments (not used).

Value

A list with the class SeroData, which contains the following items:

• age: A vector of integers containing the age of the sampled individuals at the time of the latest sampling, of length N.

• age_at_sampling: A vector of integers containing the age of the sampled individuals at the time of sampling, of length N.

• Y: A vector of seropositivity status, of length N.

• N: The number of individuals considered.

• A: The maximal age.

• NGroups: The total number of age groups.

• sampling_year: A vector of sampling years, of length N.

• location: A vector of the sampling location, of length N.

• sex: A vector of the sex of each individual, of length N.

Author(s)

Nathanael Hoze [e-mail]

Examples

## A very simple example of a serological survey with three individuals: 
data = SeroData(age_at_sampling = c(10,32,24), Y=c(0,1,1), max_age = 50, age_class = 1, sampling_year = 2017)

seroprevalence(data = data)
data2 = subset(data,c(1,3))
seroprevalence(data = data2, age_class = 5) 

## A example using categories 
sex= c('male', 'male', 'female')
data = SeroData(age_at_sampling = c(10,32,24), Y=c(0,1,1),  category= sex )

# defining the reference category 'female'

data = SeroData(age_at_sampling = c(10,32,24), Y=c(0,1,1),  category= sex, reference.category='female')

# Grouping individuals by age categories 1-10, 11-20, 21-30, etc. 
data = SeroData(age_at_sampling = c(10,32,24), Y=c(0,1,1),  category= sex, reference.category='female', age_class = 10)

nathoze/Rsero documentation built on Feb. 3, 2024, 9:58 p.m.