Data

Tools

Indexes

Applications

Experiments

Open Source Science

serosv

https://github.com/oucru-modelling/serosv

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: springer.com
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (18.7%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Basic Info
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 1
  • Open Issues: 1
  • Releases: 2
Created over 3 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%",
  dpi = 300
)
```

# serosv 



[![Codecov test coverage](https://codecov.io/gh/OUCRU-Modelling/serosv/branch/main/graph/badge.svg)](https://app.codecov.io/gh/OUCRU-Modelling/serosv?branch=main) [![R-CMD-check](https://github.com/OUCRU-Modelling/serosv/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/OUCRU-Modelling/serosv/actions/workflows/R-CMD-check.yaml)



`serosv` is an easy-to-use and efficient tool to estimate infectious diseases parameters (seroprevalence and force of infection) using serological data. The current version is based on the book "Modeling Infectious Disease Parameters Based on Serological and Social Contact Data -- A Modern Statistical Perspective" by [Hens et al., 2012 Springer](https://link.springer.com/book/10.1007/978-1-4614-4072-7).

## Installation

You can install the development version of serosv with:

```{r, eval = FALSE}
# install.packages("devtools")
devtools::install_github("OUCRU-Modelling/serosv")
```

## Feature overview

### Datasets

`serosv` contains 15 built-in serological datasets as provided by [Hens et al., 2012 Springer](https://link.springer.com/book/10.1007/978-1-4614-4072-7). Simply call the name to load a dataset, for example:

``` r
rubella <- rubella_uk_1986_1987
```

### Methods

The following methods are available to estimate seroprevalence and force of infection.

Parametric approaches:

-   Polynomial models:
    -   Muench's model
    -   Griffiths' model
    -   Grenfell and Anderson's model
-   Nonlinear models:
    -   Farrington's model
    -   Weibull model
-   Fractional polynomial models

Nonparametric approaches:

-   Local estimation by polynomials

Semiparametric approaches:

-   Penalized splines:

    -   Penalized likelihood framework

    -   Generalized Linear Mixed Model framework

Hierarchical Bayesian approaches:

-   Hierarchical Farrington model

-   Hierarchical log-logistic model

## Demo

### Fitting rubella data from the UK

Load the rubella in UK dataset.

```{r, eval=FALSE}
library(serosv)
```

Find the power for the best second degree fractional polynomial with monotonicity constraint and a logit link function. The power appears to be (-0.9,-0.9).

```{r}
rubella <- rubella_uk_1986_1987

best_2d_mn <- find_best_fp_powers(
  rubella,
  p=seq(-2,3,0.1), mc = T, degree=2, link="logit"
)

best_2d_mn
```

Finally, fit the second degree fractional polynomial.

```{r}
fpmd <- fp_model(
  rubella,
  p=c(-0.9, -0.9), link="logit")

plot(fpmd)
```

### Fitting Parvo B19 data from Finland

```{r}
parvob19 <- parvob19_fi_1997_1998

# for linelisting data, either transform it to aggregated
transform_data(
  parvob19$age, 
  parvob19$seropositive,
  heterogeneity_col = "age") %>% 
  polynomial_model(type = "Muench") %>% 
  plot()

# or fit data as is
parvob19 %>% 
  rename(status = seropositive) %>% 
  polynomial_model(type = "Muench") %>% 
  plot()
```

Owner

  • Name: OUCRU-Modelling
  • Login: OUCRU-Modelling
  • Kind: organization

GitHub Events

Total
  • Create event: 3
  • Issues event: 1
  • Release event: 2
  • Delete event: 1
  • Push event: 29
  • Pull request review event: 2
  • Pull request event: 10
  • Fork event: 1
Last Year
  • Create event: 3
  • Issues event: 1
  • Release event: 2
  • Delete event: 1
  • Push event: 29
  • Pull request review event: 2
  • Pull request event: 10
  • Fork event: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 1
  • Total pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: 9 days
  • Total issue authors: 1
  • Total pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 4
  • Average time to close issues: N/A
  • Average time to close pull requests: 9 days
  • Issue authors: 1
  • Pull request authors: 2
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • thinhong (1)
  • quingzz (1)
Pull Request Authors
  • quingzz (9)
  • andrjohns (1)
  • pntnguyen (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 130 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
cran.r-project.org: serosv

Model Infectious Disease Parameters from Serosurveys

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 130 Last month
Rankings
Dependent packages count: 28.1%
Dependent repos count: 34.6%
Average: 49.8%
Downloads: 86.7%
Maintainers (1)
anhptq@oucru.org
Last synced: 10 months ago

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/r.yml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
DESCRIPTION cran
  • R >= 2.10 depends
  • deSolve * imports
  • dplyr * imports
  • locfit * imports
  • magrittr * imports
  • stats4 * imports
  • covr * suggests
  • testthat >= 3.0.0 suggests