New site build

Author: rafalopespx

.github/workflows/pkgdown.yaml

@@ -37,7 +37,7 @@ jobs:
           needs: website
 
       - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        run: usethis::use_pkgdown_github_pages()
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀

_pkgdown.yml

@@ -0,0 +1,37 @@
+destination: docs
+authors:
+  Rafael Lopes:
+    href: https://github.com/rafalopespx
+  Leonardo Bastos:
+    href: https://github.com/lsbastos/
+  footer:
+    text: Casted by
+url: https://covid19br.github.io/nowcaster/
+template:
+  bootstrap: 5
+  bootswatch: cerulean
+navbar:
+  structure:
+    left:
+    - intro
+    - reference
+    - articles
+    - tutorials
+    - news
+    right:
+    - search
+    - github
+footer:
+  structure:
+    left: developed_by
+    right: built_with
+home:
+  sidebar:
+    structure:
+    - links
+    - license
+    - community
+    - citation
+    - authors
+    - dev
+

index.Rmd

@@ -0,0 +1,78 @@
+---
+title: "Nowcaster"
+output: github_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(
+	echo = TRUE,
+	message = FALSE,
+	warning = FALSE
+)
+library(badger)
+```
+
+
+<a href='https://github.com/covid19br/nowcaster'><img src='man/figures/nowcaster.png' align="right" width="140" /></a> <a href='https://github.com/covid19br/nowcaster'><img src='man/figures/nowcaster_rev.png' align="right" width="140" /></a>
+
+<!-- badges: start -->
+<!-- `r badger::badge_cran_checks(pkg = NULL)` -->
+<!-- `r badger::badge_dependencies(pkg = NULL)` -->
+`r badger::badge_devel(pkg = "nowcaster", color = "blue")`
+`r badger::badge_license(url = "https://github.com/covid19br/nowcaster/blob/main/LICENSE.md")`
+`r badger::badge_lifecycle(stage = "experimental")`
+<!-- badges: end -->
+
+`nowcaster` is an R package for “nowcasting” epidemiological time-series on individual level data.
+
+Every single system of notification has an intrinsic delay between the `date of onset` of the event and the `date of report`. 
+`nowcaster` can estimate how many counts of any epidemiological data of interest
+(*i.e.*, daily cases and deaths counts) by fitting a negative binomial
+model to the time steps of delay between onset date of the event,
+(*i.e.*, date of first symptoms for cases or date of occurrence of
+death) and the date of report (*i.e.*, date of notification of the case
+or death).
+
+## Installing
+
+After have a proper `INLA` installation to install `nowcaster` package simply run the code below in R:
+
+```{r Installing, eval=FALSE, message=FALSE, warning=FALSE, include=TRUE}
+devtools::install_github("https://github.com/covid19br/nowcaster")
+```
+If you have any problem installing, please refer to next section on the dependencies of the package.
+
+## Dependencies
+
+`nowcaster` is based on the
+[`R-INLA`](https://www.r-inla.org/download-install)
+and
+[`INLA`](https://inla.r-inla-download.org/r-inla.org/doc/inla-manual/inla-manual.pdf)
+packages for “**I**ntegrated **N**ested **L**aplace **A**pproximation”
+algorithm to Bayesian inference. `INLA` is a fast alternative to others
+methods for Bayesian inference like **MCMC**. An introduction to `INLA`
+can be found
+[here](https://becarioprecario.bitbucket.io/inla-gitbook/index.html).
+
+`nowcaster` it was built for epidemiological emergency use, it was
+constructed for the Brazilian Severe Acute Respiratory Illness (SARI)
+surveillance system (SIVEP-Gripe), at the time of Covid-19 pandemic.
+
+Before installing the package certify you have an active installation of `INLA`, 
+to do so you can run the following code:
+
+```{r Installing INLA, eval=FALSE, message=FALSE, warning=FALSE, include=TRUE}
+install.packages("INLA",
+                 repos=c(getOption("repos"),
+                         INLA="https://inla.r-inla-download.org/R/stable"), 
+                 dep=TRUE)
+```
+
+If you want more detail on other possible installations of `INLA`, please refer to the official [page](https://www.r-inla.org/download-install) of the package.
+
+## Similar Initiatives
+
+There are other alternative packages, that can produce nowcasting estimation, here it is some options:
+
+* [Epinowcast](https://package.epinowcast.org/)
+* [Surveillance](https://surveillance.r-forge.r-project.org/pkgdown/index.html)

index.md

@@ -0,0 +1,78 @@
+Nowcaster
+================
+
+<a href='https://github.com/covid19br/nowcaster'><img src='man/figures/nowcaster.png' align="right" width="140" /></a>
+<a href='https://github.com/covid19br/nowcaster'><img src='man/figures/nowcaster_rev.png' align="right" width="140" /></a>
+
+<!-- badges: start -->
+
+<!-- [![CRAN checks](https://badges.cranchecks.info/summary/nowcaster.svg)](https://cran.r-project.org/web/checks/check_results_nowcaster.html) -->
+
+<!-- [![Dependencies](https://tinyverse.netlify.com/badge/nowcaster)](https://cran.r-project.org/package=nowcaster) -->
+
+[![](https://img.shields.io/badge/devel%20version-0.2.3-blue.svg)](https://github.com/nowcaster)
+[![License: GPL (\>=
+3)](https://img.shields.io/badge/license-GPL%20(%3E=%203)-blue.svg)](https://github.com/covid19br/nowcaster/blob/main/LICENSE.md)
+[![](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+<!-- badges: end -->
+
+`nowcaster` is an R package for “nowcasting” epidemiological time-series
+on individual level data.
+
+Every single system of notification has an intrinsic delay between the
+`date of onset` of the event and the `date of report`. `nowcaster` can
+estimate how many counts of any epidemiological data of interest
+(*i.e.*, daily cases and deaths counts) by fitting a negative binomial
+model to the time steps of delay between onset date of the event,
+(*i.e.*, date of first symptoms for cases or date of occurrence of
+death) and the date of report (*i.e.*, date of notification of the case
+or death).
+
+## Installing
+
+After have a proper `INLA` installation to install `nowcaster` package
+simply run the code below in R:
+
+``` r
+devtools::install_github("https://github.com/covid19br/nowcaster")
+```
+
+If you have any problem installing, please refer to next section on the
+dependencies of the package.
+
+## Dependencies
+
+`nowcaster` is based on the
+[`R-INLA`](https://www.r-inla.org/download-install) and
+[`INLA`](https://inla.r-inla-download.org/r-inla.org/doc/inla-manual/inla-manual.pdf)
+packages for “**I**ntegrated **N**ested **L**aplace **A**pproximation”
+algorithm to Bayesian inference. `INLA` is a fast alternative to others
+methods for Bayesian inference like **MCMC**. An introduction to `INLA`
+can be found
+[here](https://becarioprecario.bitbucket.io/inla-gitbook/index.html).
+
+`nowcaster` it was built for epidemiological emergency use, it was
+constructed for the Brazilian Severe Acute Respiratory Illness (SARI)
+surveillance system (SIVEP-Gripe), at the time of Covid-19 pandemic.
+
+Before installing the package certify you have an active installation of
+`INLA`, to do so you can run the following code:
+
+``` r
+install.packages("INLA",
+                 repos=c(getOption("repos"),
+                         INLA="https://inla.r-inla-download.org/R/stable"), 
+                 dep=TRUE)
+```
+
+If you want more detail on other possible installations of `INLA`,
+please refer to the official
+[page](https://www.r-inla.org/download-install) of the package.
+
+## Similar Initiatives
+
+There are other alternative packages, that can produce nowcasting
+estimation, here it is some options:
+
+- [Epinowcast](https://package.epinowcast.org/)
+- [Surveillance](https://surveillance.r-forge.r-project.org/pkgdown/index.html)

vignettes/.gitignore

@@ -0,0 +1,2 @@
+*.html
+*.R