carlesmila · Jul 28, 2026 · Jul 22, 2026 · Jul 23, 2026 · Jul 28, 2026
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diff --git a/.Rproj.user/C3EAF566/sources/session-9f14958a/073730A4-contents b/.Rproj.user/C3EAF566/sources/session-9f14958a/073730A4-contents
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+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/desc-cases.R
+\name{desc_Cmed}
+\alias{desc_Cmed}
+\title{Cmed}
+\usage{
+desc_Cmed(df, x)
+}
+\arguments{
+\item{df}{A data.frame consisting of 52 rows (1 year) for a single spatial
+unit with columns 'time' (epiyearweek), 'cases', 'epiweek' and 'epiyear'.}
+
+\item{x}{Number of cases.}
+}
+\value{
+The computed Cmed epidescriptor.
+}
+\description{
+Median duration in consecutive weeks with at least 'x' cases.
+}
diff --git a/.Rproj.user/C3EAF566/sources/session-9f14958a/59A30531-contents b/.Rproj.user/C3EAF566/sources/session-9f14958a/59A30531-contents
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+# epidesc <img src="inst/figures/logo_BSC.png" align="right" width="16%"/>
+
+<!-- badges: start -->
+
+[![License](http://img.shields.io/badge/license-GPL%20%28%3E=%202%29-brightgreen.svg?style=flat)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.html) <!--  [![R-CMD-check](https://github.com/BSC-ES/epidesc/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/BSC-ES/epidesc/actions/workflows/R-CMD-check.yaml) -->
+
+<!-- badges: end -->
+
+## Overview
+
+<img src="inst/figures/epidesc.png" align="right" width="20%"/>
+
+The R package **epidesc** provides the tools to easily compute a series of epidemiological indicators to characterise different transmission profiles of infectious diseases. The work is based on the publication How heterogeneous is the dengue transmission profile in Brazil? A study in six Brazilian states (<https://doi.org/10.1371/journal.pntd.0010746>) published in PLoS Neglected Tropical Diseases by Iasmim Ferreira de Almeida, Raquel Martins Lana and Cláudia Torres Codeço in 2022.
+
+The **epidesc** pipeline to compute the indicators is the following: \* Formatting dates in *epiyearweek* format. \* Choosing descriptors and its parameters from the catalogue. \* Compute descriptors.
+
+In order to work, the data used to compute the descriptors needs to have a few simple requirements: \* The input data has to be a data.frame with the cases and spatiotemporal identifiers. \* The data needs to be weekly with dates in Date format. \* If an incidence descriptor is required, the population at risk also needs to be provided.
+
+To find out more, please have a look at the package vignette.
+
+## Included descriptors
+
+The current version of the package includes the following descriptors:
+
+``` r
+library("epidesc")
+knitr::kable(desc_list())
+```
+
+| class | fun | description | param1 | param2 |
+|:---|:---|:---|:---|:---|
+| Peak | Ap | Maximum cases peak |  |  |
+| Peak | Tp | Week where the maximum peak occurred |  |  |
+| Period with cases | Cnf | Frequency of periods of consecutive 'n' weeks or longer with at least 'x' cases | n | x |
+| Period with cases | Cmax | Maximum duration in consecutive weeks with at least 'x' cases | x |  |
+| Period with cases | Cmed | Median duration in consecutive weeks with at least 'x' cases | x |  |
+| Period with cases | Isof | Number of weeks with isolated cases |  |  |
+| Period with cases | p | Proportion of weeks with at least 'x' cases | x |  |
+| Period without cases | Cwf | Frequency of periods of consecutive weeks with at least 'n' weeks without cases. | n |  |
+| Period without cases | Cwmax | Maximum duration in consecutive weeks without cases |  |  |
+| Period without cases | Cwmed | Median duration in consecutive weeks without cases |  |  |
+| Incidence | Inc | Annual incidence per 'p' persons | p |  |
+
+## Contributions
+
+We are very interested in keep expanding **epidesc** with new descriptors and we are open to contributions. If would like to contribute, please open an issue with your idea or get in touch with Raquel Martins Lana ([raquel.lana\@bsc.es](mailto:raquel.lana@bsc.es){.email}, [raquelmlana\@gmail.com](mailto:raquelmlana@gmail.com){.email}) or Carles Milà ([carles.milagarcia\@bsc.es](mailto:carles.milagarcia@bsc.es){.email}) to discuss its inclusion.
+
+## Installation
+
+`epidesc` is still in development and not on CRAN. You can install the development version of epidesc as follows:
+
+``` r
+pak::pak("https://github.com/BSC-ES/epidesc.git")
+```
+
+## Package authors
+
+[**Raquel Martins Lana, PhD**](https://www.bsc.es/martins-lana-raquel) <a href="https://orcid.org/0000-0002-7573-1364" style="margin-left: 15px;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" alt="ORCID" style="width: 16px; height: 16px;"/></a>\
+Barcelona Supercomputing Center
+
+[**Carles Milà, PhD**](https://www.bsc.es/mila-garcia-carles) <a href="https://orcid.org/0000-0003-0470-0760" style="margin-left: 15px;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" alt="ORCID" style="width: 16px; height: 16px;"/></a>\
+Barcelona Supercomputing Center
+
+**Iasmin Ferreira de Almeida, PhD** <a href="https://orcid.org/0000-0002-9334-4093" style="margin-left: 15px;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" alt="ORCID" style="width: 16px; height: 16px;"/></a>\
+Getulio Vargas Foundation (FGV)
+
+**Claudia Torres Codeço, PhD** <a href="https://orcid.org/0000-0003-1174-178X" style="margin-left: 15px;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" alt="ORCID" style="width: 16px; height: 16px;"/></a>\
+Oswaldo Cruz Foundation (Fiocruz)
+
+[**Daniela Lührsen, MSc**](https://www.bsc.es/luhrsen-daniela-sofie) <a href="https://orcid.org/0009-0002-6340-5964" style="margin-left: 15px;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" alt="ORCID" style="width: 16px; height: 16px;"/></a>\
+Barcelona Supercomputing Center
+
+**Diego Ricardo Xavier Silva, PhD** <a href="https://orcid.org/0000-0001-5259-7732" style="margin-left: 15px;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" alt="ORCID" style="width: 16px; height: 16px;"/></a>\
+Oswaldo Cruz Foundation (Fiocruz)
+
+**Christovam Barcellos, PhD** <a href="https://orcid.org/0000-0002-1161-2753" style="margin-left: 15px;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" alt="ORCID" style="width: 16px; height: 16px;"/></a>\
+Oswaldo Cruz Foundation (Fiocruz)
+
+**Raphael Saldanha, PhD** <a href="https://orcid.org/0000-0003-0652-8466" style="margin-left: 15px;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" alt="ORCID" style="width: 16px; height: 16px;"/></a>\
+Oswaldo Cruz Foundation (Fiocruz)
+
+[**Rachel Lowe, PhD**](https://www.bsc.es/lowe-rachel) <a href="https://orcid.org/0000-0003-3939-7343" style="margin-left: 15px;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" alt="ORCID" style="width: 16px; height: 16px;"/></a>\
+Barcelona Supercomputing Center
diff --git a/.Rproj.user/C3EAF566/sources/session-9f14958a/64442212-contents b/.Rproj.user/C3EAF566/sources/session-9f14958a/64442212-contents
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+#' Cnf
+#'
+#' @description Frequency of periods of consecutive 'n' weeks or longer with at
+#' least 'x' cases.
+#'
+#' @param df A data.frame consisting of 52 rows (1 year) for a single spatial
+#' unit with columns 'time' (epiyearweek), 'cases', 'epiweek' and 'epiyear'.
+#' @param n Number of consecutive weeks.
+#' @param x Number of cases.
+#'
+#' @returns The computed Cnf epidescriptor.
+#' @export
+desc_Cnf <- function(df, n, x) {
+  res <- nseq::trle_cond(df$cases, a_op = "gte", a = n, b_op = "gte", b = x)
+
+  return(res)
+}
+
+#' Cmax
+#'
+#' @description Maximum duration in consecutive weeks with at least 'x' cases.
+#'
+#' @param df A data.frame consisting of 52 rows (1 year) for a single spatial
+#' unit with columns 'time' (epiyearweek), 'cases', 'epiweek' and 'epiyear'.
+#' @param x Number of cases.
+#'
+#' @returns The computed Cmax epidescriptor.
+#' @export
+desc_Cmax <- function(df, x) {
+  res <- nseq::trle_cond_stat(df$cases, b_op = "gte", b = x, stat = "max")
+
+  # If no sequences are found
+  if (is.na(res)) {
+    res <- 0
+  }
+
+  return(res)
+}
+
+#' Cmed
+#'
+#' @description Median duration in consecutive weeks with at least 'x' cases.
+#'
+#' @param df A data.frame consisting of 52 rows (1 year) for a single spatial
+#' unit with columns 'time' (epiyearweek), 'cases', 'epiweek' and 'epiyear'.
+#' @param x Number of cases.
+#'
+#' @returns The computed Cmed epidescriptor.
+#' @export
+desc_Cmed <- function(df, x) {
+  res <- nseq::trle_cond_stat(df$cases, b_op = "gte", b = x, stat = "median")
+
+  # If no sequences are found
+  if (is.na(res)) {
+    res <- 0
+  }
+
+  return(res)
+}
+
+#' Isof
+#'
+#' @description Number of weeks with isolated cases, i.e. weeks with 0 cases
+#' both in the previous and following week.
+#'
+#' @param df A data.frame consisting of 52 rows (1 year) for a single spatial
+#' unit with columns 'time' (epiyearweek), 'cases', 'epiweek' and 'epiyear'.
+#'
+#' @returns The computed Isof epidescriptor.
+#' @export
+desc_Isof <- function(df) {
+  res <- nseq::trle_cond(
+    df$cases,
+    a_op = "e",
+    a = 1,
+    b_op = "gt",
+    b = 0,
+    isolated = TRUE
+  )
+
+  return(res)
+}
+
+#' p
+#'
+#' @description Proportion fo weeks with at least 'x' cases.
+#'
+#' @param df A data.frame consisting of 52 rows (1 year) for a single spatial
+#' unit with columns 'time' (epiyearweek), 'cases', 'epiweek' and 'epiyear'.
+#' @param x Number of cases.
+#'
+#' @returns The computed p epidescriptor.
+#' @export
+desc_p <- function(df, x) {
+  res <- df$cases >= x
+  res <- sum(res) / length(res)
+
+  return(res)
+}
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