From fb097fe1009cd4064f697e2870d09744ace52c43 Mon Sep 17 00:00:00 2001 From: Douglas Ezra Morrison Date: Wed, 10 Jul 2024 14:02:09 -0400 Subject: [PATCH] try a fix --- .github/workflows/document.yaml | 3 ++- R/est.incidence.R | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/document.yaml b/.github/workflows/document.yaml index d1ced7ea..aefa0924 100644 --- a/.github/workflows/document.yaml +++ b/.github/workflows/document.yaml @@ -6,7 +6,8 @@ on: name: Document -permissions: read-all +permissions: + contents: write jobs: document: diff --git a/R/est.incidence.R b/R/est.incidence.R index 435fb899..7572ae85 100644 --- a/R/est.incidence.R +++ b/R/est.incidence.R @@ -3,7 +3,7 @@ #' This function models seroincidence using maximum likelihood estimation; that is, it finds the value of the seroincidence parameter which maximizes the likelihood (i.e., joint probability) of the data. #' @inheritParams log_likelihood #' @inheritParams stats::nlm -#' @param pop_data a [data.frame()] with cross-sectional serology data per antibody and age, and additional columns +#' @param pop_data a [data.frame(] with cross-sectional serology data per antibody and age, and additional columns #' @param lambda_start starting guess for incidence rate, in years/event. #' @param antigen_isos Character vector with one or more antibody names. Values must match `pop_data` #' @param build_graph whether to graph the log-likelihood function across a range of incidence rates (lambda values)