Merge branch 'main' into main

.github/CONTRIBUTING.md

@@ -0,0 +1,47 @@
+# Contributing to serocalculator
+
+This outlines how to propose a change to serocalculator.
+For a detailed discussion on contributing to this and other tidyverse packages, please see the [development contributing guide](https://rstd.io/tidy-contrib) and our [code review principles](https://code-review.tidyverse.org/).
+
+## Fixing typos
+
+You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the _source_ file. 
+This generally means you'll need to edit [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`, not a `.Rd` file. 
+You can find the `.R` file that generates the `.Rd` by reading the comment in the first line.
+
+## Bigger changes
+
+If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed. 
+If you’ve found a bug, please file an issue that illustrates the bug with a minimal 
+[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed).
+See our guide on [how to create a great issue](https://code-review.tidyverse.org/issues/) for more advice.
+
+### Pull request process
+
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("UCD-SERG/serocalculator", fork = TRUE)`.
+
+*   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
+    If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 
+*   Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`.
+
+*   Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
+    The title of your PR should briefly describe the change.
+    The body of your PR should contain `Fixes #issue-number`.
+
+*  For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tidyverse.org/news.html>.
+
+### Code style
+
+*   New code should follow the tidyverse [style guide](https://style.tidyverse.org). 
+    You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.  
+
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.  
+
+*  We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. 
+   Contributions with test cases included are easier to accept.  
+
+## Code of Conduct
+
+Please note that the serocalculator project is released with a
+[Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this
+project you agree to abide by its terms.

.github/workflows/pkgdown.yaml

@@ -1,8 +1,10 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
     branches: [main, master]
+  pull_request:
+    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
@@ -12,24 +14,35 @@ name: pkgdown
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: pkgdown
+          extra-packages: any::pkgdown, local::.
           needs: website
 
-      - name: Deploy package
-        run: |
-          git config --local user.name "$GITHUB_ACTOR"
-          git config --local user.email "[email protected]"
-          Rscript -e 'pkgdown::deploy_to_branch(new_process = FALSE)'
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -5,15 +5,13 @@ Version: 0.1.0.9000
 Date: 2022-03-29
 Authors@R: c(
   person(given = "Peter", family = "Teunis", email = "[email protected]", role = c("aut", "cph"), comment = "Author of the method and original code."),
-  person(given = "Jan", family = "van Eijkeren", role = c("ctb"), comment = "Author of the method and original code."), 
-  person(given = "Daniel", family = "Lewandowski", email = "[email protected]", role = c("ctb"), comment = "Creator of the `seroincidence` R package."), 
-  person(given = "Chantal", family = "Quinten", email = "[email protected]", role = c("ctb")),
-  person(given = "Kristen", family = "Aiemjoy", email = "[email protected]", role = c("aut", "ctb")),
-  person(given = "Douglas Ezra", family = "Morrison", email = "[email protected]", role = c("aut", "ctb", "cre"), comment = "Package maintainer."))
+  person(given = "Kristina", family = "Lai", role = c("aut")), 
+  person(given = "Kristen", family = "Aiemjoy", email = "[email protected]", role = c("aut")),
+  person(given = "Douglas Ezra", family = "Morrison", email = "[email protected]", role = c("aut", "cre")))
 Description: Translates antibody levels measured in a (cross-sectional)
   population sample into an estimate of the frequency with which
   seroconversions (infections) occur in the sampled population.
-  Fork of the "seroincidence" package v2.0.0 on CRAN (https://cran.r-project.org/web/packages/seroincidence/index.html)
+  Forked from the "seroincidence" package v2.0.0 on CRAN (https://cran.r-project.org/web/packages/seroincidence/index.html)
 Depends: R (>= 2.10)
 License: GPL-3
 Imports: 
@@ -32,8 +30,8 @@ Suggests:
 VignetteBuilder: knitr
 LazyData: true
 Encoding: UTF-8
-URL: https://github.com/UCD-SEG/serocalculator, https://ucd-seg.github.io/serocalculator/
-RoxygenNote: 7.1.2
+URL: https://github.com/UCD-SERG/serocalculator, https://ucd-serg.github.io/serocalculator/
+RoxygenNote: 7.2.3
 NeedsCompilation: no
 LinkingTo: 
     Rcpp

R/nll.R

@@ -15,7 +15,7 @@
 #' @param start  starting value for \code{log(lambda)}. Value of -6 corresponds roughly to 1 day
 #'   (log(1/365.25)), -4 corresponds roughly to 1 week (log(7 / 365.25)). Default = -6.
 #'
-#' @return
+#' @return the log-likelihood of the data with the current parameter values
 .nll <- function(stratumData, antibodies, params, censorLimits, ivc = FALSE, m = 0, par0, start)
 {
   # Start with zero total

R/serocalculator-package.R

@@ -12,81 +12,83 @@
 #' estimate of the frequency with which seroconversions (infections) occur in the sampled population.
 #'
 #' @details
-#' For detailed documentation type the following in the R console:\cr
+#' For detailed documentation type the following in the R console:
 #'
-#' \code{vignette("installation", package = "serocalculator")}\cr
-#' \code{vignette("tutorial", package = "serocalculator")}\cr
+#' \code{vignette("installation", package = "serocalculator")}
+#' \code{vignette("tutorial", package = "serocalculator")}
 #' \code{vignette("methodology", package = "serocalculator")}
 #'
 #' @author
-#' Author: Peter Teunis \email{<[email protected]>}\cr
-#' Maintainer: Doug Ezra Morrison \email{<[email protected]>}
+#' Author: Peter Teunis \email{p.teunis@@emory.edu}
+#' Author: Doug Ezra Morrison \email{demorrison@@ucdavis.edu}
+#' Author: Kristen Aiemjoy \email{kaiemjoy@@ucdavis.edu}
+#' Author: Kristina Lai \email{kaiemjoy@@ucdavis.edu}
 #'
 #' @references
 #'
 #' \strong{\emph{Methods for estimating seroincidence}}
 #'
 #' \itemize{
-#' \item Teunis, P. F., van Eijkeren, J. C., Ang, C. W., van Duynhoven, Y. T., Simonsen, J. B., Strid, M. A., van Pelt, W.\cr
-#' "Biomarker dynamics: estimating infection rates from serological data"\cr
+#' \item Teunis, P. F., van Eijkeren, J. C., Ang, C. W., van Duynhoven, Y. T., Simonsen, J. B., Strid, M. A., van Pelt, W.
+#' "Biomarker dynamics: estimating infection rates from serological data"
 #' Statistics in Medicine 31, no. 20 (September 9, 2012): 2240--48. doi:10.1002/sim.5322.
 #'
-#' \item Simonsen, J., Molbak, K., Falkenhorst, G., Krogfelt, K. A., Linneberg, A., Teunis, P. F.\cr
-#' "Estimation of incidences of infectious diseases based on antibody measurements"\cr
+#' \item Simonsen, J., Molbak, K., Falkenhorst, G., Krogfelt, K. A., Linneberg, A., Teunis, P. F.
+#' "Estimation of incidences of infectious diseases based on antibody measurements"
 #' Statistics in Medicine 28, no. 14 (June 30, 2009): 1882--95. doi:10.1002/sim.3592.
 #' }
 #'
 #' \strong{\emph{Applications}}
 #'
 #' \itemize{
 #'
-#' \item Monge, S., Teunis, P. F., Friesema, I., Franz, E., Ang, W., van Pelt, W., Mughini-Gras, L.\cr
+#' \item Monge, S., Teunis, P. F., Friesema, I., Franz, E., Ang, W., van Pelt, W., Mughini-Gras, L.
 #' "Immune response-eliciting exposure to Campylobacter vastly exceeds the incidence of clinically
-#' overt campylobacteriosis but is associated with similar risk factors: A nationwide serosurvey in the Netherlands"\cr
+#' overt campylobacteriosis but is associated with similar risk factors: A nationwide serosurvey in the Netherlands"
 #' Journal of Infection, 2018, 1--7, doi:10.1016/j.jinf.2018.04.016
 #'
-#' \item Kretzschmar, M., Teunis, P. F., Pebody, R. G.\cr
-#' "Incidence and reproduction numbers of pertussis: estimates from serological and social contact data in five European countries"\cr
+#' \item Kretzschmar, M., Teunis, P. F., Pebody, R. G.
+#' "Incidence and reproduction numbers of pertussis: estimates from serological and social contact data in five European countries"
 #' PLoS Medicine 7, no. 6 (June 1, 2010):e1000291. doi:10.1371/journal.pmed.1000291.
 #'
-#' \item Simonsen, J., Strid, M. A., Molbak, K., Krogfelt, K. A., Linneberg, A., Teunis, P.\cr
-#' "Sero-epidemiology as a tool to study the incidence of Salmonella infections in humans"\cr
+#' \item Simonsen, J., Strid, M. A., Molbak, K., Krogfelt, K. A., Linneberg, A., Teunis, P.
+#' "Sero-epidemiology as a tool to study the incidence of Salmonella infections in humans"
 #' Epidemiology and Infection 136, no. 7 (July 1, 2008): 895--902. doi:10.1017/S0950268807009314
 #'
-#' \item Simonsen, J., Teunis, P. F., van Pelt, W., van Duynhoven, Y., Krogfelt, K. A., Sadkowska-Todys, M., Molbak K.\cr
-#' "Usefulness of seroconversion rates for comparing infection pressures between countries"\cr
+#' \item Simonsen, J., Teunis, P. F., van Pelt, W., van Duynhoven, Y., Krogfelt, K. A., Sadkowska-Todys, M., Molbak K.
+#' "Usefulness of seroconversion rates for comparing infection pressures between countries"
 #' Epidemiology and Infection, April 12, 2010, 1--8. doi:10.1017/S0950268810000750.
 #'
-#' \item Falkenhorst, G., Simonsen, J., Ceper, T. H., van Pelt, W., de Valk, H., Sadkowska-Todys, M., Zota, L., Kuusi, M., Jernberg, C., Rota, M. C., van Duynhoven, Y. T., Teunis, P. F., Krogfelt, K. A., Molbak, K.\cr
-#' "Serological cross-sectional studies on salmonella incidence in eight European countries: no correlation with incidence of reported cases"\cr
+#' \item Falkenhorst, G., Simonsen, J., Ceper, T. H., van Pelt, W., de Valk, H., Sadkowska-Todys, M., Zota, L., Kuusi, M., Jernberg, C., Rota, M. C., van Duynhoven, Y. T., Teunis, P. F., Krogfelt, K. A., Molbak, K.
+#' "Serological cross-sectional studies on salmonella incidence in eight European countries: no correlation with incidence of reported cases"
 #' BMC Public Health 12, no. 1 (July 15, 2012): 523--23. doi:10.1186/1471-2458-12-523.
 #'
-#' \item Teunis, P. F., Falkenhorst, G., Ang, C. W., Strid, M. A., De Valk, H., Sadkowska-Todys, M., Zota, L., Kuusi, M., Rota, M. C., Simonsen, J. B., Molbak, K., Van Duynhoven, Y. T., van Pelt, W.\cr
-#' "Campylobacter seroconversion rates in selected countries in the European Union"\cr
+#' \item Teunis, P. F., Falkenhorst, G., Ang, C. W., Strid, M. A., De Valk, H., Sadkowska-Todys, M., Zota, L., Kuusi, M., Rota, M. C., Simonsen, J. B., Molbak, K., Van Duynhoven, Y. T., van Pelt, W.
+#' "Campylobacter seroconversion rates in selected countries in the European Union"
 #' Epidemiology and Infection 141, no. 10 (2013): 2051--57. doi:10.1017/S0950268812002774.
 #'
-#' \item de Melker, H. E., Versteegh, F. G., Schellekens, J. F., Teunis, P. F., Kretzschmar, M.\cr
-#' "The incidence of Bordetella pertussis infections estimated in the population from a combination of serological surveys"\cr
+#' \item de Melker, H. E., Versteegh, F. G., Schellekens, J. F., Teunis, P. F., Kretzschmar, M.
+#' "The incidence of Bordetella pertussis infections estimated in the population from a combination of serological surveys"
 #' The Journal of Infection 53, no. 2 (August 1, 2006): 106--13. doi:10.1016/j.jinf.2005.10.020
 #' }
 #'
 #' \strong{\emph{Quantification of seroresponse}}
 #'
 #' \itemize{
-#' \item de Graaf, W. F., Kretzschmar, M. E., Teunis, P. F., Diekmann, O.\cr
-#' "A two-phase within-host model for immune response and its application to serological profiles of pertussis"\cr
+#' \item de Graaf, W. F., Kretzschmar, M. E., Teunis, P. F., Diekmann, O.
+#' "A two-phase within-host model for immune response and its application to serological profiles of pertussis"
 #' Epidemics 9 (2014):1--7. doi:10.1016/j.epidem.2014.08.002.
 #'
-#' \item Berbers, G. A., van de Wetering, M. S., van Gageldonk, P. G., Schellekens, J. F., Versteegh, F. G., Teunis, P.F.\cr
-#' "A novel method for evaluating natural and vaccine induced serological responses to Bordetella pertussis antigens"\cr
+#' \item Berbers, G. A., van de Wetering, M. S., van Gageldonk, P. G., Schellekens, J. F., Versteegh, F. G., Teunis, P.F.
+#' "A novel method for evaluating natural and vaccine induced serological responses to Bordetella pertussis antigens"
 #' Vaccine 31, no. 36 (August 12, 2013): 3732--38. doi:10.1016/j.vaccine.2013.05.073.
 #'
-#' \item Versteegh, F. G., Mertens, P. L., de Melker, H. E., Roord, J. J., Schellekens, J. F., Teunis, P. F.\cr
-#' "Age-specific long-term course of IgG antibodies to pertussis toxin after symptomatic infection with Bordetella pertussis"\cr
+#' \item Versteegh, F. G., Mertens, P. L., de Melker, H. E., Roord, J. J., Schellekens, J. F., Teunis, P. F.
+#' "Age-specific long-term course of IgG antibodies to pertussis toxin after symptomatic infection with Bordetella pertussis"
 #' Epidemiology and Infection 133, no. 4 (August 1, 2005): 737--48.
 #'
 #' \item Teunis, P. F., van der Heijden, O. G., de Melker, H. E., Schellekens, J. F., Versteegh, F. G., Kretzschmar, M. E.
-#' "Kinetics of the IgG antibody response to pertussis toxin after infection with B. pertussis"\cr
+#' "Kinetics of the IgG antibody response to pertussis toxin after infection with B. pertussis"
 #' Epidemiology and Infection 129, no. 3 (December 10, 2002):479. doi:10.1017/S0950268802007896.
 #' }
 #'

README.md

@@ -4,7 +4,7 @@ serocalculator package
 ------------------------------------------------------------------------
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/UCD-SERG/serocalculator/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/UCD-SERG/serocalculator/actions/workflows/R-CMD-check.yaml)
+[![R-CMD-check](https://github.com/UCD-SERG/serocalculator/workflows/R-CMD-check/badge.svg)](https://github.com/UCD-SERG/serocalculator/actions)
 <!-- badges: end -->
 
 Antibody levels measured in a (cross–sectional) population sample can be
@@ -25,7 +25,7 @@ You can install the development version from
 
 ``` r
 install.packages("devtools")
-devtools::install_github("ucd-seg/serocalculator")
+devtools::install_github("ucd-serg/serocalculator")
 ```
 
 **A Note for Windows Users**

_pkgdown.yml

@@ -1,4 +1,4 @@
-url: https://ucd-seg.github.io/serocalculator/
+url: https://ucd-serg.github.io/serocalculator/
 template:
   bootstrap: 5