Merge pull request #4 from UCD-SERG/main

catch up

.github/workflows/R-CMD-check.yaml

@@ -1,4 +1,4 @@
-# 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:
@@ -18,7 +18,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,18 +29,21 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     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:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

DESCRIPTION

@@ -33,7 +33,7 @@ VignetteBuilder: knitr
 LazyData: true
 Encoding: UTF-8
 URL: https://github.com/UCD-SEG/serocalculator, https://ucd-seg.github.io/serocalculator/
-RoxygenNote: 7.1.2
+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/seroincidence-package.R → R/serocalculator-package.R

@@ -12,84 +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{<p.teunis@@emory.edu>}\cr
-#' Author: Jan van Eijkeren\cr
-#' Contributor: Daniel Lewandowski \email{<daniel@@nextpagesoft.net>}\cr
-#' Contributor: Chantal Quinten \email{<seroincidence@@ecdc.europa.eu>}
-#' Maintainer: Doug Ezra Morrison \email{<demorrison@@ucdavis.edu>}
+#' 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-SEG/serocalculator/workflows/R-CMD-check/badge.svg)](https://github.com/UCD-SEG/serocalculator/actions)
+[![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)
 <!-- badges: end -->
 
 Antibody levels measured in a (cross–sectional) population sample can be