From 8dd760b02d6d94684bd40ee4d75229fc100f3ec1 Mon Sep 17 00:00:00 2001 From: Douglas Ezra Morrison Date: Thu, 27 Jul 2023 23:31:45 -0400 Subject: [PATCH 1/5] removed \cr (carriage return) symbols, and <> from emails in roxygen. added Kristen and Kristina to authors list. added return value information in .nll() function documentation. --- DESCRIPTION | 2 +- R/nll.R | 2 +- R/serocalculator-package.R | 62 ++++++++++++++++++----------------- man/dot-nll.Rd | 2 +- man/serocalculator.Rd | 67 +++++++++++++++++++------------------- 5 files changed, 68 insertions(+), 67 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e11c0cbf..c1c1c490 100644 --- a/DESCRIPTION +++ b/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 diff --git a/R/nll.R b/R/nll.R index 88a4e0ee..dddf5b34 100644 --- a/R/nll.R +++ b/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 diff --git a/R/serocalculator-package.R b/R/serocalculator-package.R index da314d79..289c779d 100644 --- a/R/serocalculator-package.R +++ b/R/serocalculator-package.R @@ -12,27 +12,29 @@ #' 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{}\cr -#' Maintainer: Doug Ezra Morrison \email{} +#' 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. #' } #' @@ -40,53 +42,53 @@ #' #' \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. #' } #' diff --git a/man/dot-nll.Rd b/man/dot-nll.Rd index 8e6d1deb..337bebb1 100644 --- a/man/dot-nll.Rd +++ b/man/dot-nll.Rd @@ -39,7 +39,7 @@ for true seronegatives (i.e. those who never seroconverted), by named antibody t (log(1/365.25)), -4 corresponds roughly to 1 week (log(7 / 365.25)). Default = -6.} } \value{ - +the log-likelihood of the data with the current parameter values } \description{ Calculate log-likelihood diff --git a/man/serocalculator.Rd b/man/serocalculator.Rd index 5b48ba59..0c138293 100644 --- a/man/serocalculator.Rd +++ b/man/serocalculator.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/seroincidence-package.R +% Please edit documentation in R/serocalculator-package.R \docType{package} \name{serocalculator} \alias{serocalculator} @@ -10,22 +10,22 @@ Translates antibody levels measured in a (cross-sectional) population sample int 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")} } \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. } @@ -33,60 +33,59 @@ Statistics in Medicine 28, no. 14 (June 30, 2009): 1882--95. doi:10.1002/sim.359 \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. } } \author{ -Author: Peter Teunis \email{}\cr -Author: Jan van Eijkeren\cr -Contributor: Daniel Lewandowski \email{}\cr -Contributor: Chantal Quinten \email{} -Maintainer: Doug Ezra Morrison \email{} +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} } From b9f1b3f02fd59df3c31e6bf14b58ea8ef30470a7 Mon Sep 17 00:00:00 2001 From: Douglas Ezra Morrison Date: Fri, 28 Jul 2023 16:13:35 -0400 Subject: [PATCH 2/5] adding contribution instructions --- .github/CONTRIBUTING.md | 47 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 .github/CONTRIBUTING.md diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md new file mode 100644 index 00000000..56d4d565 --- /dev/null +++ b/.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 . + +### 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. From 1146c85ea97b5906bd3507e090920b86f5d59a9b Mon Sep 17 00:00:00 2001 From: Douglas Ezra Morrison Date: Thu, 17 Aug 2023 14:02:35 -0400 Subject: [PATCH 3/5] fixing pkgdown auto-build system. --- .github/workflows/pkgdown.yaml | 35 +++++++++++++------- DESCRIPTION | 2 +- README.md | 58 +++++++++++++++++----------------- _pkgdown.yml | 2 +- 4 files changed, 55 insertions(+), 42 deletions(-) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 63cbb18a..ed7650c7 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.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 "$GITHUB_ACTOR@users.noreply.github.com" - 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/github-pages-deploy-action@v4.4.1 + with: + clean: false + branch: gh-pages + folder: docs diff --git a/DESCRIPTION b/DESCRIPTION index e11c0cbf..2da8b69e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -32,7 +32,7 @@ Suggests: VignetteBuilder: knitr LazyData: true Encoding: UTF-8 -URL: https://github.com/UCD-SEG/serocalculator, https://ucd-seg.github.io/serocalculator/ +URL: https://github.com/UCD-SERG/serocalculator, https://ucd-serg.github.io/serocalculator/, https://ucd-serg.github.io/serocalculator/ RoxygenNote: 7.1.2 NeedsCompilation: no LinkingTo: diff --git a/README.md b/README.md index a270e261..61504bcf 100644 --- a/README.md +++ b/README.md @@ -1,29 +1,29 @@ -serocalculator package -===================== - ------------------------------------------------------------------------- - - -[![R-CMD-check](https://github.com/UCD-SEG/serocalculator/workflows/R-CMD-check/badge.svg)](https://github.com/UCD-SEG/serocalculator/actions) - - -Antibody levels measured in a (cross–sectional) population sample can be -translated into an estimate of the frequency with which seroconversions -(infections) occur in the sampled population. Formulated simply: the -presence of many high titres indicates that many subjects likely -experienced infection recently, while low titres indicate a low -frequency of infections in the sampled population. - -The serocalculator script was designed to use the longitudinal -response characteristics by means of a set of parameters characterizing -the longitudinal response of the selected serum antibodies. - -## Installation - -You can install the development version from -[GitHub](https://github.com/) with: - -``` r -install.packages("devtools") -devtools::install_github("ucd-seg/serocalculator") -``` +serocalculator package +===================== + +------------------------------------------------------------------------ + + +[![R-CMD-check](https://github.com/UCD-SERG/serocalculator/workflows/R-CMD-check/badge.svg)](https://github.com/UCD-SERG/serocalculator/actions) + + +Antibody levels measured in a (cross–sectional) population sample can be +translated into an estimate of the frequency with which seroconversions +(infections) occur in the sampled population. Formulated simply: the +presence of many high titres indicates that many subjects likely +experienced infection recently, while low titres indicate a low +frequency of infections in the sampled population. + +The serocalculator script was designed to use the longitudinal +response characteristics by means of a set of parameters characterizing +the longitudinal response of the selected serum antibodies. + +## Installation + +You can install the development version from +[GitHub](https://github.com/) with: + +``` r +install.packages("devtools") +devtools::install_github("ucd-serg/serocalculator") +``` diff --git a/_pkgdown.yml b/_pkgdown.yml index 42d2bd0d..b6f5aed0 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,4 +1,4 @@ -url: https://ucd-seg.github.io/serocalculator/ +url: https://ucd-serg.github.io/serocalculator/ template: bootstrap: 5 From 2004fca33636a11aade05e34650e5c216ac60269 Mon Sep 17 00:00:00 2001 From: Douglas Ezra Morrison Date: Thu, 17 Aug 2023 14:12:29 -0400 Subject: [PATCH 4/5] merging with main --- .github/CONTRIBUTING.md | 47 +++++++++++++ .github/workflows/R-CMD-check.yaml | 19 +++--- DESCRIPTION | 12 ++-- R/nll.R | 2 +- ...nce-package.R => serocalculator-package.R} | 65 +++++++++--------- man/dot-nll.Rd | 2 +- man/serocalculator.Rd | 67 +++++++++---------- 7 files changed, 130 insertions(+), 84 deletions(-) create mode 100644 .github/CONTRIBUTING.md rename R/{seroincidence-package.R => serocalculator-package.R} (75%) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md new file mode 100644 index 00000000..56d4d565 --- /dev/null +++ b/.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 . + +### 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. diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 271d466e..a3ac6182 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.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 diff --git a/DESCRIPTION b/DESCRIPTION index 2da8b69e..d241a6c2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -5,15 +5,13 @@ Version: 0.1.0.9000 Date: 2022-03-29 Authors@R: c( person(given = "Peter", family = "Teunis", email = "p.teunis@emory.edu", 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 = "daniel@nextpagesoft.net", role = c("ctb"), comment = "Creator of the `seroincidence` R package."), - person(given = "Chantal", family = "Quinten", email = "seroincidence@ecdc.europa.eu", role = c("ctb")), - person(given = "Kristen", family = "Aiemjoy", email = "kaiemjoy@ucdavis.edu", role = c("aut", "ctb")), - person(given = "Douglas Ezra", family = "Morrison", email = "demorrison@ucdavis.edu", role = c("aut", "ctb", "cre"), comment = "Package maintainer.")) + person(given = "Kristina", family = "Lai", role = c("aut")), + person(given = "Kristen", family = "Aiemjoy", email = "kaiemjoy@ucdavis.edu", role = c("aut")), + person(given = "Douglas Ezra", family = "Morrison", email = "demorrison@ucdavis.edu", role = c("aut"))) 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: @@ -33,7 +31,7 @@ VignetteBuilder: knitr LazyData: true Encoding: UTF-8 URL: https://github.com/UCD-SERG/serocalculator, https://ucd-serg.github.io/serocalculator/, https://ucd-serg.github.io/serocalculator/ -RoxygenNote: 7.1.2 +RoxygenNote: 7.2.3 NeedsCompilation: no LinkingTo: Rcpp diff --git a/R/nll.R b/R/nll.R index 88a4e0ee..dddf5b34 100644 --- a/R/nll.R +++ b/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 diff --git a/R/seroincidence-package.R b/R/serocalculator-package.R similarity index 75% rename from R/seroincidence-package.R rename to R/serocalculator-package.R index fdaa3960..289c779d 100644 --- a/R/seroincidence-package.R +++ b/R/serocalculator-package.R @@ -12,30 +12,29 @@ #' 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{}\cr -#' Author: Jan van Eijkeren\cr -#' Contributor: Daniel Lewandowski \email{}\cr -#' Contributor: Chantal Quinten \email{} -#' Maintainer: Doug Ezra Morrison \email{} +#' 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. #' } #' @@ -43,53 +42,53 @@ #' #' \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. #' } #' diff --git a/man/dot-nll.Rd b/man/dot-nll.Rd index 8e6d1deb..337bebb1 100644 --- a/man/dot-nll.Rd +++ b/man/dot-nll.Rd @@ -39,7 +39,7 @@ for true seronegatives (i.e. those who never seroconverted), by named antibody t (log(1/365.25)), -4 corresponds roughly to 1 week (log(7 / 365.25)). Default = -6.} } \value{ - +the log-likelihood of the data with the current parameter values } \description{ Calculate log-likelihood diff --git a/man/serocalculator.Rd b/man/serocalculator.Rd index 5b48ba59..0c138293 100644 --- a/man/serocalculator.Rd +++ b/man/serocalculator.Rd @@ -1,5 +1,5 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/seroincidence-package.R +% Please edit documentation in R/serocalculator-package.R \docType{package} \name{serocalculator} \alias{serocalculator} @@ -10,22 +10,22 @@ Translates antibody levels measured in a (cross-sectional) population sample int 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")} } \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. } @@ -33,60 +33,59 @@ Statistics in Medicine 28, no. 14 (June 30, 2009): 1882--95. doi:10.1002/sim.359 \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. } } \author{ -Author: Peter Teunis \email{}\cr -Author: Jan van Eijkeren\cr -Contributor: Daniel Lewandowski \email{}\cr -Contributor: Chantal Quinten \email{} -Maintainer: Doug Ezra Morrison \email{} +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} } From fdd9d7e571de5cd004afc963f646cce89e9e2ac4 Mon Sep 17 00:00:00 2001 From: Douglas Ezra Morrison Date: Thu, 17 Aug 2023 14:24:35 -0400 Subject: [PATCH 5/5] adding myself as maintainer; required for checks to pass --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d241a6c2..cc0d44a8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -7,7 +7,7 @@ Authors@R: c( person(given = "Peter", family = "Teunis", email = "p.teunis@emory.edu", role = c("aut", "cph"), comment = "Author of the method and original code."), person(given = "Kristina", family = "Lai", role = c("aut")), person(given = "Kristen", family = "Aiemjoy", email = "kaiemjoy@ucdavis.edu", role = c("aut")), - person(given = "Douglas Ezra", family = "Morrison", email = "demorrison@ucdavis.edu", role = c("aut"))) + person(given = "Douglas Ezra", family = "Morrison", email = "demorrison@ucdavis.edu", 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.