Snake case lint

.Rbuildignore

@@ -29,11 +29,6 @@ allpopsamples_hlye.csv$
 ^vignettes/methodology\.qmd$
 ^\.quarto$
 ^revdep$
-^man/ab\.Rd$
-^man/baseline\.Rd$
-^man/mk_baseline\.Rd$
+^NEWS_files$
+^NEWS\.html$
 ^man/check_strata\.Rd$
-^man/df_to_array\.Rd$
-^man/ldpar\.Rd$
-^man/simcs.tinf\.Rd$
-^man/simresp.tinf\.Rd$

.gitignore

@@ -17,3 +17,4 @@ README.html
 README_files
 /.quarto/
 NEWS.html
+NEWS_files

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: serocalculator
 Title: Estimating Infection Rates from Serological Data
-Version: 1.3.0.9005
+Version: 1.3.0.9006
 Authors@R: c(
     person("Peter", "Teunis", , "[email protected]", role = c("aut", "cph"),
            comment = "Author of the method and original code."),
@@ -15,15 +15,15 @@ Description: Translates antibody levels measured in cross-sectional
     seroconversions (infections) occur in the sampled populations.
     Replaces the previous `seroincidence` package.
 License: GPL-3
-URL: https://github.com/UCD-SERG/serocalculator,
-    https://ucd-serg.github.io/serocalculator/
+URL: https://ucd-serg.github.io/serocalculator/,
+    https://github.com/UCD-SERG/serocalculator
 BugReports: https://github.com/UCD-SERG/serocalculator/issues
 Depends: 
     R (>= 4.1.0)
 Imports: 
     cli,
     doParallel,
-    dplyr (>= 1.1.1),
+    dplyr,
     foreach,
     ggplot2,
     ggpubr,
@@ -42,15 +42,15 @@ Imports:
     purrr,
     and,
     glue,
-    stringr
+    stringr,
+    parallel
 Suggests:
     bookdown,
     DT,
     fs,
     ggbeeswarm,
     knitr,
     pak,
-    parallel,
     readr,
     quarto,
     rmarkdown,

NAMESPACE

@@ -32,8 +32,8 @@ export(load_noise_params)
 export(load_pop_data)
 export(log_likelihood)
 export(serocalculator_example)
-export(sim.cs)
-export(sim.cs.multi)
+export(sim_pop_data)
+export(sim_pop_data_multi)
 importFrom(Rcpp,sourceCpp)
 importFrom(doParallel,registerDoParallel)
 importFrom(dplyr,across)
@@ -48,6 +48,7 @@ importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
 importFrom(dplyr,if_all)
 importFrom(dplyr,if_any)
+importFrom(dplyr,if_else)
 importFrom(dplyr,inner_join)
 importFrom(dplyr,is.grouped_df)
 importFrom(dplyr,mutate)

NEWS.md

@@ -2,6 +2,10 @@
 
 ## New features
 
+* Renamed variables for consistency (#281):
+  - `sim.cs()` -> `sim_pop_data()` 
+  - `sim.cs.multi()` -> `sim_pop_data_multi()`
+
 ## Internal changes
 
 * Removed `ldpar()` from API (#345)

R/ab.R

@@ -29,9 +29,9 @@
 #'    ncol = 2L,
 #'    dimnames = list(c("HlyE_IgA", "HlyE_IgG"), c("min", "max"))
 #'    )
-#' preds <- ab(t = t, par = par1, blims = blims)
+#' preds <- serocalculator:::ab(t = t, par = par1, blims = blims)
 #'
-#' @dev
+#' @keywords internal
 ab <- function(t, par, ...) {
   t1 <- t1func(par)
   y1 <- y1func(par)

R/baseline.R

@@ -11,7 +11,7 @@
 #' @param ... unused
 #'
 #' @returns an altered version of `yvec`
-#' @dev
+#' @keywords internal
 #'
 baseline <- function(kab, yvec, blims, ...) {
   subst <- which(yvec < blims[kab, 2])
@@ -29,9 +29,8 @@ baseline <- function(kab, yvec, blims, ...) {
 #' @param blims range of possible baseline antibody levels
 #' @param ... not currently used
 #' @return a [numeric()] vector
-#' @dev
+#' @keywords internal
 mk_baseline <- function(kab, n = 1, blims, ...) {
-  # yset <- rlnorm(n=1,meanlog=negpar[1],sdlog=negpar[2]);
   if (blims[kab, 2] == 0) {
     yset <- rep(0, n)
   } else {

R/df_to_array.R

@@ -38,10 +38,10 @@ df.to.array <- function( # nolint: object_name_linter
 #'   ) %>%
 #'   mutate(parameter = factor(parameter, levels = unique(parameter)))
 #' arr <- df %>%
-#'   serocalculator::df_to_array(
+#'   serocalculator:::df_to_array(
 #'      dim_var_names = c("parameter", "Species"))
 #' ftable(arr[,,1:5])
-#' @dev
+#' @keywords internal
 df_to_array <- function(
     df,
     dim_var_names,

R/ldpar.R

@@ -9,7 +9,7 @@
 #' @param npar number of parameters
 #' @returns an array of parameters:
 #'  c(y0,b0,mu0,mu1,c1,alpha,shape)
-#' @dev
+#' @keywords internal
 ldpar <- function(age, antigen_isos, nmc, npar, ...) {
   dimnames1 <- list(
     params = c("y0", "b0", "mu0", "mu1", "c1", "alpha", "shape_r"),
@@ -24,8 +24,7 @@ ldpar <- function(age, antigen_isos, nmc, npar, ...) {
     dimnames = dimnames1
   )
 
-  for (k.test in antigen_isos)
-  {
+  for (k.test in antigen_isos) {
     spar[, k.test] <- simpar(age, k.test, nmc, ...)
   }
   return(spar)

R/serocalculator-package.R

@@ -1,128 +1,5 @@
-#' _PACKAGE
-#'
-#' @name serocalculator
-#'
-#' @aliases serocalculator serocalculator-package
-#'
-#' @title
-#' Estimating Infection Rates from Serological Data
-#'
-#' @description
-#' This package 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.
-#'
-#' @author
-#' * Peter Teunis \email{p.teunis@@emory.edu}
-#' * Doug Ezra Morrison \email{demorrison@@ucdavis.edu}
-#' * Kristen Aiemjoy \email{kaiemjoy@@ucdavis.edu}
-#' * Kristina Lai \email{kwlai@@ucdavis.edu}
-#'
-#' @references
-#'
-#' ***Methods for estimating seroincidence***
-#'
-#' * Teunis, P. F. M., and J. C. H. van Eijkeren.
-#' "Estimation of seroconversion rates for infectious diseases:
-#' Effects of age and noise."
-#' Statistics in Medicine 39, no. 21 (2020): 2799-2814.
-#'
-#' * Teunis, P. F. M., J. C. H. van Eijkeren, W. F. de Graaf,
-#' A. Bonačić Marinović, and M. E. E. Kretzschmar.
-#' "Linking the seroresponse to infection to within-host heterogeneity
-#'  in antibody production." Epidemics 16 (2016): 33-39.
-#'
-#'
-#' ***Applications***
-#'
-#' * Aiemjoy, Kristen, Jessica C. Seidman, Senjuti Saha,
-#' Sira Jam Munira, Mohammad Saiful Islam Sajib,
-#' Syed Muktadir Al Sium, Anik Sarkar et al.
-#' "Estimating typhoid incidence from community-based serosurveys:
-#' a multicohort study." The Lancet Microbe 3, no. 8 (2022): e578-e587.
-#'
-#' * Aiemjoy, Kristen, John Rumunu, Juma John Hassen,
-#' Kirsten E. Wiens, Denise Garrett, Polina Kamenskaya,
-#' Jason B. Harris et al. "Seroincidence of enteric fever, Juba,
-#' South Sudan." Emerging infectious diseases 28, no. 11 (2022): 2316.
-#'
-#' * 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"
-#' Journal of Infection, 2018, 1--7, doi:10.1016/j.jinf.2018.04.016
-#'
-#' * 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.
-#'
-#' * 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
-#'
-#' * 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.
-#'
-#' * 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.
-#'
-#' * 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.
-#'
-#' * 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
-#'
-#'
-#' ***Quantification of seroresponse***
-#'
-#' * 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.
-#'
-#' * 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.
-#'
-#' * 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.
-#'
-#' * 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"
-#' Epidemiology and Infection 129, no. 3 (December 10, 2002):479. doi:10.1017/S0950268802007896.
-#'
-#'
+#' @keywords internal
+"_PACKAGE"
 
 ## usethis namespace: start
 #' @importFrom doParallel registerDoParallel
@@ -138,6 +15,7 @@
 #' @importFrom dplyr group_by
 #' @importFrom dplyr if_all
 #' @importFrom dplyr if_any
+#' @importFrom dplyr if_else
 #' @importFrom dplyr inner_join
 #' @importFrom dplyr is.grouped_df
 #' @importFrom dplyr mutate