add error message for missing strata

DESCRIPTION

@@ -31,7 +31,8 @@ Imports:
     tidyr,
     utils,
     tidyselect,
-    cli
+    cli,
+    purrr
 Suggests:
     parallel,
     knitr,

NEWS.md

@@ -1,4 +1,7 @@
-# serocalculator (development version)
+# serocalculator 1.3.0
+* Add test for `est.incidence` 
+
+* Add option to test `strata` in `pop_data`
 
 # serocalculator 1.2.0
 * Added `test-summary.pop_data` test

R/est.incidence.by.R

@@ -1,14 +1,22 @@
 #' Estimate Seroincidence
-#'
 #' @description
-#' Function to estimate seroincidences based on cross-section serology data and longitudinal
+#' Function to estimate seroincidences based on cross-section
+#' serology data and longitudinal
 #' response model.
 #'
-#' @param pop_data a [data.frame] with cross-sectional serology data per antibody and age, and additional columns corresponding to each element of the `strata` input
-#' @param strata a [character] vector of stratum-defining variables. Values must be variable names in `pop_data`.
-#' @param curve_strata_varnames A subset of `strata`. Values must be variable names in `curve_params`. Default = "".
-#' @param noise_strata_varnames A subset of `strata`. Values must be variable names in `noise_params`. Default = "".
-#' @param num_cores Number of processor cores to use for calculations when computing by strata. If set to more than 1 and package \pkg{parallel} is available, then the computations are executed in parallel. Default = 1L.
+#' @param pop_data a [data.frame] with cross-sectional serology data per
+#' antibody and age, and additional columns corresponding to
+#' each element of the `strata` input
+#' @param strata a [character] vector of stratum-defining variables.
+#' Values must be variable names in `pop_data`.
+#' @param curve_strata_varnames A subset of `strata`.
+#' Values must be variable names in `curve_params`. Default = "".
+#' @param noise_strata_varnames A subset of `strata`.
+#' Values must be variable names in `noise_params`. Default = "".
+#' @param num_cores Number of processor cores to use for
+#' calculations when computing by strata. If set to
+#' more than 1 and package \pkg{parallel} is available,
+#' then the computations are executed in parallel. Default = 1L.
 
 #' @details
 #'
@@ -17,7 +25,8 @@
 #' and then the data will be passed to [est.incidence()].
 #' If for some reason you want to use [est.incidence.by()]
 #' with no strata instead of calling [est.incidence()],
-#' you may use `NA`, `NULL`, or `""` as the `strata` argument to avoid that warning.
+#' you may use `NA`, `NULL`, or `""` as the `strata`
+#' argument to avoid that warning.
 #'
 #'
 #' @inheritParams est.incidence
@@ -26,7 +35,9 @@
 #'
 #' @return
 #' * if `strata` has meaningful inputs:
-#' An object of class `"seroincidence.by"`; i.e., a list of `"seroincidence"` objects from [est.incidence()], one for each stratum, with some meta-data attributes.
+#' An object of class `"seroincidence.by"`; i.e., a list of `
+#' "seroincidence"` objects from [est.incidence()], one for each stratum,
+#' with some meta-data attributes.
 #' * if `strata` is missing, `NULL`, `NA`, or `""`:
 #' An object of class `"seroincidence"`.
 #'
@@ -39,7 +50,7 @@
 #'
 #' curve <- load_curve_params("https://osf.io/download/rtw5k/") %>%
 #'   filter(antigen_iso %in% c("HlyE_IgA", "HlyE_IgG")) %>%
-#'   slice(1:100, .by = antigen_iso) # Reduce dataset for the purposes of this example
+#'   slice(1:100, .by = antigen_iso)
 #'
 #' noise <- load_noise_params("https://osf.io/download//hqy4v/")
 #'
@@ -49,13 +60,13 @@
 #'   curve_params = curve,
 #'   noise_params = noise %>% filter(Country == "Pakistan"),
 #'   antigen_isos = c("HlyE_IgG", "HlyE_IgA"),
-#'   #num_cores = 8 # Allow for parallel processing to decrease run time
+#'   # num_cores = 8 # Allow for parallel processing to decrease run time
 #'   iterlim = 5 # limit iterations for the purpose of this example
 #' )
 #'
 #' summary(est2)
 #'
 est.incidence.by <- function(
     pop_data,
     curve_params,
     noise_params,
@@ -75,16 +86,19 @@
     warning(
       "The `strata` argument to `est.incidence.by()` is missing.",
       "\n\n  If you do not want to stratify your data, ",
-      "consider using the `est.incidence()` function to simplify your code and avoid this warning.",
-      "\n\n Since the `strata` argument is empty, `est.incidence.by()` will return a `seroincidence` object, instead of a `seroincidence.by` object.\n"
+      "consider using the `est.incidence()` function to
+      simplify your code and avoid this warning.",
+      "\n\n Since the `strata` argument is empty, `est.incidence.by()`
+      will return a `seroincidence` object, instead of a
+      `seroincidence.by` object.\n"
     )
   }
 
   strata_is_empty <-
     missing(strata) ||
-      is.null(strata) ||
-      setequal(strata, NA) ||
-      setequal(strata, "")
+    is.null(strata) ||
+    setequal(strata, NA) ||
+    setequal(strata, "")
 
   if (strata_is_empty) {
     to_return <-
@@ -110,7 +124,7 @@
   )
 
   # Split data per stratum
   stratumDataList <- stratify_data(
     antigen_isos = antigen_isos,
     data = pop_data %>% filter(.data$antigen_iso %in% antigen_isos),
     curve_params = curve_params %>% filter(.data$antigen_iso %in% antigen_isos),
@@ -130,8 +144,10 @@
 
   if (num_cores > 1L && !requireNamespace("parallel", quietly = TRUE)) {
     warning(
-      "The `parallel` package is not installed, so `num_cores > 1` has no effect.",
-      "To install `parallel`, run `install.packages('parallel')` in the console."
+      "The `parallel` package is not installed,
+      so `num_cores > 1` has no effect.",
+      "To install `parallel`, run `install.packages('parallel')`
+      in the console."
     )
   }
 
@@ -142,11 +158,12 @@
     num_cores <- num_cores %>% check_parallel_cores()
 
     if (verbose) {
-      message("Setting up parallel processing with `num_cores` = ", num_cores, ".")
+      message("Setting up parallel processing with
+              `num_cores` = ", num_cores, ".")
     }
 
 
     libPaths <- .libPaths()
     cl <-
       num_cores %>%
       parallel::makeCluster() %>%
@@ -158,11 +175,11 @@
     parallel::clusterExport(cl, c("libPaths"), envir = environment())
     parallel::clusterEvalQ(cl, {
       .libPaths(libPaths)
-      require(serocalculator) # note - this gets out of sync when using load_all() in development
+      require(serocalculator) # note - this gets out of sync" %>%
+      "when using load_all() in development"
       require(dplyr)
     })
-
     {
       fits <- parallel::parLapplyLB(
         cl = cl,
         X = stratumDataList,
@@ -183,23 +200,16 @@
           )
         }
       )
     } %>% system.time() -> time
 
     if (verbose) {
       message("Elapsed time for parallelized code: ")
       print(time)
     }
   } else {
-    # fits <- lapply(
-    #   X = stratumDataList,
-    #   FUN = function(x) est.incidence(dataList = x, verbose = verbose, ...))
-
     fits <- list()
-
     { # time progress
-
-      for (cur_stratum in names(stratumDataList))
-      {
+      for (cur_stratum in names(stratumDataList)) {
         cur_stratum_vars <-
           strata_table %>%
           dplyr::filter(.data$Stratum == cur_stratum)
@@ -225,7 +235,8 @@
             )
           )
       }
-    } %>% system.time() -> time
+    }
+
 
     if (verbose) {
       message("Elapsed time for loop over strata: ")
@@ -233,7 +244,7 @@
     }
   }
 
   incidenceData <- structure(
     fits,
     antigen_isos = antigen_isos,
     Strata = strata_table,