address most of the CRAN issues

DESCRIPTION

@@ -8,11 +8,11 @@ Authors@R:
            comment = c(ORCID = "0000-0002-0380-1503")),
       person("Lucy", "Goodfellow", , "lucy.goodfellow@lshtm.ac.uk", role = c("aut"),
            comment = c(ORCID = "0009-0004-0434-5863")))
-Description: The `paramix` package provides a convenient framework for aggregating
+Description: A convenient framework for aggregating
     and disaggregating continuously varying parameters (for example, case fatality
     ratio, with age) for proper parametrization of lower-resolution compartmental
     models (for example, with broad age categories) and subsequent upscaling of
-    model outputs at high resolution (for example, as needed when calculating
+    model outputs to high resolution (for example, as needed when calculating
     age-sensitive measures like years-life-lost).
 License: MIT + file LICENSE
 Encoding: UTF-8

R/aggregate.R

@@ -8,11 +8,7 @@
 #' @param ... any number of numeric vectors
 #'
 #' @return a sorted numeric vector with unique values
-#'
-#' @examples
-#' paramix:::make_partition(1:5)
-#' paramix:::make_partition(5:1, 4, 6)
-#'
+#' @keywords internal
 make_partition <- function(
   ...
 ) {

R/plotting.R

@@ -27,7 +27,7 @@
 #'    uses `integrate()`
 #'
 #' @examples
-#' # from Levin et al 2020 https://doi.org/10.1007/s10654-020-00698-1
+#' # COVID IFR from Levin et al 2020 https://doi.org/10.1007/s10654-020-00698-1
 #' f_param <- function(age_in_years) {
 #'   (10^(-3.27 + 0.0524 * age_in_years))/100
 #' }
@@ -115,6 +115,19 @@ utils::globalVariables(c(
 #'
 #' @inheritParams blend
 #'
+#' @return a `data.table`, columns:
+#'  - `partition`, the feature point corresponding to the value
+#'  - `value`, the translated `model_outcomes_dt$value`
+#'  - `method`, a factor with levels indicating how feature points are selected,
+#'  and how `value` is weighted to those features:
+#'    * `f_mid`: features at the `alembic_dt` outcome partitions, each with
+#'    value corresponding to the total value of the corresponding model
+#'    partition, divided by the number of outcome partitions in that model
+#'    partition
+#'    * `f_mean`: ...
+#'    * `mean_f`: ...
+#'    * `wm_f`: the
+#'
 #' @examples
 #' library(data.table)
 #' f_param <- function(age_in_years) {
@@ -174,7 +187,7 @@ distill_summary <- function(
       distill(alembic_dt, model_outcomes_dt)[, method := "wm_f"],
       "new_from", "partition"
     )
-  ))
+  )[, method := factor(method)])
 
 }
 

vignettes/intro.Rmd

@@ -1,6 +1,8 @@
 ---
 title: "Introductory Usage: `paramix`"
-output: rmarkdown::html_vignette
+output:
+  rmarkdown::html_vignette:
+    check_title: False
 vignette: >
   %\VignetteIndexEntry{paramix-intro}
   %\VignetteEngine{knitr::rmarkdown}
@@ -12,10 +14,6 @@ knitr::opts_chunk$set(
   collapse = TRUE,
   comment = "#>"
 )
-options(
-  scipen = 100000,
-  rmarkdown.html_vignette.check_title = FALSE
-)
 ```
 
 ```{r setup, echo = FALSE}