Merge pull request #400 from cmu-delphi/ndefries/specialized-slide-mean

Add a specialized function for calculating rolling averages

Author: nmdefries

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: epiprocess
 Title: Tools for basic signal processing in epidemiology
-Version: 0.7.5
+Version: 0.7.6
 Authors@R: c(
     person("Jacob", "Bien", role = "ctb"),
     person("Logan", "Brooks", email = "[email protected]", role = c("aut", "cre")),

NAMESPACE

@@ -46,6 +46,7 @@ export(detect_outlr_stl)
 export(epi_archive)
 export(epi_cor)
 export(epi_slide)
+export(epi_slide_mean)
 export(epix_as_of)
 export(epix_merge)
 export(epix_slide)
@@ -74,6 +75,7 @@ importFrom(checkmate,assert)
 importFrom(checkmate,assert_character)
 importFrom(checkmate,assert_class)
 importFrom(checkmate,assert_data_frame)
+importFrom(checkmate,assert_function)
 importFrom(checkmate,assert_int)
 importFrom(checkmate,assert_list)
 importFrom(checkmate,assert_logical)
@@ -93,11 +95,13 @@ importFrom(data.table,address)
 importFrom(data.table,as.data.table)
 importFrom(data.table,between)
 importFrom(data.table,copy)
+importFrom(data.table,frollmean)
 importFrom(data.table,key)
 importFrom(data.table,rbindlist)
 importFrom(data.table,set)
 importFrom(data.table,setDF)
 importFrom(data.table,setkeyv)
+importFrom(dplyr,"%>%")
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,dplyr_col_modify)
@@ -114,17 +118,21 @@ importFrom(dplyr,relocate)
 importFrom(dplyr,rename)
 importFrom(dplyr,select)
 importFrom(dplyr,slice)
+importFrom(dplyr,tibble)
 importFrom(dplyr,ungroup)
 importFrom(ggplot2,autoplot)
+importFrom(lubridate,as.period)
 importFrom(lubridate,days)
 importFrom(lubridate,weeks)
 importFrom(magrittr,"%>%")
+importFrom(purrr,map)
 importFrom(purrr,map_lgl)
 importFrom(rlang,"!!!")
 importFrom(rlang,"!!")
 importFrom(rlang,.data)
 importFrom(rlang,.env)
 importFrom(rlang,arg_match)
+importFrom(rlang,as_label)
 importFrom(rlang,caller_arg)
 importFrom(rlang,caller_env)
 importFrom(rlang,enquo)
@@ -139,6 +147,7 @@ importFrom(rlang,is_missing)
 importFrom(rlang,is_quosure)
 importFrom(rlang,missing_arg)
 importFrom(rlang,new_function)
+importFrom(rlang,quo_get_expr)
 importFrom(rlang,quo_is_missing)
 importFrom(rlang,sym)
 importFrom(rlang,syms)

NEWS.md

@@ -9,6 +9,8 @@ Pre-1.0.0 numbering scheme: 0.x will indicate releases, while 0.x.y will indicat
 - `epi_slide` computations are now 2-4 times faster after changing how
   reference time values, made accessible within sliding functions, are
   calculated (#397).
+- Add new `epi_slide_mean` function to allow much (~30x) faster rolling
+  average computations in some cases (#400).
 - regenerated the `jhu_csse_daily_subset` dataset with the latest versions of
   the data from the API
 - changed approach to versioning, see DEVELOPMENT.md for details

R/slide.R

@@ -67,6 +67,7 @@ reference:
     desc: Functions that act on `epi_df` objects.
   - contents:
       - epi_slide
+      - epi_slide_mean
       - epi_cor
   - title: Vector functions
     desc: Functions that act directly on signal variables.