Merge pull request epiforecasts#437 from epiforecasts/fewer-deps

Reduce the number of `Imports`
RichardMN · Dec 3, 2021 · b93e19d · b93e19d
2 parents f6c9759 + 007b535
commit b93e19d
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -93,19 +93,14 @@ Imports:
     jsonlite,
     lifecycle,
     lubridate,
-    magrittr,
     memoise,
     purrr,
     R6,
     readxl,
     rlang,
-    stringi,
     stringr,
-    tibble,
     tidyr (>= 1.0.0),
-    tidyselect,
     vroom,
-    withr,
     xml2
 Suggests:
     ggplot2,

diff --git a/NAMESPACE b/NAMESPACE
@@ -48,12 +48,14 @@ importFrom(countrycode,countrycode)
 importFrom(countrycode,countryname)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,across)
+importFrom(dplyr,all_of)
 importFrom(dplyr,arrange)
 importFrom(dplyr,as_tibble)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,count)
 importFrom(dplyr,distinct)
 importFrom(dplyr,do)
+importFrom(dplyr,ends_with)
 importFrom(dplyr,everything)
 importFrom(dplyr,filter)
 importFrom(dplyr,full_join)
@@ -78,6 +80,7 @@ importFrom(dplyr,summarise)
 importFrom(dplyr,tally)
 importFrom(dplyr,tibble)
 importFrom(dplyr,transmute)
+importFrom(dplyr,tribble)
 importFrom(dplyr,ungroup)
 importFrom(dplyr,vars)
 importFrom(httr,GET)
@@ -95,7 +98,6 @@ importFrom(lubridate,month)
 importFrom(lubridate,year)
 importFrom(lubridate,ymd)
 importFrom(lubridate,ymd_hms)
-importFrom(magrittr,"%>%")
 importFrom(memoise,cache_filesystem)
 importFrom(memoise,memoise)
 importFrom(purrr,compact)
@@ -114,17 +116,12 @@ importFrom(rlang,"!!")
 importFrom(rlang,":=")
 importFrom(rlang,.data)
 importFrom(rlang,syms)
-importFrom(stringi,stri_replace_all)
-importFrom(stringi,stri_trans_general)
-importFrom(stringi,stri_trim_both)
+importFrom(stringr,str_conv)
 importFrom(stringr,str_detect)
 importFrom(stringr,str_replace_all)
 importFrom(stringr,str_to_sentence)
 importFrom(stringr,str_to_title)
-importFrom(tibble,add_column)
-importFrom(tibble,as_tibble)
-importFrom(tibble,tibble)
-importFrom(tibble,tribble)
+importFrom(stringr,str_trim)
 importFrom(tidyr,complete)
 importFrom(tidyr,drop_na)
 importFrom(tidyr,fill)
@@ -134,13 +131,8 @@ importFrom(tidyr,pivot_longer)
 importFrom(tidyr,pivot_wider)
 importFrom(tidyr,replace_na)
 importFrom(tidyr,separate)
-importFrom(tidyselect,all_of)
-importFrom(tidyselect,ends_with)
-importFrom(tidyselect,starts_with)
-importFrom(tidyselect,vars_select_helpers)
 importFrom(utils,download.file)
 importFrom(utils,untar)
 importFrom(vroom,vroom)
-importFrom(withr,with_envvar)
 importFrom(xml2,xml_find_first)
 importFrom(xml2,xml_text)
diff --git a/R/Belgium.R b/R/Belgium.R
@@ -57,13 +57,13 @@ Belgium <- R6::R6Class("Belgium",
     source_url = "https://epistat.wiv-isp.be/covid/",
 
     #' @description Set up a table of region codes for clean data
-    #' @importFrom tibble tibble tribble
+    #' @importFrom dplyr tibble tribble
     set_region_codes = function() {
-      self$codes_lookup$`1` <- tibble::tibble(
+      self$codes_lookup$`1` <- tibble(
         level_1_region_code = c("BE-BRU", "BE-VLG", "BE-WAL"),
         level_1_region = c("Brussels", "Flanders", "Wallonia")
       )
-      self$codes_lookup$`2` <- tibble::tribble(
+      self$codes_lookup$`2` <- tribble(
         ~level_2_region_code, ~level_2_region, ~level_1_region_code,
         "BE-VAN", "Antwerpen", "BE-VLG",
         "BE-WBR", "BrabantWallon", "BE-WAL",
@@ -82,8 +82,7 @@ Belgium <- R6::R6Class("Belgium",
 
     #' @description Downloads data from source and (for Belgium)
     #' applies an initial data patch.
-    #' @importFrom dplyr select mutate filter bind_rows
-    #' @importFrom tibble tribble
+    #' @importFrom dplyr select mutate filter bind_rows tribble
     download = function() {
       # do the actual downloading using the parent download method
       super$download()
@@ -92,7 +91,7 @@ Belgium <- R6::R6Class("Belgium",
       # For now, we filter out the broken lines and replace them
       # with the following data shim
 
-      fixed_lines <- tibble::tribble(
+      fixed_lines <- tribble(
         ~DATE, ~PROVINCE, ~REGION, ~AGEGROUP, ~SEX, ~CASES,
         "2020-04-22", "Limburg", "Flanders", "50-59", "F", 10,
         "2021-02-17", "VlaamsBrabant", "Flanders", "10-19", "M", 12

diff --git a/R/Brazil.R b/R/Brazil.R
@@ -47,7 +47,7 @@ Brazil <- R6::R6Class("Brazil",
     source_url = "https://github.com/wcota/covid19br/blob/master/README.en.md",
 
     #' @description Set up a table of region codes for clean data
-    #' @importFrom tibble tribble
+    #' @importFrom dplyr tibble
     set_region_codes = function() {
       self$codes_lookup <- tibble(
         state_name = c(

diff --git a/R/Canada.R b/R/Canada.R
@@ -44,7 +44,7 @@ Canada <- R6::R6Class("Canada",
     source_url = "https://open.canada.ca/data/en/dataset/261c32ab-4cfd-4f81-9dea-7b64065690dc", # nolint
 
     #' @description Set up a table of region codes for clean data
-    #' @importFrom tibble tibble
+    #' @importFrom dplyr tibble
     set_region_codes = function() {
       canada_codes <- tibble(
         code = c(

diff --git a/R/Colombia.R b/R/Colombia.R
@@ -41,7 +41,6 @@ Colombia <- R6::R6Class("Colombia",
     source_url = "https://github.com/danielcs88/colombia_covid-19/",
 
     #' @description Set up a table of region codes for clean data
-    #' @importFrom tibble tibble
     #' @importFrom dplyr mutate
     set_region_codes = function() {
       self$codes_lookup$`1` <- covidregionaldata::colombia_codes

diff --git a/R/Cuba.R b/R/Cuba.R
@@ -42,7 +42,7 @@ Cuba <- R6::R6Class("Cuba",
 
 
     #' @description Set up a table of region codes for clean data
-    #' @importFrom tibble tibble
+    #' @importFrom dplyr tibble
     set_region_codes = function() {
       self$codes_lookup$`1` <- tibble(
         code = c(

diff --git a/R/Estonia.R b/R/Estonia.R
@@ -43,7 +43,7 @@ Estonia <- R6::R6Class("Estonia",
 
 
     #' @description Set up a table of region codes for clean data
-    #' @importFrom tibble tibble
+    #' @importFrom dplyr tibble
     set_region_codes = function() {
       self$codes_lookup$`1` <- tibble(
         code = c("EE-37",

diff --git a/R/France.R b/R/France.R
@@ -50,7 +50,6 @@ France <- R6::R6Class("France",
 
 
     #' @description Set up a table of region codes for clean data
-    #' @importFrom tibble tibble
     #' @importFrom dplyr select
     set_region_codes = function() {
       self$codes_lookup$`1` <- france_codes %>%

diff --git a/R/Germany.R b/R/Germany.R
@@ -44,8 +44,7 @@ Germany <- R6::R6Class("Germany",
 
 
     #' @description Set up a table of region codes for clean data
-    #' @importFrom tibble tibble
-    #' @importFrom dplyr mutate
+    #' @importFrom dplyr tibble
     set_region_codes = function() {
       self$codes_lookup$`1` <- tibble(
         code = c(

diff --git a/R/India.R b/R/India.R
@@ -37,7 +37,7 @@ India <- R6::R6Class("India",
     source_url = "https://www.covid19india.org",
 
     #' @description Set up a table of region codes for clean data
-    #' @importFrom tibble tibble
+    #' @importFrom dplyr tibble
     set_region_codes = function() {
       self$codes_lookup$`1` <- tibble(
         code = c(

diff --git a/R/Italy.R b/R/Italy.R
@@ -42,7 +42,7 @@ Italy <- R6::R6Class("Italy",
     source_url = "https://github.com/pcm-dpc/COVID-19/blob/master/README_EN.md",
 
     #' @description Set up a table of region codes for clean data
-    #' @importFrom tibble tibble
+    #' @importFrom dplyr tibble
     set_region_codes = function() {
       self$codes_lookup$`1` <- tibble(
         code = c(

diff --git a/R/JHU.R b/R/JHU.R
@@ -84,7 +84,6 @@ JHU <- R6::R6Class("JHU", # rename to country name
     source_url = "https://github.com/CSSEGISandData/COVID-19/",
 
     #' @description Set up a table of region codes for clean data
-    #' @importFrom tibble tibble
     set_region_codes = function() {
       self$codes_lookup$`1` <- JHU_codes
     },

diff --git a/R/Lithuania.R b/R/Lithuania.R
@@ -184,8 +184,7 @@ Lithuania <- R6::R6Class("Lithuania",
     #' @description Common data cleaning for both levels
     #'
     # nolint start
-    #' @importFrom dplyr mutate group_by summarise if_else filter select bind_rows rename left_join everything across lead
-    #' @importFrom tidyselect all_of
+    #' @importFrom dplyr mutate group_by summarise if_else filter select bind_rows rename left_join everything across lead all_of
     #' @importFrom lubridate as_date
     # nolint end
     clean_common = function() {
@@ -244,7 +243,7 @@ Lithuania <- R6::R6Class("Lithuania",
       # or qualitative)
       sum_cols <- names(select(
         self$data$raw$main,
-        "population":tidyselect::last_col()
+        "population":dplyr::last_col()
       ))
       sum_cols <- sum_cols[!grepl("prc|map_colors", sum_cols)]
 
@@ -345,7 +344,6 @@ Lithuania <- R6::R6Class("Lithuania",
     #' provided by the source at the level 2 (municipality) regional level.
     #'
     #' @importFrom dplyr group_by summarise ungroup full_join across if_else
-    #' @importFrom tidyselect vars_select_helpers
     clean_level_1 = function() {
       self$data$clean <- self$data$clean %>%
         group_by(
@@ -354,7 +352,7 @@ Lithuania <- R6::R6Class("Lithuania",
         ) %>%
         summarise(
           across(
-            tidyselect::vars_select_helpers$where(is.numeric),
+            where(is.numeric),
             sum
           )
         ) %>%

diff --git a/R/Mexico.R b/R/Mexico.R
@@ -54,7 +54,6 @@ Mexico <- R6::R6Class("Mexico",
     source_url = "https://datos.covid-19.conacyt.mx",
 
     #' @description Set up a table of region codes for clean data
-    #' @importFrom tibble tibble
     #' @importFrom dplyr select
     set_region_codes = function() {
       self$codes_lookup$`1` <- covidregionaldata::mexico_codes %>%

diff --git a/R/Netherlands.R b/R/Netherlands.R
@@ -46,7 +46,6 @@ Netherlands <- R6::R6Class("Netherlands",
     source_url = "https://data.rivm.nl/covid-19/",
 
     #' @description Set up a table of region codes for clean data
-    #' @importFrom tibble tibble
     set_region_codes = function() {
 
     },

diff --git a/R/SouthAfrica.R b/R/SouthAfrica.R
@@ -41,7 +41,7 @@ SouthAfrica <- R6::R6Class("SouthAfrica",
     source_url = "https://github.com/dsfsi/covid19za",
 
     #' @description Set up a table of region codes for clean data
-    #' @importFrom tibble tibble
+    #' @importFrom dplyr tibble
     set_region_codes = function() {
       self$codes_lookup$`1` <- tibble(
         code = c(

diff --git a/R/Switzerland.R b/R/Switzerland.R
@@ -44,7 +44,7 @@ Switzerland <- R6::R6Class("Switzerland",
     source_url = "https://www.covid19.admin.ch/en/overview",
 
     #' @description Set up a table of region codes for clean data
-    #' @importFrom tibble tibble
+    #' @importFrom dplyr tibble
     set_region_codes = function() {
       self$codes_lookup$`1` <- tibble(
         code = c(

diff --git a/R/UK.R b/R/UK.R
@@ -450,8 +450,7 @@ UK <- R6::R6Class("UK",
     #'     Section 2, "2. Estimated new hospital cases"
     #' @importFrom lubridate year month
     #' @importFrom readxl read_excel cell_limits
-    #' @importFrom tibble as_tibble
-    #' @importFrom dplyr mutate select %>% group_by summarise left_join
+    #' @importFrom dplyr mutate select %>% group_by summarise left_join as_tibble
     #' @importFrom tidyr pivot_longer
     #' @param clean_data Cleaned UK covid-19 data
     #' @param nhs_data NHS region data

diff --git a/R/USA.R b/R/USA.R
@@ -49,7 +49,7 @@ USA <- R6::R6Class("USA",
     source_url = "https://github.com/nytimes/covid-19-data",
 
     #' @description Set up a table of region codes for clean data
-    #' @importFrom tibble tribble
+    #' @importFrom dplyr tibble
     set_region_codes = function() {
       self$codes_lookup <- usa_codes <- tibble(
         level_1_region_code = c(

diff --git a/R/Vietnam.R b/R/Vietnam.R
@@ -47,7 +47,6 @@ Vietnam <- R6::R6Class("Vietnam",
     source_url = "https://covid19.ncsc.gov.vn",
 
     #' @description Set up a table of region codes for clean data
-    #' @importFrom tibble tibble
     set_region_codes = function() {
       self$codes_lookup$`1` <- covidregionaldata::vietnam_codes
     },
@@ -65,8 +64,7 @@ Vietnam <- R6::R6Class("Vietnam",
     #' @importFrom dplyr filter select mutate rename tibble as_tibble full_join
     #' @importFrom tidyr replace_na drop_na separate
     #' @importFrom purrr map
-    #' @importFrom stringi stri_trans_general stri_trim_both stri_replace_all
-    #' @importFrom stringr str_to_title str_replace_all
+    #' @importFrom stringr str_conv str_trim str_to_title str_replace_all
     #' @importFrom lubridate dmy
     clean_common = function() {
       # The first three elements of self$data$raw are the data
@@ -121,8 +119,8 @@ Vietnam <- R6::R6Class("Vietnam",
         #
         #tidyr::drop_na(date, region_name) %>%
         mutate(
-          level_1_region = stri_trans_general(level_1_region, "latin-ascii"),
-          level_1_region = stri_trim_both(level_1_region),
+          level_1_region = str_conv(level_1_region, "ASCII"),
+          level_1_region = str_trim(level_1_region, side = "both"),
           level_1_region = str_replace_all(level_1_region,
                                            "\\(.*\\)|-| ", ""),
           level_1_region = str_to_title(level_1_region),

diff --git a/R/get_available_datasets.R b/R/get_available_datasets.R
@@ -18,7 +18,6 @@
 #' @family interface
 #' @importFrom rlang .data
 #' @importFrom dplyr select bind_rows filter
-#' @importFrom tibble as_tibble
 #' @export
 #' @examples
 #' # see all available datasets

diff --git a/R/get_linelist.R b/R/get_linelist.R
@@ -24,7 +24,6 @@
 #' @importFrom lifecycle deprecate_warn
 #' @importFrom dplyr if_else select mutate filter
 #' @importFrom lubridate dmy
-#' @importFrom tibble as_tibble
 #' @importFrom utils download.file untar
 #' @examples
 #' \dontrun{