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Fix 104 #109

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merged 2 commits into from
Jul 22, 2024
+11 −6
Merged

Fix 104 #109

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f8544ce
Use readr to read in parameter type mapping
sangeetabhatia03 Jul 19, 2024
aef8c71
Bump up version number and update NEWS
sangeetabhatia03 Jul 19, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: epireview
Title: Tools to update and summarise the latest pathogen data from the Pathogen Epidemiology Review Group (PERG)
Version: 1.3.0
Version: 1.3.1
Authors@R: c(
person("Rebecca", "Nash", email = "r.nash@imperial.ac.uk", role = "aut",
comment = c(ORCID = "0000-0002-5213-4364")),
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2 changes: 1 addition & 1 deletion NAMESPACE
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Expand Up @@ -124,6 +124,7 @@ importFrom(readr,col_double)
importFrom(readr,col_integer)
importFrom(readr,col_logical)
importFrom(readr,read_csv)
importFrom(readr,read_delim)
importFrom(readr,write_csv)
importFrom(scales,squish)
importFrom(stats,na.omit)
Expand All @@ -139,7 +140,6 @@ importFrom(tidyr,pivot_wider)
importFrom(tidyr,replace_na)
importFrom(tm,removeNumbers)
importFrom(utils,globalVariables)
importFrom(utils,read.csv2)
importFrom(validate,"%vin%")
importFrom(validate,confront)
importFrom(validate,summary)
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4 changes: 4 additions & 0 deletions NEWS.md
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@@ -1,3 +1,7 @@
# epireview 1.3.1

* BUG-FIX: Fixes #104 using readr::read_delim to read in parameter type short names

# epireview 1.3.0

* MAJOR RELEASE
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9 changes: 5 additions & 4 deletions R/load_epidata.R
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Propose that perhaps @sangeetabhatia03 if we have varying delimiters we move all read_csv() to read_delim() so that we can handle multiple delimiters without coding for exceptions. Not urgent, but relates to lowering our dependency footprint and variability in function convention.

Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ short_parameter_type <- function(x, parameter_type_full, parameter_type_short) {
#' of the outbreaks extracted for this pathogen, where available.
#'
#' @importFrom dplyr left_join
#' @importFrom utils read.csv2
#' @importFrom readr read_delim
#' @importFrom cli cli_alert_info cli_alert_warning cli_abort cli_alert_success
#' @export
load_epidata <- function(pathogen, mark_multiple = TRUE) {
Expand Down Expand Up @@ -138,9 +138,10 @@ load_epidata <- function(pathogen, mark_multiple = TRUE) {
)
articles_everything <- articles
articles <- articles[, cols]

param_names <- read.csv2(
system.file("extdata", "param_name.csv", package = "epireview")

param_names <- read_delim(
system.file("extdata", "param_name.csv", package = "epireview"),
delim = ";"
)
params <- short_parameter_type(
params, param_names$parameter_type_full, param_names$parameter_type_short
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