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Avoid underscored function names #21

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2 changes: 1 addition & 1 deletion R/internal_functions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -355,7 +355,7 @@ aggAtlasExport <- function(x, input){

#-- Aggregation by time and place
RegionName <- NumValue <- NULL
x <- dplyr::group_by_(x, c("StudyPeriod") )
x <- dplyr::group_by(x, dplyr::pick(dplyr::all_of(c("StudyPeriod"))))
x <- dplyr::summarise(x,
"CasesByCountry" = paste(RegionName, " (", NumValue, ")", sep = "", collapse = ", "),
"NumValue" = sum(NumValue, na.rm = TRUE) )
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4 changes: 2 additions & 2 deletions inst/SignalDetectionReport_HTML/SignalDetectionReport.Rmd
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Expand Up @@ -146,7 +146,7 @@ country(ies) reporting at least 1 case in the signal detection period.
if(input$country == "EU-EEA - complete series") {

datasetByCountry <- datasetTP %>%
dplyr::group_by_( c("RegionName") ) %>%
dplyr::group_by( dplyr::pick(dplyr::all_of(c("RegionName"))) ) %>%
dplyr::summarise( NumValue = sum(NumValue) ) %>%
dplyr::ungroup()

Expand Down Expand Up @@ -193,7 +193,7 @@ Result <- data.frame( Time = "" ,
#-- Creation of a EU/EEA
if(input$country == "EU-EEA - complete series"){
datasetEU <- dataset %>%
dplyr::group_by_( c("StudyPeriod") ) %>%
dplyr::group_by( dplyr::pick(dplyr::all_of(c("StudyPeriod"))) ) %>%
dplyr::summarise( NumValue = sum(NumValue) ) %>%
dplyr::ungroup()
datasetEU <- data.frame(RegionName = "EU-EEA - complete series", datasetEU)
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4 changes: 2 additions & 2 deletions inst/StratifiedSignalDetectionReport_HTML/StratifiedSignalDetectionReport.Rmd
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Expand Up @@ -167,7 +167,7 @@ in the signal detection period, all strata added up.
if(input$country == "EU-EEA - complete series") {

datasetByCountry <- datasetTP %>%
dplyr::group_by_( c("RegionName") ) %>%
dplyr::group_by( dplyr::pick(dplyr::all_of(c("RegionName"))) ) %>%
dplyr::summarise( NumValue = sum(NumValue) ) %>%
dplyr::ungroup()

Expand Down Expand Up @@ -265,7 +265,7 @@ Result <- data.frame( Time = "" ,
#-- Creation of a EU/EEA
if(input$country == "EU-EEA - complete series"){
datasetEU <- dataset %>%
dplyr::group_by_("StudyPeriod", "Population" ) %>%
dplyr::group_by(dplyr::pick(dplyr::all_of(c("StudyPeriod", "Population")))) %>%
dplyr::summarise( NumValue = sum(NumValue) ) %>%
dplyr::ungroup()
datasetEU <- data.frame(RegionName = "EU-EEA - complete series", datasetEU)
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2 changes: 1 addition & 1 deletion vignettes/EpiSignalDetection_Vignette.R
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Expand Up @@ -34,7 +34,7 @@ knitr::kable(head(my_dataset),
## ---- echo=FALSE, results='asis'-----------------------------------------
my_dataset <- EpiSignalDetection::SignalData
my_dataset <- dplyr::filter(my_dataset, my_dataset$HealthTopic == "Salmonellosis")
my_dataset <- dplyr::group_by_(my_dataset, c("Population") )
my_dataset <- dplyr::group_by(my_dataset, dplyr::pick(dplyr::all_of(c("Population"))))
my_dataset <- dplyr::summarise(my_dataset, "NumValue" = sum(NumValue, na.rm = TRUE))
my_dataset <- dplyr::ungroup(my_dataset)
my_dataset <- dplyr::arrange(my_dataset, desc(my_dataset$NumValue))
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2 changes: 1 addition & 1 deletion vignettes/EpiSignalDetection_Vignette.Rmd
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Expand Up @@ -179,7 +179,7 @@ knitr::kable(head(my_dataset),
```{r, echo=FALSE, results='asis'}
my_dataset <- EpiSignalDetection::SignalData
my_dataset <- dplyr::filter(my_dataset, my_dataset$HealthTopic == "Salmonellosis")
my_dataset <- dplyr::group_by_(my_dataset, c("Population") )
my_dataset <- dplyr::group_by(my_dataset, dplyr::pick(dplyr::all_of("Population")) )
my_dataset <- dplyr::summarise(my_dataset, "NumValue" = sum(NumValue, na.rm = TRUE))
my_dataset <- dplyr::ungroup(my_dataset)
my_dataset <- dplyr::arrange(my_dataset, desc(my_dataset$NumValue))
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