diff --git a/R/internal_functions.R b/R/internal_functions.R index 9b32d17..624b157 100644 --- a/R/internal_functions.R +++ b/R/internal_functions.R @@ -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) ) diff --git a/inst/SignalDetectionReport_HTML/SignalDetectionReport.Rmd b/inst/SignalDetectionReport_HTML/SignalDetectionReport.Rmd index d2dc6a8..cbb26ce 100644 --- a/inst/SignalDetectionReport_HTML/SignalDetectionReport.Rmd +++ b/inst/SignalDetectionReport_HTML/SignalDetectionReport.Rmd @@ -146,7 +146,7 @@ country(ies) reporting at least 1 case in the signal detection period. if(input$country == "EU-EEA - complete series") { datasetByCountry <- datasetTP %>% - dplyr::group_by_( c("RegionName") ) %>% + dplyr::group_by( dplyr::pick(dplyr::all_of(c("RegionName"))) ) %>% dplyr::summarise( NumValue = sum(NumValue) ) %>% dplyr::ungroup() @@ -193,7 +193,7 @@ Result <- data.frame( Time = "" , #-- Creation of a EU/EEA if(input$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) diff --git a/inst/StratifiedSignalDetectionReport_HTML/StratifiedSignalDetectionReport.Rmd b/inst/StratifiedSignalDetectionReport_HTML/StratifiedSignalDetectionReport.Rmd index f9d745b..c63cfb4 100644 --- a/inst/StratifiedSignalDetectionReport_HTML/StratifiedSignalDetectionReport.Rmd +++ b/inst/StratifiedSignalDetectionReport_HTML/StratifiedSignalDetectionReport.Rmd @@ -167,7 +167,7 @@ in the signal detection period, all strata added up. if(input$country == "EU-EEA - complete series") { datasetByCountry <- datasetTP %>% - dplyr::group_by_( c("RegionName") ) %>% + dplyr::group_by( dplyr::pick(dplyr::all_of(c("RegionName"))) ) %>% dplyr::summarise( NumValue = sum(NumValue) ) %>% dplyr::ungroup() @@ -265,7 +265,7 @@ Result <- data.frame( Time = "" , #-- Creation of a EU/EEA if(input$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) diff --git a/vignettes/EpiSignalDetection_Vignette.R b/vignettes/EpiSignalDetection_Vignette.R index 6657724..1e47e4f 100644 --- a/vignettes/EpiSignalDetection_Vignette.R +++ b/vignettes/EpiSignalDetection_Vignette.R @@ -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)) diff --git a/vignettes/EpiSignalDetection_Vignette.Rmd b/vignettes/EpiSignalDetection_Vignette.Rmd index d1ea78d..74f50b4 100644 --- a/vignettes/EpiSignalDetection_Vignette.Rmd +++ b/vignettes/EpiSignalDetection_Vignette.Rmd @@ -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))