## ----setup, include = FALSE----------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ---- echo = FALSE-------------------------------------------------------
pkgVersion <- packageDescription("EpiSignalDetection")$Version
pkgDate <- packageDescription("EpiSignalDetection")$Date
authorsString <- gsub("^ *|(?<= ) |\n| *$", "",
packageDescription("EpiSignalDetection")$Authors, perl = TRUE)
authorList <- eval(parse(text = authorsString))
pkgAuthors <- paste(format(authorList,
include = c("given", "family", "email", "comment"),
braces = list(email = c("<", ">,<br />"), comment = c("", ""))),
collapse = "<br /><br />")
pkgMaintainer <- packageDescription("EpiSignalDetection")$Maintainer
pkgLicense <- packageDescription("EpiSignalDetection")$License
pkgUrl <- packageDescription("EpiSignalDetection")$URL
## ---- eval=FALSE, echo=TRUE----------------------------------------------
# install.packages("EpiSignalDetection")
# library(EpiSignalDetection)
# EpiSignalDetection::runEpiSDApp()
## ---- echo=FALSE, results='asis'-----------------------------------------
my_dataset <- EpiSignalDetection::importAtlasExport("./data/ECDC_surveillance_data_Pertussis_20180717.csv")
knitr::kable(head(my_dataset),
format = "html", table.attr = 'class="myTable"',
format.args = list(decimal.mark = ".", big.mark = ","),
align = 'c',
caption = "__Tab.1 Example of Pertussis data exported from the ECDC Atlas__")
## ---- echo=FALSE, results='asis'-----------------------------------------
my_dataset <- EpiSignalDetection::SignalData
my_dataset <- dplyr::filter(my_dataset, my_dataset$HealthTopic == "Salmonellosis")
my_dataset <- dplyr::group_by_(my_dataset, c("Population") )
my_dataset <- dplyr::summarise(my_dataset, "NumValue" = sum(NumValue, na.rm = TRUE))
my_dataset <- dplyr::ungroup(my_dataset)
my_dataset <- dplyr::arrange(my_dataset, desc(my_dataset$NumValue))
knitr::kable(my_dataset,
format = "html", table.attr = 'class="myTable"',
format.args = list(decimal.mark = ".", big.mark = ","),
align = 'c',
caption = "__Tab.2 Number of cases in each stratum using Salmonellosis data exported from the ECDC Atlas__")
## ------------------------------------------------------------------------
my_parameters <- EpiSignalDetection::AlgoParam
names(my_parameters)
## ---- echo = FALSE-------------------------------------------------------
knitr::kable(my_parameters$FarringtonFlexible,
format = "html", table.attr = 'class="myTable"',
format.args = list(decimal.mark = ".", big.mark = ","),
align = 'c',
caption = "__Tab.3 Parameters for the Farrington Flexible algorithm__")
knitr::kable(my_parameters$GLRNB,
format = "html", table.attr = 'class="myTable"',
format.args = list(decimal.mark = ".", big.mark = ","),
align = 'c',
caption = "__Tab.4 Parameters for the GLRNB algorithm__")
## ---- echo = FALSE, results = 'hide'-------------------------------------
my_input <- list(
disease = "Salmonellosis",
country = "EU-EEA - complete series",
indicator = "Reported cases",
stratification = "Confirmed cases",
unit = "Month",
daterange = c("2012-01-01", "2016-12-31"),
algo = "FarringtonFlexible",
testingperiod = 5
)
png(file = "plots/plot_time_series.png", width = 1450, height = 500, res=90)
EpiSignalDetection::plotSD(input = my_input)
dev.off()
## ------------------------------------------------------------------------
my_dataset <- EpiSignalDetection::SignalData
knitr::kable(head(my_dataset))
## ------------------------------------------------------------------------
my_input <- list(
disease = "Salmonellosis",
country = "EU-EEA - complete series",
indicator = "Reported cases",
stratification = "Confirmed cases",
unit = "Month",
daterange = c("2012-01-01", "2016-12-31"),
algo = "FarringtonFlexible",
testingperiod = 5
)
## ---- eval = FALSE-------------------------------------------------------
# EpiSignalDetection::plotSD(input = my_input)
## ---- eval = FALSE-------------------------------------------------------
# EpiSignalDetection::runEpiSDReport(
# outputfile = "C:/R/test.html",
# input = my_input)
## ---- eval = FALSE-------------------------------------------------------
# EpiSignalDetection::runEpiSDReport(
# outputfile = "C:/R/test.html",
# input = my_input,
# stratified = TRUE)
## ---- eval = FALSE-------------------------------------------------------
# EpiSignalDetection::runEpiSDReport()
# [1] "Dataset (please enter the full path to the csv file, or just press 'Enter' to use the default dataset)"
# 1:
# Read 0 items
# [1] "Disease / Health topic (e.g. Salmonellosis):"
# 1: Salmonellosis
# Read 1 item
# [1] "Region name (e.g. EU-EEA - complete series):"
## ------------------------------------------------------------------------
my_dataset <- EpiSignalDetection::importAtlasExport("./data/ECDC_surveillance_data_Pertussis_20180717.csv")
## ------------------------------------------------------------------------
my_dataset <- EpiSignalDetection::cleanAtlasExport(my_dataset)
## ------------------------------------------------------------------------
my_input <- list(
disease = "Pertussis",
country = "EU-EEA - complete series",
indicator = "Reported cases",
stratification = "All cases",
unit = "Month",
daterange = c("2012-01-01", "2016-12-31"),
algo = "FarringtonFlexible",
testingperiod = 6
)
## ------------------------------------------------------------------------
my_dataset <- EpiSignalDetection::filterAtlasExport(my_dataset, my_input)
## ------------------------------------------------------------------------
my_dataset <- EpiSignalDetection::aggAtlasExport(my_dataset, my_input)
## ---- eval = FALSE-------------------------------------------------------
# EpiSignalDetection::plotSD(x = my_dataset, input = my_input)
## ---- echo = FALSE, results = 'hide'-------------------------------------
png(file = "plots/plot_time_series_external.png", width = 1450, height = 500, res=90)
EpiSignalDetection::plotSD(x = my_dataset, input = my_input)
dev.off()
## ---- eval = FALSE-------------------------------------------------------
# my_input <- list(
# file = list(datapath = "C:/data/ECDC_surveillance_data_Pertussis_20180717.csv"),
# disease = "Pertussis",
# country = "Greece",
# indicator = "Reported cases",
# stratification = "All cases",
# unit = "Month",
# daterange = c("2011-12-01", "2016-12-01"),
# algo = "FarringtonFlexible",
# testingperiod = 3
# )
#
# EpiSignalDetection::runEpiSDReport(input = my_input)
## ---- eval = FALSE-------------------------------------------------------
# my_input <- list(
# file = list(datapath = "C:/data/ECDC_surveillance_data_Salmonella_20180717.csv"),
# disease = "Salmonellosis",
# country = "EU-EEA - complete series",
# indicator = "Reported cases",
# stratification = "Confirmed cases",
# unit = "Month",
# daterange = c("2011-12-01", "2016-12-01"),
# algo = "FarringtonFlexible",
# testingperiod = 6
# )
#
# EpiSignalDetection::runEpiSDReport(input = my_input, stratified = TRUE)
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