## ----echo = FALSE------------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) library(episomer) package_name <- "episomer" package_desc <- packageDescription(package_name) pkg_version <- package_desc$Version pkg_date <- package_desc$Date authors_str <- gsub("^ *|(?<= ) |\n| *$", "", package_desc$Authors, perl = TRUE) author_list <- eval(parse(text = authors_str)) pkg_authors <- paste( format( author_list, include = c("given", "family", "email", "comment"), braces = list( email = c("<", ">,
"), comment = c("", "") ) ), collapse = "

" ) pkg_maintainer <- package_desc$Maintainer pkg_license <- package_desc$License pkg_url <- package_desc$URL ## ----echo=FALSE, fig.cap="", out.width = '100%'------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/dashboard.png") ## ----echo=FALSE, fig.cap="", out.width = '100%'------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/alerts.png") ## ----echo=FALSE, fig.cap="", out.width = '100%'------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/geotag_evaluation.png") ## ----echo=FALSE, fig.cap="", out.width = '100%'------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/data_protection.png") ## ----echo=FALSE, fig.cap="", out.width = '100%'------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/config.png") ## ----echo=FALSE, fig.cap="", out.width = '100%'------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/troubleshoot.png") ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # install.packages(episomer) ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # system("java -version") ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # Sys.getenv("JAVA_HOME") ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # library(episomer) # episomer_app("data_dir") ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # library(episomer) # episomer_app("data_dir") ## ----echo=FALSE, fig.cap="", out.width = '50%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/run_tasks.png") ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # library(episomer) # fs_loop("data_dir") ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # library(episomer) # search_loop("data_dir") ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # library(episomer) # detect_loop("data_dir") ## ----echo=FALSE, fig.cap="", out.width = '50%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/bluesky_authentication.png") ## ----echo=FALSE, fig.cap="", out.width = '100%'------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/topics.png") ## ----echo=FALSE, fig.cap="", out.width = '80%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/Example_topics_list.png") ## ----echo=FALSE, fig.cap="", out.width = '80%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/Schedule_plan_image.png") ## ----echo=FALSE, fig.cap="", out.width = '80%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/Search_plan_queues.png") ## ----echo=FALSE, fig.cap="", out.width = '80%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/config_languages.png") ## ----echo=FALSE, fig.cap="", out.width = '100%'------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/subscribers.png") ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # episomer_app("data_dir") ## ----eval=FALSE, echo=TRUE---------------------------------------------------- # # Opens only the interactive dashboard # dashboard_app("data_dir") # # # Opens only the rest of the features with the administrative # admin_app("data_dir") ## ----echo=FALSE, fig.cap="", out.width = '40%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/topics_countries.png") ## ----echo=FALSE, fig.cap="", out.width = '40%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/period.png") ## ----echo=FALSE, fig.cap="", out.width = '30%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/time_unit.png") ## ----echo=FALSE, fig.cap="", out.width = '30%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/include_quotes.png") ## ----echo=FALSE, fig.cap="", out.width = '30%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/signal_detection_fpr.png") ## ----echo=FALSE, fig.cap="", out.width = '40%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/outlier_dashboard.png") ## ----echo=FALSE, fig.cap="", out.width = '30%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/Bonferroni_correction.png") ## ----echo=FALSE, fig.cap="", out.width = '30%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/days_in_baseline.png") ## ----echo=FALSE, fig.cap="", out.width = '30%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/same_weekday_baseline.png") ## ----echo=FALSE, fig.cap="", out.width = '30%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/hover_trendline.png") ## ----echo=FALSE, fig.cap="", out.width = '60%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/hover_map.png") ## ----echo=FALSE, fig.cap="", out.width = '50%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/top_words.png") ## ----echo=FALSE, fig.cap="", out.width = '100%'------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/alerts.png") ## ----echo=FALSE, fig.cap="", out.width = '100%'------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/geotag_evaluation.png") ## ----echo=FALSE, fig.cap="", out.width = '100%'------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/config.png") ## ----echo=FALSE, fig.cap="", out.width = '50%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/status.png") ## ----echo=FALSE, fig.cap="", out.width = '70%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/detection_pipeline.png") ## ----echo=FALSE, fig.cap="", out.width = '50%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/signal_detection_config.png") ## ----echo=FALSE, fig.cap="", out.width = '40%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/general.png") ## ----echo=FALSE, fig.cap="", out.width = '30%'-------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/region_disclaimer.png") ## ----echo=FALSE, fig.cap="", out.width = '100%'------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/topics.png") ## ----echo=FALSE, fig.cap="", out.width = '100%'------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/languages.png") ## ----echo=FALSE, fig.cap="", out.width = '100%'------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/troubleshoot.png") ## ----echo=FALSE, fig.cap="", out.width = '100%'------------------------------- knitr::include_graphics("https://raw.githubusercontent.com/EU-ECDC/episomer/main/img/ebola.png")