## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----echo = FALSE------------------------------------------------------------- pkgVersion <- packageDescription("EpiReport")$Version pkgDate <- packageDescription("EpiReport")$Date authorsString <- gsub("^ *|(?<= ) |\n| *$", "", packageDescription("EpiReport")$Authors, perl = TRUE) authorList <- eval(parse(text = authorsString)) pkgAuthors <- paste(format(authorList, include = c("given", "family", "email", "comment"), braces = list(email = c("<", ">,<br />"), comment = c("", ""))), collapse = "<br /><br />") pkgMaintainer <- packageDescription("EpiReport")$Maintainer pkgLicense <- packageDescription("EpiReport")$License pkgUrl <- packageDescription("EpiReport")$URL ## ----echo=FALSE, results='asis'----------------------------------------------- my_dataset <- EpiReport::SALM2016 my_dataset <- dplyr::select(my_dataset, c("HealthTopicCode", "MeasurePopulation", "MeasureCode", "TimeUnit", "TimeCode", "GeoCode", "XLabel", "YLabel", "ZValue", "YValue", "N")) knitr::kable(my_dataset[sample(1:nrow(EpiReport::SALM2016), 10), ], row.names = FALSE, format = "html", table.attr = 'class="myTable"', caption = "__Tab.1 Example of Salmonellosis data 2012-2016__") ## ----echo=FALSE, results='asis'----------------------------------------------- my_dataset <- EpiReport::AERparams my_dataset <- dplyr::select(my_dataset, c("HealthTopic", "MeasurePopulation", "TableUse", "AgeGenderUse", "TSTrendGraphUse", "TSSeasonalityGraphUse", "MapNumbersUse", "MapRatesUse", "MapASRUse")) knitr::kable(my_dataset[sample(1:nrow(EpiReport::AERparams), 5), ], row.names = FALSE, format = "html", table.attr = 'class="myTable"', caption = "__Tab.2 Example of the main columns of the parameter dataset__") ## ----echo=FALSE, results='asis'----------------------------------------------- my_dataset <- EpiReport::MSCode knitr::kable(my_dataset[sample(1:nrow(EpiReport::MSCode), 5), ], row.names = FALSE, format = "html", table.attr = 'class="myTable"', caption = "__Tab.3 Example of geographical codes and associated labels__") ## ----eval=FALSE--------------------------------------------------------------- # getAER() ## ----eval=FALSE--------------------------------------------------------------- # output <- "C:/EpiReport/doc/" # getAER(outputPath = output) ## ----warning=FALSE------------------------------------------------------------ # --- Importing the dataset PERT2016 <- read.table("data/PERT2016.csv", sep = ",", header = TRUE, stringsAsFactors = FALSE) # --- Specifying the folder containing pertussis maps pathMap <- paste(getwd(), "/maps", sep = "") # --- (optional) Setting the local language in English for month label Sys.setlocale("LC_TIME", "C") # --- Producing the report EpiReport::getAER(disease = "PERT", year = 2016, x = PERT2016, pathPNG = pathMap) ## ----eval = FALSE------------------------------------------------------------- # getTemplate(output_path = "C:/EpiReport/template") ## ----eval = FALSE------------------------------------------------------------- # getAER(template = "C:/EpiReport/template/New_AER_Template.docx", # outputPath = "C:/EpiReport/doc/") ## ----eval = FALSE------------------------------------------------------------- # EpiReport::getTableByMS() ## ----echo = FALSE------------------------------------------------------------- knitr::knit_print(EpiReport::getTableByMS()) ## ----eval = FALSE------------------------------------------------------------- # ZIKV2016 <- read.table("data/ZIKV2016.csv", # sep = ",", # header = TRUE, # stringsAsFactors = FALSE) # EpiReport::getTableByMS(x = ZIKV2016, # disease = "ZIKV", # year = 2016) ## ----echo = FALSE------------------------------------------------------------- ZIKV2016 <- read.table("data/ZIKV2016.csv", sep = ",", header = TRUE, stringsAsFactors = FALSE) knitr::knit_print(EpiReport::getTableByMS(x = ZIKV2016, disease = "ZIKV", year = 2016)) ## ----fig.width = 7------------------------------------------------------------ # --- Salmonellosis 2016 plot EpiReport::getSeason() ## ----fig.width = 7------------------------------------------------------------ # --- Pertussis 2016 plot EpiReport::getSeason(x = PERT2016, disease = "PERT", year = 2016) ## ----fig.width = 7------------------------------------------------------------ # --- Salmonellosis 2016 plot EpiReport::getTrend() ## ----fig.width = 7------------------------------------------------------------ # --- Pertussis 2016 plot EpiReport::getTrend(x = PERT2016, disease = "PERT", year = 2016) ## ----fig.width = 7, fig.height=5, fig.retina=4, results='hide'---------------- # --- Salmonellosis 2016 map EpiReport::getMap() ## ----eval = FALSE------------------------------------------------------------- # # --- Pertussis 2016 map # EpiReport::getMap(disease = "PERT", # year = 2016, # pathPNG = "C:/EpiReport/maps/") ## ----fig.width = 7------------------------------------------------------------ # --- Salmonellosis 2016 bar graph EpiReport::getAgeGender() ## ----fig.width = 7------------------------------------------------------------ # --- Zika 2016 bar graph EpiReport::getAgeGender(x = ZIKV2016, disease = "ZIKV", year = 2016)