Initial commit

.gitattributes

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+# Auto detect text files and perform LF normalization
+* text=auto

.gitignore

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+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+/*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md

CoV19.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX

DESCRIPTION

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+Package: CoV19
+Type: Package
+Title: Eli's package for figures and data on CoV-19 epidemic
+Version: 1.0
+Date: 2020-03-22
+Depends: 
+   R (>= 2.15.0), 
+   stringr, 
+   rmarkdown, 
+   knitr, 
+   ggplot2,
+   grid
+Imports: Rdpack
+Author: Eli Holmes, Seattle, USA
+Maintainer: [email protected]
+Description: Code, figures and data
+License: GPL-2
+LazyData: yes
+BuildVignettes: yes
+ByteCompile: TRUE
+RdMacros: Rdpack
+VignetteBuilder: knitr
+RoxygenNote: 7.0.2
+Remotes: github::rstudio/rmarkdown
+Encoding: UTF-8

NAMESPACE

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+## export functions
+export(
+  getdatacovidtracking,
+  getdatajhu
+)
+
+## Imports
+import(ggplot2)

R/README.md

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+This is a package for exploring some of the CoV-19 data. The world data is downloaded from JHU. The US data is downloaded from JHU and CovidTracking. The Italy data is downloaded from the Italian CDC (Protezione Civile) 
+
+Sources:
+* https://github.com/CSSEGISandData/COVID-19
+* https://covidtracking.com/api/ 
+* https://github.com/pcm-dpc/COVID-19
+
+To install the package
+
+```
+library(devtools)
+install_github(eeholmes/CoV19)
+```
+
+To get the data:
+```
+statedata
+italydata
+worlddata
+```
+Use `head()` to look at it. Should be pretty self-evident what it is.
+
+
+

R/getdatacovidtracking.R

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+#' Download state data from Covid Tracking
+#' 
+#' @param append Whether to append current numbers to an existing data frame (append=TRUE) or to download the whole time series again (append=FALSE).
+#' @return Saves a data frame to the data folder.
+#' @examples
+#' getdatacovidtrackint
+getdatacovidtracking <- function(append=TRUE){
+  if(append){
+    if(max(statedatadate) < Sys.Date()-1){
+      cat(paste0("No update because the state data file max date is ", max(statedatadate), " and appending would skip a day.\n"))
+      return()
+      }
+    }
+  if(!append){
+    url <- "http://covidtracking.com/api/states/daily.csv"
+    statedata <- try(read.csv(url), silent=TRUE)
+    if(!inherits(statedata, "try-error")){
+      save(statedata, file="states.RData")
+    }else{
+      cat("Server error. Data could not be downloaded.\n")
+      return()
+    }
+  }else{
+    load("data/states.RData")
+    statedatadate <- as.Date(statedata$dateChecked)
+    if(max(statedatadate) == Sys.Date()){
+      ans <- readline("The state data is has the same date as current date. Still update? (y/n)")
+      if(ans != "y"){ cat("No update.\n"); return() }
+    }
+    save(statedata, file="data/statesold.RData")
+    url <- "https://covidtracking.com/api/states.csv"
+    stateday <- read.csv(url)
+    stateday$date <- format(as.Date(stateday$dateChecked),"%Y%m%d")
+    daydate <- as.Date(stateday$dateChecked)[1]
+    statedata <- statedata[statedatadate != daydate,]
+    statecols <- colnames(statedata)
+    statedata <- rbind(stateday[,statecols],statedata)
+    save(statedata, file="data/states.RData")
+  }
+}

R/getdataitaly.R

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+#' Download confirmed, deaths and recovered from github/pcm-dpc/COVID-19
+#' 
+#' @return Saves a data frame with region, date, positive, death, recovered, total hospitalized, and ICU to the data folder.
+#' @examples
+#' getdatajhu
+getdataitaly <- function(){
+  getx <- function(x, val){
+    x <- x[, !(colnames(x) %in% c("Lat","Long"))]
+    library(tidyr)
+    x %>% pivot_longer(cols=starts_with("X"),names_to="date", values_to = val)
+  }
+    url <- "https://raw.githubusercontent.com/pcm-dpc/COVID-19/master/dati-regioni/dpc-covid19-ita-regioni.csv"
+    italydata <- try(read.csv(url), silent=TRUE)
+    italydata$recovered <- italydata$totale_casi-italydata$totale_attualmente_positivi
+    #rename
+    iname <- c("data", "denominazione_regione", "totale_casi", "deceduti", "recovered", "totale_ospedalizzati", "terapia_intensiva")
+    italydata <- italydata[,iname]
+    colnames(italydata) <- c("date", "region", "positive", "death", "recovered", "hospitalized", "ICU")
+
+    italydata$date <- as.Date(italydata$date)
+    save(italydata, file="data/italy.RData")
+  }
+}

R/getdatajhu.R

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+#' Download confirmed, deaths and recovered from JHU
+#' 
+#' @return Saves a data frame with Province.State, Country.Region, date, positive, death, and recovered to the data folder.
+#' @examples
+#' getdatajhu
+getdatajhu <- function(){
+  getx <- function(x, val){
+    x <- x[, !(colnames(x) %in% c("Lat","Long"))]
+    library(tidyr)
+    x %>% pivot_longer(cols=starts_with("X"),names_to="date", values_to = val)
+  }
+    url <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Confirmed.csv"
+    worlddataconfirmed <- try(read.csv(url), silent=TRUE)
+    url <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Deaths.csv"
+    worlddatadeaths <- try(read.csv(url), silent=TRUE)
+    url <- "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Recovered.csv"
+    worlddatarecovered <- try(read.csv(url), silent=TRUE)
+
+    worlddata <- cbind(getx(worlddataconfirmed,"positive"),death=getx(worlddatadeaths,"death")$death, recovered=getx(worlddatarecovered,"recovered")$recovered)
+
+    worlddata$date <- as.Date(str_remove(worlddata$date,"X"),"%m.%d.%y")
+    save(worlddata, file="data/world.RData")
+  }
+}