From 615547285506ac3f73849c16e98e996943a914c4 Mon Sep 17 00:00:00 2001
From: boB Rudis <bob@rud.is>
Date: Sun, 12 Nov 2017 16:12:38 -0500
Subject: [PATCH] ilinet years parameter added

---
 .Rbuildignore     |  1 +
 Makefile          | 44 ++++++++++++++++++++++++++++++++++++++++++++
 R/ilinet.r        | 33 ++++++++++++++++++++++++++++++---
 man/ilinet.Rd     |  9 ++++++++-
 man/who_nrevss.Rd |  3 ++-
 5 files changed, 85 insertions(+), 5 deletions(-)
 create mode 100644 Makefile

diff --git a/.Rbuildignore b/.Rbuildignore
index 172071b..1f58f13 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -14,6 +14,7 @@
 ^\.Rproj\.user$
 ^\.travis\.yml$
 ^.*md$
+^crunch
 ^crunch/
 ^crunch/.*
 ^README_files/
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..194d0ce
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,44 @@
+PACKAGE := $(shell grep '^Package:' DESCRIPTION | sed -E 's/^Package:[[:space:]]+//')
+RSCRIPT = Rscript --no-init-file
+
+all: install
+
+test:
+	${RSCRIPT} -e 'library(methods); devtools::test()'
+
+roxygen:
+	@mkdir -p man
+	${RSCRIPT} -e "library(methods); devtools::document()"
+
+install:
+	R CMD INSTALL .
+
+build:
+	R CMD build .
+
+check:
+	_R_CHECK_CRAN_INCOMING_=FALSE make check_all
+
+check_all:
+	${RSCRIPT} -e "rcmdcheck::rcmdcheck(args = c('--as-cran', '--no-manual'))"
+
+staticdocs:
+	@mkdir -p inst/staticdocs
+	${RSCRIPT} -e "library(methods); staticdocs::build_site()"
+	rm -f vignettes/*.html
+	@rmdir inst/staticdocs
+website: staticdocs
+	./update_web.sh
+
+README.md: README.Rmd
+	Rscript -e 'library(methods); devtools::load_all(); knitr::knit("README.Rmd")'
+	sed -i.bak 's/[[:space:]]*$$//' $@
+	rm -f $@.bak
+
+vignettes/%.Rmd: vignettes/src/%.R
+	${RSCRIPT} -e 'library(sowsear); sowsear("$<", output="$@")'
+vignettes: vignettes/cyphr.Rmd vignettes/data.Rmd
+	${RSCRIPT} -e 'library(methods); devtools::build_vignettes()'
+
+# No real targets!
+.PHONY: all test document install vignettes
diff --git a/R/ilinet.r b/R/ilinet.r
index 9625f58..75d76d4 100644
--- a/R/ilinet.r
+++ b/R/ilinet.r
@@ -10,6 +10,12 @@
 #'
 #' @md
 #' @param region one of "`national`", "`hhs`", "`census`", or "`state`"
+#' @param years a vector of years to retrieve data for (i.e. `2014` for CDC
+#'        flu season 2014-2015). CDC has data for this API going back to 1997.
+#'        Default value (`NULL`) means retrieve **all** years. NOTE: if you
+#'        happen to specify a 2-digit season value (i.e. `57` == 2017-2018)
+#'        the function is smart enough to retrieve by season ID vs convert that
+#'        to a year.
 #' @references
 #' - [CDC FluView Portal](https://gis.cdc.gov/grasp/fluview/fluportaldashboard.html)
 #' - [ILINet Portal](https://wwwn.cdc.gov/ilinet/) (Login required)
@@ -26,10 +32,12 @@
 #'   c("national", "hhs", "census", "state"),
 #'   ~ilinet(.x) %>% readr::type_convert())
 #' }
-ilinet <- function(region=c("national", "hhs", "census", "state")) {
+ilinet <- function(region=c("national", "hhs", "census", "state"), years=NULL) {
 
   region <- match.arg(tolower(region), c("national", "hhs", "census", "state"))
 
+  meta <- jsonlite::fromJSON("https://gis.cdc.gov/grasp/flu2/GetPhase02InitApp?appVersion=Public")
+
   list(
     AppVersion = "Public",
     DatasourceDT = list(list(ID = 1, Name = "ILINet")),
@@ -43,8 +51,27 @@ ilinet <- function(region=c("national", "hhs", "census", "state")) {
     state = { lapply(1:59, function(i) list(ID=i, Name=as.character(i))) }
   )
 
-  seasons <- 37:((unclass(as.POSIXlt(Sys.time()))[["year"]] + 1900) - 1960)
-  params$SeasonsDT <- lapply(seasons, function(i) list(ID=i, Name=as.character(i)))
+  available_seasons <- sort(meta$seasons$seasonid)
+
+  if (is.null(years)) { # ALL YEARS
+    years <- available_seasons
+  } else { # specified years or seasons or a mix
+
+    years <- as.numeric(years)
+    years <- ifelse(years > 1996, years - 1960, years)
+    years <- sort(unique(years))
+    years <- years[years %in% available_seasons]
+
+    if (length(years) == 0) {
+      years <- rev(sort(meta$seasons$seasonid))[1]
+      curr_season_descr <- meta$seasons[meta$seasons$seasonid == years, "description"]
+      message(sprintf("No valid years specified, defaulting to this flu season => ID: %s [%s]",
+                      years, curr_season_descr))
+    }
+
+  }
+
+  params$SeasonsDT <- lapply(years, function(i) list(ID=i, Name=as.character(i)))
 
   tf <- tempfile(fileext = ".zip")
   td <- tempdir()
diff --git a/man/ilinet.Rd b/man/ilinet.Rd
index ada5bc9..1f110a3 100644
--- a/man/ilinet.Rd
+++ b/man/ilinet.Rd
@@ -4,10 +4,17 @@
 \alias{ilinet}
 \title{Retrieve ILINet Surveillance Data}
 \usage{
-ilinet(region = c("national", "hhs", "census", "state"))
+ilinet(region = c("national", "hhs", "census", "state"), years = NULL)
 }
 \arguments{
 \item{region}{one of "\code{national}", "\code{hhs}", "\code{census}", or "\code{state}"}
+
+\item{years}{a vector of years to retrieve data for (i.e. \code{2014} for CDC
+flu season 2014-2015). CDC has data for this API going back to 1997.
+Default value (\code{NULL}) means retrieve \strong{all} years. NOTE: if you
+happen to specify a 2-digit season value (i.e. \code{57} == 2017-2018)
+the function is smart enough to retrieve by season ID vs convert that
+to a year.}
 }
 \description{
 The CDC FluView Portal provides in-season and past seasons' national, regional,
diff --git a/man/who_nrevss.Rd b/man/who_nrevss.Rd
index ffcb728..60a4536 100644
--- a/man/who_nrevss.Rd
+++ b/man/who_nrevss.Rd
@@ -32,7 +32,8 @@ HHS, Census and State data retrieval is not as "instantaneous" as their ILINet
 counterparts.\cr\cr
 Also, beginning for the 2015-16 season, reports from public health and clinical
 laboratories are presented separately in the weekly influenza update. This is
-the reason why a list of data frames is returned.
+the reason why a list of data frames is returned.\cr\cr
+\strong{ALSO} The new CDC API seems to be missing some public health lab data fields.
 }
 \examples{
 \dontrun{