Improve documentation and README

DESCRIPTION

@@ -1,15 +1,14 @@
 Package: HeatStress
 Type: Package
 Title: Calculate heat stress indices
-Version: 1.0.6
-Date: 2019-03-11
+Version: 1.0.7
+Date: 2019-07-01
 Author: A. Casanueva
 Maintainer: A.Casanueva <ana.casanueva@meteoswiss.ch>
 Description: Calculate heat stress indices based on meteorological data.
-License: file LICENCE
-RoxygenNote: 6.0.1
-Depends: R (>= 2.10.0)
+License: file LICENSE
+RoxygenNote: 6.1.1
+Depends: R (>= 2.10.0), magrittr
 Suggests: testthat, assertthat
 Imports: stats
-Encoding: ISO-8859-1
-
+Encoding: UTF-8

NAMESPACE

@@ -9,9 +9,13 @@ export(fTg)
 export(fTnwb)
 export(hi)
 export(humidex)
+export(indexShow)
 export(swbgt)
 export(tashurs2vap.pres)
 export(wbgt.Bernard)
 export(wbgt.Liljegren)
 export(wbt.Stull)
+importFrom(magrittr,"%>%")
 importFrom(stats,optimize)
+importFrom(utils,packageDescription)
+importFrom(utils,read.table)

NEWS

@@ -15,4 +15,10 @@ Changes in version 1.0.4
   * Inclusion of more heat indices.
 
 Changes in version 1.0.5
-  * Arrange assert statments in wrapper function to speed up calculation of wbgt.Liljegren.
+  * Arrange assert statments in wrapper function to speed up calculation of wbgt.Liljegren.
+
+Changes in version 1.0.6
+  * Correct bug in assertion statement.
+
+Changes in version 1.0.7
+  * Update README.md

R/HeatStress.R

@@ -4,8 +4,14 @@
 #' 
 #' The package \code{HeatStress} provides methods to calculate heat stress indices.
 #' 
-#' @name HeatStress 
-#' @docType package 
+#' Check the details of the indices and input variables: 
+#' 
+#' \code{library(HeatStress)}
+#' 
+#' \code{indexShow()}
+#' 
+#' 
+#' 
 #' @details 
 #' 
 #' The following calculation methods are implemented:
@@ -21,6 +27,9 @@
 #'  \item \code{discomInd}: Calculation of the discomfort index (Coccolo et al. 2016 and references therein).
 #'  \item \code{hi}: Calculation of the heat index (Buzan et al. 2015 and references therein).
 
-#'  } 
+#'  }
+#' @name HeatStress 
+#' @docType package 
+#'  
 NULL 
 #"_PACKAGE"

R/indexShow.R

@@ -0,0 +1,27 @@
+#' @title List all available heat indices
+#' @description Print a table with a summary of the available indices
+#' @return Print a table on the screen with the following columns:
+#' \itemize{
+#' \item \strong{code}: Code of the index.
+#' \item \strong{longname}: Long description of the index
+#' \item \strong{index.fun}: The name of the internal function used to calculate it
+#' \item \strong{tas, dewp, hurs, wind, radiation}: A logical value (0/1) indicating the input variables required for index calculation. Temperature and either dew point temperature or relative humidity need to be always provided.
+#' \item \strong{units}: The units of the index. 
+#' }
+#' @author A. Casanueva
+#' @export
+
+indexShow <- function() {
+  read.master()
+}
+
+#' @keywords internal
+#' @importFrom magrittr %>%
+#' @importFrom utils read.table
+
+read.master <- function() {
+  system.file("master", package = "HeatStress") %>% read.table(header = TRUE,
+                                                                      sep = ";",
+                                                                      stringsAsFactors = FALSE,
+                                                                      na.strings = "")
+}

R/rhooks.R

@@ -0,0 +1,32 @@
+#' @importFrom utils packageDescription
+
+.onAttach <- function(...) {
+  pkgname <- "HeatStress"
+  ver <- packageDescription(pkgname)$Version
+  builddate <- packageDescription(pkgname)$Date
+  mess <- paste(pkgname, " version ", ver, " (", builddate,") is loaded", sep = "")
+  packageStartupMessage(mess)
+  url <- paste0("https://raw.githubusercontent.com/anacv/", pkgname, "/master/DESCRIPTION")
+  b <- tryCatch(suppressWarnings(readLines(url)), error = function(er) {
+    er <- NULL
+    return(er)
+  })
+  if (!is.null(b)) {
+    latest.ver <- package_version(gsub("Version: ", "", b[grep("^Version", b)]))
+    if (ver < latest.ver) {
+      ver.mess1 <- paste0("WARNING: Your current version of ", pkgname, " (v", ver, ") is not up-to-date")
+      ver.mess <- paste0("Get the latest stable version (", latest.ver,
+                         ") using <devtools::install_github('anacv/", pkgname, "')>")
+      packageStartupMessage(ver.mess1)
+      packageStartupMessage(ver.mess)
+    } else if (ver > latest.ver) {
+      ver.mess1 <- paste0("WARNING: Your current version of ", pkgname, " (v", ver,
+                          ") is ahead of the master branch version (", latest.ver, ")")
+      ver.mess <- paste0("Development version may have an unexpected behaviour")
+      packageStartupMessage(ver.mess1)
+      packageStartupMessage(ver.mess)
+    }
+  }
+  packageStartupMessage("Use 'indexShow()' for an overview of the available heat indices")
+}
+# End

README.md

@@ -1,2 +1,29 @@
 # HeatStress
 Heat Stress indices for Heat-Shield
+
+## What is `HeatStress`?
+
+**HeatStress** is a R package for the calculation of heat stress indices. It has been developed in the framework of the Horizon2020 [HEAT-SHIELD project](www.heat-shield.eu).
+
+****
+
+### Installation
+
+The recommended procedure for installing the package is using the devtools package. 
+
+```R
+devtools::install_github("anacv/HeatStress")
+```
+
+A list of all available indices and the atomic functions calculating them is printed on screen with:
+
+```R
+library(HeatStress)
+indexShow()
+```
+
+### Reference and further information: 
+
+This package was used in the development of climate change scenarios of heat stress, in the following publications:
+* Casanueva et al. 2019. Climate projections of a multi-variate heat stress index: the role of downscaling and bias correction, *Geoscientific Model Development*, https://www.geosci-model-dev-discuss.net/gmd-2018-294/
+* Casanueva et al. 2019. Escalating environmental heat exposure – a future threat for the European workforce, *Regional Environmental Change*.

inst/master

@@ -0,0 +1,11 @@
+code;longname;indexfun;tas;dewp;hurs;wind;radiation;units
+wbt;Wet Bulb Temperature; wbt.Stull;1;0;1;0;0;degC 
+wbgt_shade;Wet Bulb Globe Temperature (shade);wbgt.Bernard;1;1;0;0;0;degC
+wbgt_sun;Wet Bulb Globe Temperature (sun);wbgt.Liljegren;1;1;0;1;1;degC 
+swbgt;simplified wet bulb globe temperature;swbgt;1;0;1;0;0;degC
+apparentTemp;apparent temperature;apparentTemp;1;0;1;1;0;degC
+effectiveTemp;effective temperature;effectiveTemp;1;0;1;1;0;degC
+humidex;humidex;humidex;1;0;1;0;0;degC
+discomInd;discomfort index;discomInd;1;0;1;0;0;degC
+hi;heat index;hi;1;0;1;0;0;degF 
+