Merge pull request #30 from jread-usgs/master

v0.2.1 example data w/ pkg and check fixes according to as-cran

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rGLM
 Type: Package
 Title: rGLM
-Version: 0.2.0
+Version: 0.2.1
 Date: 2013-07-23
 Author: Jordan S Read, Luke A Winslow
 Maintainer: Jordan S Read <jread@usgs.gov>, Luke A Winslow <lawinslow@wisc.edu>

LICENSE

@@ -0,0 +1,19 @@
+U.S.Geological Survey Software User Rights Notice
+
+Copied from http://water.usgs.gov/software/help/notice/ on September 7, 2012.  Please check webpage for updates.
+
+Software and related material (data and (or) documentation), contained in or furnished in connection with a software distribution, are made available by the U.S. Geological Survey (USGS) to be used in the public interest and in the advancement of science. You may, without any fee or cost, use, copy, modify, or distribute this software, and any derivative works thereof, and its supporting documentation, subject to the following restrictions and understandings.
+
+If you distribute copies or modifications of the software and related material, make sure the recipients receive a copy of this notice and receive or can get a copy of the original distribution. If the software and (or) related material are modified and distributed, it must be made clear that the recipients do not have the original and they must be informed of the extent of the modifications. For example, modified files must include a prominent notice stating the modifications made, the author of the modifications, and the date the modifications were made. This restriction is necessary to guard against problems introduced in the software by others, reflecting negatively on the reputation of the USGS.
+
+The software is public property and you therefore have the right to the source code, if desired.
+
+You may charge fees for distribution, warranties, and services provided in connection with the software or derivative works thereof. The name USGS can be used in any advertising or publicity to endorse or promote any products or commercial entity using this software if specific written permission is obtained from the USGS.
+
+The user agrees to appropriately acknowledge the authors and the USGS in publications that result from the use of this software or in products that include this software in whole or in part.
+
+Because the software and related material are free (other than nominal materials and handling fees) and provided "as is," the authors, the USGS, and the United States Government have made no warranty, express or implied, as to accuracy or completeness and are not obligated to provide the user with any support, consulting, training or assistance of any kind with regard to the use, operation, and performance of this software nor to provide the user with any updates, revisions, new versions or "bug fixes".
+
+The user assumes all risk for any damages whatsoever resulting from loss of use, data, or profits arising in connection with the access, use, quality, or performance of this software.
+
+R and other package dependencies have more restrictive licenses.

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2 (4.0.1): do not edit by hand
 
+export(get_evaporation)
 export(get_hypsography)
 export(get_ice)
 export(get_nml_value)

R/get_evaporation.R

@@ -0,0 +1,26 @@
+#'@title get evaporation from GLM simulation
+#'@description 
+#'Creates a data.frame with DateTime and E (mm/day).  \cr
+#'
+#'@param file a string with the path to the netcdf output from GLM
+#'@return a data.frame with DateTime and evaporation (in mm/day)
+#'@keywords methods
+#'@author
+#'Jordan S. Read
+#'@examples 
+#'file <- system.file('extdata', 'output.nc', package = 'rGLM')
+#'evap <- get_evaporation(file)
+#'plot(evap)
+#'@import ncdf4
+#'@export
+get_evaporation <-  function(file){
+  day_secs <- 86400
+  m_to_mm <- 1000
+  glm_nc <- get_glm_nc(file)
+  evaporation <- ncvar_get(glm_nc, "evap")*day_secs*m_to_mm
+  time <- get_time(glm_nc)
+
+  glm_evaporation <- data.frame('DateTime'=time, 'evaporation(mm/d)'=evaporation)
+  close_glm_nc(glm_nc)
+  return(glm_evaporation)
+}

R/get_hypsography.R

@@ -1,7 +1,8 @@
-#'@title retrieve hypsography information from glm_nml object or file
+#'@title retrieve hypsography information
 #'@description 
-#'Retrieves hypsography information from glm_nml object or file  \cr
-#'
+#'Retrieves hypsography information from glm_nml object or file.  \cr
+#'Hypsography is the relationship between depth and area of a lake. 
+#''Depth' is referenced from the lake surface and downward values are positive in meters. Areas are in square meters.
 #'
 #'@param glm_nml a nml (a list) for GLM config
 #'@param file a string with the path to the GLM glm.nml file
@@ -11,16 +12,16 @@
 #'Jordan S. Read
 #'@seealso \link{write_lvl}, \link{read_nml}, \link{get_nml_value}
 #'@examples 
-#'nml_file <- '../resources/glm.nml'
+#'nml_file <- system.file('extdata', 'glm.nml', package = 'rGLM')
 #'glm_nml <- read_nml(nml_file)
 #'get_hypsography(glm_nml)
-#'get_hypsography(file=nml_file)
+#'get_hypsography(file = nml_file)
 #'@export
-get_hypsography <- function(glm_nml=NULL, file=NULL){
+get_hypsography <- function(glm_nml, file){
   # if both are passed, glm_nml is used and 'file' is ignored
-  if (is.null(file) & is.null(glm_nml)){stop('glm.nml file path OR glm_nml must be specified')}
+  if (missing(file) & missing(glm_nml)){stop('glm.nml file path OR glm_nml must be specified')}
 
-  if (is.null(glm_nml)){
+  if (missing(glm_nml)){
     glm_nml <- read_nml(file)
   }
 

R/get_ice.R

@@ -1,24 +1,32 @@
 #'@title get ice depth from GLM simulation
 #'@description 
 #'Creates a data.frame with DateTime and ice.  \cr
-#'
+#'This function sums the thickness of the clear ice, white ice, 
+#'and optionally, the thickness of snow for each timestep in the GLM model.
 #'
 #'@param file a string with the path to the netcdf output from GLM
-#'@return a data.frame with DateTime and ice 
+#'@param snow.rm a boolean for ignoring snow depth in the calculation of ice thickness
+#'@return a data.frame with DateTime and ice (in meters)
 #'@keywords methods
 #'@author
 #'Luke A. Winslow, Jordan S. Read
 #'@examples 
-#'file = '../test/output.nc'
+#'file <- system.file('extdata', 'output.nc', package = 'rGLM')
 #'ice <- get_ice(file)
+#'ice_and_snow <- get_ice(file, snow.rm = FALSE)
+#'plot(ice)
+#'points(ice_and_snow, col = "red")
 #'@import ncdf4
 #'@export
-get_ice <-  function(file){
+get_ice <-  function(file, snow.rm = TRUE){
   glm_nc <- get_glm_nc(file)
-  ice <- ncvar_get(glm_nc, "hice")+ncvar_get(glm_nc, "hwice")+ncvar_get(glm_nc, "hsnow")
+  ice <- ncvar_get(glm_nc, "hice") + ncvar_get(glm_nc, "hwice")
+  if (!snow.rm){
+    ice <- ice + ncvar_get(glm_nc, "hsnow")
+  }
   time <- get_time(glm_nc)
 
-  glm_ice <- data.frame('DateTime'=time, 'ice'=ice)
+  glm_ice <- data.frame('DateTime'=time, 'ice(m)'=ice)
   close_glm_nc(glm_nc)
   return(glm_ice)
 }

R/get_nml_value.R

@@ -7,11 +7,11 @@
 #'@author
 #'Jordan S. Read
 #'@examples
-#'file = '../resources/glm.nml'
-#'glm_nml <- read_nml(file)
-#'get_nml_value(glm_nml,arg_name='Kw')
+#'nml_file <- system.file('extdata', 'glm.nml', package = 'rGLM')
+#'glm_nml <- read_nml(nml_file)
+#'get_nml_value(glm_nml,arg_name = 'Kw')
 #'@export
-get_nml_value  <-	function(glm_nml,arg_name){
+get_nml_value  <-	function(glm_nml, arg_name){
 
   blckI	<-	findBlck(glm_nml,arg_name)
 

R/get_surface_height.R

@@ -5,17 +5,18 @@
 #'
 #'@param file a string with the path to the netcdf output from GLM
 #'@param ice.rm a boolean for including ice thickness in surface height
+#'@param snow.rm a boolean for including snow depth thickness in surface height
 #'@return a data.frame with DateTime and surface_height (in meters)
 #'@keywords methods
 #'@author
 #'Jordan S. Read, Luke A. Winslow
 #'@examples 
-#'file = '../test/output.nc'
+#'file <- system.file('extdata', 'output.nc', package = 'rGLM')
 #'surface <- get_surface_height(file)
-#'surface_w_ice <- get_surface_height(file, ice.rm = FALSE)
+#'surface_w_ice <- get_surface_height(file, ice.rm = FALSE, snow.rm = FALSE)
 #'@import ncdf4
 #'@export
-get_surface_height  <-	function(file, ice.rm = TRUE){
+get_surface_height  <-	function(file, ice.rm = TRUE, snow.rm = TRUE){
   glm_nc <- get_glm_nc(file)
   NS	<- 	ncvar_get(glm_nc, "NS")
   elev <- ncvar_get(glm_nc, "z")
@@ -27,7 +28,11 @@ get_surface_height  <-	function(file, ice.rm = TRUE){
     surface_height[j] <- elev[NS[j],j]
   }
   if (!ice.rm){
-    surface_height <- surface_height + get_ice(file)[, 2]
+    surface_height <- surface_height + get_ice(file, snow.rm = TRUE)[, 2]
+  }
+  if (!snow.rm){
+    snow <- get_ice(file, snow.rm = TRUE)[, 2] - get_ice(file, snow.rm = TRUE)[, 2]
+    surface_height <- surface_height + snow
   }
 
   glm_surface <- data.frame('DateTime'=time, 'surface_height'=surface_height)

R/get_temp.R

@@ -1,7 +1,9 @@
 #'@title get water temperatures from a GLM simulation
 #'@description 
 #'Creates a data.frame with DateTime and temperatures (in deg C).  \cr
-#'
+#'Temperatures that are sampled out of the GLM output are taken relative 
+#'to the surface (\code{reference = 'surface'}) or the bottom of the lake 
+#'(\code{reference = 'bottom'}).
 #'
 #'@param file a string with the path to the netcdf output from GLM
 #'@param reference a string which specifies the vertical reference ('surface' or 'bottom')
@@ -11,12 +13,12 @@
 #'@author
 #'Jordan S. Read, Luke A. Winslow
 #'@examples 
-#'file = '../test/output.nc'
-#'temp_surf <- get_temp(file,reference='surface',z_out=c(0,1,2))
-#'temp_bot <- get_temp(file,reference='bot',z_out=c(0,1,2))
+#'file <- system.file('extdata', 'output.nc', package = 'rGLM')
+#'temp_surf <- get_temp(file, reference = 'surface', z_out = c(0,1,2))
+#'temp_bot <- get_temp(file, reference = 'bottom', z_out = c(0,1,2))
 #'@import ncdf4
 #'@export
-get_temp <-  function(file, reference='bottom', z_out){
+get_temp <-  function(file, reference = 'bottom', z_out){
   if (reference!='bottom' & reference!='surface'){
     stop('reference input must be either "surface" or "bottom"')
   }

R/get_wind.R

@@ -9,8 +9,8 @@
 #'@author
 #'Luke A. Winslow, Jordan S. Read
 #'@examples 
-#'file = '../test/output.nc'
-#'ice <- get_wind(file)
+#'file <- system.file('extdata', 'output.nc', package = 'rGLM')
+#'wind <- get_wind(file)
 #'@import ncdf4
 #'@export
 get_wind <-  function(file){

R/nc_helpers.R

@@ -1,6 +1,5 @@
 
 get_glm_nc  <-  function(file){
-	require(ncdf4)
 	glm_nc	<- 	nc_open(file)
 	return(glm_nc)
 }
@@ -12,7 +11,6 @@ close_glm_nc <- function(glm_nc){
 
 # Summary: Returns the converted time vector in R format
 get_time  <-  function(glm_nc){
-  require(ncdf4)
 	hours_since  <-   ncvar_get(glm_nc, "time")
 	time_info <- get_time_info(glm_nc)
 
@@ -23,7 +21,6 @@ get_time  <-  function(glm_nc){
 }
 
 get_time_info <- function(glm_nc){
-  require(ncdf4)
 	day_secs = 86400
   time_unit <- 3600/day_secs
 

R/nml_helpers.R

@@ -60,14 +60,14 @@ findBlck	<-	function(nml,argName){
 }
 
 # private function
-setnmlList <- function(nml,argList){
-  if (!is.list(argList)){stop("argList must be a list")}
+setnmlList <- function(glm_nml,arg_list){
+  if (!is.list(arg_list)){stop("argList must be a list")}
 
-  argNames  <-	names(argList)
-  for (i in 1:length(argNames)){
-    nml <- set_nml(nml,argName=argNames[i],argVal=argList[[i]])
+  arg_names  <-	names(arg_list)
+  for (i in 1:length(arg_names)){
+    glm_nml <- set_nml(glm_nml,arg_name=arg_names[i],arg_val=arg_list[[i]])
   }
-  return(nml)
+  return(glm_nml)
 }
 
 

R/pretty_nml.R

@@ -4,8 +4,8 @@
 #'@author
 #'Jordan S. Read
 #'@examples
-#'file = '../resources/glm.nml'
-#'glm_nml <- read_nml(file)
+#'nml_file <- system.file('extdata', 'glm.nml', package = 'rGLM')
+#'glm_nml <- read_nml(nml_file)
 #'pretty_nml(glm_nml)
 #'@export
 pretty_nml <- function(glm_nml){

R/read_nml.R

@@ -10,11 +10,11 @@
 #'Jordan S. Read
 #'@seealso \link{get_nml_value}
 #'@examples 
-#'file = '../resources/glm.nml'
-#'glm_nml <- read_nml(file)
+#'nml_file <- system.file('extdata', 'glm.nml', package = 'rGLM')
+#'glm_nml <- read_nml(nml_file)
 #'pretty_nml(glm_nml)
 #'@export
-read_nml  <-	function(file = '../resources/glm.nml'){
+read_nml  <-	function(file){
   # skip all commented lines, return all variables and associated values
   # requires NO return line variables (all variables must be completely defined on a single line)
   c <- file(file,"r")