Merge pull request #189 from jread-usgs/master

updating to ncdf4 instead of ncdf

.travis.yml

@@ -12,7 +12,7 @@ before_install:
   - ./travis-tool.sh bootstrap
 install:
   - ./travis-tool.sh install_deps
-  - ./travis-tool.sh github_package jimhester/covr
+  - ./travis-tool.sh r_install covr
   - ./travis-tool.sh install_github GLEON/GLMr
 script: ./travis-tool.sh run_tests
 

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: glmtools
 Type: Package
 Title: glmtools
-Version: 0.10.3
-Date: 2013-09-18
+Version: 0.11.0
+Date: 2016-01-15
 Authors@R: c( person("Jordan", "Read", role = c("aut","cre"),
     email = "jread@usgs.gov"),
     person("Luke", "Winslow", role = "aut",
@@ -19,7 +19,7 @@ Depends:
     GLMr,
     rLakeAnalyzer
 Imports:
-    ncdf,
+    ncdf4,
     tools,
     akima
 Suggests:

NAMESPACE

@@ -35,7 +35,10 @@ export(validate_sim)
 export(water.temperature)
 export(write_nml)
 import(GLMr)
-import(ncdf)
 import(rLakeAnalyzer)
 import(tools)
 importFrom(akima,interp)
+importFrom(ncdf4,nc_close)
+importFrom(ncdf4,nc_open)
+importFrom(ncdf4,ncatt_get)
+importFrom(ncdf4,ncvar_get)

R/get_raw.R

@@ -31,12 +31,12 @@
 #'sim_folder <- run_example_sim(verbose = FALSE)
 #'nc_file <- file.path(sim_folder, 'output.nc')
 #'wind <- get_raw(nc_file, 'wind') #raw wind data
-#'@import ncdf
+#'@importFrom ncdf4 ncvar_get
 #'@seealso \code{\link{sim_vars}}
 #'@export
 get_raw <-  function(file='output.nc', param_name){
   glm_nc <- get_glm_nc(file)
-  raw_data <- get.var.ncdf(glm_nc, param_name)
+  raw_data <- ncvar_get(glm_nc, param_name)
 
   close_glm_nc(glm_nc)
   return(raw_data)

R/get_surface_height.R

@@ -16,12 +16,12 @@
 #'nc_file <- file.path(sim_folder, 'output.nc')
 #'surface <- get_surface_height(file = nc_file)
 #'surface_w_ice <- get_surface_height(file = nc_file, ice.rm = FALSE, snow.rm = FALSE)
-#'@import ncdf
+#'@importFrom ncdf4 ncvar_get
 #'@export
 get_surface_height  <-	function(file='output.nc', ice.rm = TRUE, snow.rm = TRUE, ...){
   glm_nc <- get_glm_nc(file)
-  NS	<- 	get.var.ncdf(glm_nc, "NS")
-  elev <- get.var.ncdf(glm_nc, "z")
+  NS	<- 	ncvar_get(glm_nc, "NS")
+  elev <- ncvar_get(glm_nc, "z")
   time <- get_time(glm_nc)
   close_glm_nc(glm_nc)
 

R/get_var.R

@@ -26,17 +26,17 @@
 #'print(sim_vars(nc_file))
 #'evaporation <- get_var(nc_file, var_name = "evap")
 #'plot(evaporation)
-#'@import ncdf
+#'@importFrom ncdf4 ncvar_get
 #'@export
 get_var <-  function(file='output.nc',  var_name, reference = 'bottom', z_out = NULL, t_out = NULL, ...){
 
 
 
   glm_nc <- get_glm_nc(file)
 
-  tallest_layer <- get.var.ncdf(glm_nc, "NS") #The last useful index
-  elev <- get.var.ncdf(glm_nc, "z" )
-  temp <- get.var.ncdf(glm_nc, var_name)
+  tallest_layer <- ncvar_get(glm_nc, "NS") #The last useful index
+  elev <- ncvar_get(glm_nc, "z" )
+  temp <- ncvar_get(glm_nc, var_name)
   time <- get_time(glm_nc)
 
   close_glm_nc(glm_nc)

R/nc_helpers.R

@@ -1,20 +1,22 @@
 
+#' @importFrom ncdf4 nc_open
 get_glm_nc  <-  function(file){
 	if(length(file) < 1 || is.na(file)){
 		stop('glm_nc file must be supplied string or proper file handle')
 	}
-	glm_nc	<- 	open.ncdf(file, readunlim=TRUE)
+	glm_nc	<- 	nc_open(file, readunlim=TRUE)
 	return(glm_nc)
 }
-
+#' @importFrom ncdf4 nc_close
 close_glm_nc <- function(glm_nc){
-  close.ncdf(glm_nc)
+  nc_close(glm_nc)
 }
 
 
 # Summary: Returns the converted time vector in R format
+#' @importFrom ncdf4 ncvar_get
 get_time  <-  function(glm_nc){
-	hours_since  <-   get.var.ncdf(glm_nc, "time")
+	hours_since  <- ncvar_get(glm_nc, "time")
 	time_info <- get_time_info(glm_nc)
 
 	time <- time_info$startDate + time_info$time_unit * hours_since * 60*60*24
@@ -23,6 +25,7 @@ get_time  <-  function(glm_nc){
 
 }
 
+#' @importFrom ncdf4 ncatt_get ncvar_get
 get_time_info <- function(glm_nc, file = NULL){
 
 	day_secs = 86400
@@ -34,7 +37,7 @@ get_time_info <- function(glm_nc, file = NULL){
     glm_nc <- get_glm_nc(file)
     close_nc <- TRUE
   }
-	time_units <- att.get.ncdf(glm_nc,'time','units')$value
+	time_units <- ncatt_get(glm_nc,'time','units')$value
 
 
 	#It is written in prose instead of machine-readable format. Check to makes sure
@@ -59,7 +62,7 @@ get_time_info <- function(glm_nc, file = NULL){
   time_info  <-  cbind(time_info,"startDate"=start_date)
 
 	#End date/time 
-	endT <- time_info$startDate + get.var.ncdf(glm_nc, 'time', start=tLen, count=1) * time_unit * day_secs
+	endT <- time_info$startDate + ncvar_get(glm_nc, 'time', start=tLen, count=1) * time_unit * day_secs
 
   time_info  <-  cbind(time_info,"stopDate"=endT[1])
 	if (close_nc){

README.md

@@ -51,7 +51,7 @@ How do I install `glmtools`? It isn't on CRAN!
 
 What libraries does `glmtools` need?
 ===
-This version requires the NetCDF version R library (called `ncdf`), and `rLakeAnalyzer`, and `tools` if you would like to run all examples. 
+This version requires the NetCDF version R library (called `ncdf4`), and `rLakeAnalyzer`, and `tools` if you would like to run all examples. 
 
 How do I contribute new code back to the glmtools project?
 ===