Merge pull request #205 from jread-usgs/master

conversions for units

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: glmtools
 Type: Package
 Title: glmtools
-Version: 0.13.2
-Date: 2016-01-15
+Version: 0.14.0
+Date: 2016-03-28
 Authors@R: c( person("Jordan", "Read", role = c("aut","cre"),
     email = "jread@usgs.gov"),
     person("Luke", "Winslow", role = "aut",
@@ -21,7 +21,8 @@ Depends:
 Imports:
     ncdf4,
     tools,
-    akima
+    akima,
+    lazyeval
 Suggests:
     testthat,
     knitr,

NAMESPACE

@@ -4,6 +4,7 @@ S3method(print,nml)
 S3method(summary,nml)
 export(.compare_to_field)
 export(compare_to_field)
+export(convert_sim_var)
 export(epi.temperature)
 export(get_evaporation)
 export(get_hypsography)
@@ -41,7 +42,12 @@ import(GLMr)
 import(rLakeAnalyzer)
 import(tools)
 importFrom(akima,interp)
+importFrom(lazyeval,lazy_dots)
+importFrom(lazyeval,lazy_eval)
 importFrom(ncdf4,nc_close)
 importFrom(ncdf4,nc_open)
 importFrom(ncdf4,ncatt_get)
+importFrom(ncdf4,ncvar_add)
+importFrom(ncdf4,ncvar_def)
 importFrom(ncdf4,ncvar_get)
+importFrom(ncdf4,ncvar_put)

R/convert_sim_var.R

@@ -0,0 +1,78 @@
+
+#' convert an existing simulation variable into a different one
+#' 
+#' allows you to provide specific variable or unit conversions to create a new variable 
+#' that can be used with \code{\link{plot_var_compare}}, and others. 
+#' 
+#' @param nc_file the netcdf output file
+#' @param \dots an expression to convert variable based on other variables or offsets
+#' @param unit the units for the new variable
+#' @param longname the longname for the new variable
+#' @export
+#' @importFrom lazyeval lazy_dots lazy_eval
+#' @importFrom ncdf4 ncvar_def ncvar_put ncvar_add
+#' @examples 
+#' \dontrun{
+#'sim_folder <- run_example_sim(verbose = FALSE)
+#'nc_file <- file.path(sim_folder, 'output.nc')
+#'convert_sim_var(nc_file, tempF = temp/5*9+32, unit='degF',longname='temperature degrees Farenheit')
+#'plot_var(nc_file, 'tempF')
+#'convert_sim_var(nc_file, crazy_var = temp-u_mean*1000)
+#'plot_var(nc_file, 'crazy_var')
+#'
+#'temp2f <- function(c) c/5*9+32
+#'convert_sim_var(nc_file, tempf = temp2f(temp), unit='degF',longname='temperature degrees Farenheit')
+#' }
+#' 
+convert_sim_var <- function(nc_file='output.nc', ..., unit='', longname='', overwrite=FALSE){
+
+
+  sim.vars <- sim_vars(nc_file)$name
+  message('convert_sim_var is untested and in development')
+
+  # // here, vals would be defined by the function passed in by `...`. Probably captured w/ lazyeval?
+  # lazyeval::lazy_eval(convert, data=list(temp=ncvar_get(nc, 'temp')))
+  convert <- lazyeval::lazy_dots(...)
+  if (length(convert) > 1)
+    stop('not yet ready to handle multi-var expressions')
+
+  var.name <- names(convert)
+  var.exists <- var.name %in% sim.vars
+  if (var.exists & !overwrite)
+    stop(var.name, ' cannot be added, it already exists and overwrite = FALSE.', call. = FALSE)
+
+  fun.string <- deparse(convert[[1]]$expr)
+  variables <- strsplit(fun.string,"[^a-zA-Z_]")[[1]]
+  variables <- variables[variables != '']
+  nc.vars <- variables[variables %in% sim.vars]
+
+  data <- lapply(nc.vars, function(v) get_raw(nc_file, v))
+  names(data) <- nc.vars
+  vals <- lazyeval::lazy_eval(convert, data=data)[[1]]
+
+  nc <- nc_open(nc_file, readunlim=TRUE, write=TRUE)
+
+
+  if (!var.exists){
+    #depending on conversion, dims can be [time], [lon,lat,time], or [lon,lat,z,time] 
+    lon <- nc$dim$lon
+    lat <- nc$dim$lon
+    time <- nc$dim$time
+    if (length(dim(vals)) > 1){
+      z <- nc$dim$z
+      dim = list(lon,lat,z,time)
+    } else {
+      dim = list(lon,lat,time)
+    }
+
+    missval = 9.96920996838687e36
+    var_new <- ncvar_def(name=var.name, unit, dim = dim, missval, prec="double")
+    nc <- ncvar_add(nc, var_new)
+  } else {
+    var_new <- var.name
+  }
+
+
+  ncvar_put(nc, var_new, vals=vals)
+  nc_close(nc)
+}

tests/testthat/test-convert_sim_var.R

@@ -0,0 +1,43 @@
+context("convert variables in netcdf output")
+
+test_that("errors with poor matches", {
+  sim_folder <- run_example_sim(verbose = FALSE)
+  nc_file <<- file.path(sim_folder, 'output.nc')
+  expect_error(convert_sim_var(nc_file, temp = temp*2), "temp cannot be added, it already exists.")
+  expect_error(convert_sim_var(nc_file, temp.new = garbage))
+})
+
+test_that("can add variable", {
+  convert_sim_var(nc_file, temp.new = temp*2)
+  expect_true('temp.new' %in% sim_vars(nc_file)$name)
+  expect_is(get_var(nc_file, var_name = 'temp.new'), 'data.frame')
+})
+
+test_that("errors when you try to add it again", {
+  expect_error(convert_sim_var(nc_file, temp.new = temp*2))
+})
+
+test_that("can modify variable with more than one variable function", {
+
+  convert_sim_var(nc_file, crazy_var = temp-u_mean*1000)
+  expect_true('crazy_var' %in% sim_vars(nc_file)$name)
+})
+
+test_that("can modify variable with a function", {
+
+  temp2f <- function(c) c/5*9+32
+  convert_sim_var(nc_file, tempf = temp2f(temp), unit='degF',longname='temperature degrees Farenheit')
+  expect_true('tempf' %in% sim_vars(nc_file)$name)
+  expect_error(convert_sim_var(nc_file, tempf2 = garbagefun(temp)))
+
+})
+
+test_that("can overwrite existing variable", {
+
+  temp2f <- function(c) c/5*9+32
+  tempf <- get_raw(nc_file, 'tempf')
+  convert_sim_var(nc_file, tempf = temp2f(temp), overwrite = TRUE)
+  expect_equal(tempf, get_raw(nc_file, 'tempf'))
+  convert_sim_var(nc_file, tempf = temp2f(temp)+5, overwrite = TRUE)
+  expect_equal(tempf, get_raw(nc_file, 'tempf')-5)
+})