Merge pull request #143 from jread-usgs/master

v0.7.0 updates

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: glmtools
 Type: Package
 Title: glmtools
-Version: 0.6.2
+Version: 0.7.0
 Date: 2013-09-18
 Author: Jordan S Read, Luke A Winslow
 Maintainer: Jordan S Read <jread@usgs.gov>

NAMESPACE

@@ -26,6 +26,8 @@ export(resample_to_field)
 export(run_example_sim)
 export(set_nml)
 export(sim_metrics)
+export(sim_var_longname)
+export(sim_var_units)
 export(sim_vars)
 export(summarize_sim)
 export(validate_sim)

R/nml_helpers.R

@@ -1,12 +1,14 @@
 
 
 # private function
-buildVal	<-	function(textLine){
+buildVal	<-	function(textLine, lineNum, blckName){
 	#-----function appends nml list with new values-----
 	# remove all text after comment string
 	textLine	<-	strsplit(textLine,'!')[[1]][1]
 
-	if (!any(grep("=",textLine))){stop(c("no hanging lines allowed in .nml, used ",textLine))}
+	if (!any(grep("=",textLine))){
+    stop(c("no hanging lines allowed in .nml, used ",textLine,'.\nSee line number:',lineNum,' in "&',blckName,'" section.'))
+	}
 	params	<-	strsplit(textLine,"=") # break text at "="
 	parNm	<-	params[[1]][1]
 	parVl	<-	params[[1]][2]
@@ -101,3 +103,14 @@ ascii_only <- function(file){
   }
 
 }
+
+.validate_nml <- function(nml){
+  # test for required blocks:
+  required_blks <- c('outflow', 'inflow', 'meteorology', 'init_profiles', 'output', 'time', 'morphometry', 'glm_setup')
+  blk_match <- required_blks %in% names(nml)
+  if (!all(blk_match)){
+    stop('parsing error in nml file.',required_blks[blk_match],'missing.')
+  }
+  return(TRUE)
+
+}

R/plot_var.R

@@ -6,9 +6,9 @@
 #'@param num_cells number of vertical cells to use for heatmap
 #'@param fig_path F if plot to screen, string path if save plot as .png
 #'@param add F if create new figure, T if add to existing
-#'@param bar_title NULL if use var_name, or specify as a string to name plot variable
+#'@param bar_title NULL if use \code{\link{sim_var_longname}}, or specify as a string to name plot variable
 #'@keywords methods
-#'@seealso \link{get_temp}
+#'@seealso \code{\link{get_temp}}, \code{\link{sim_var_longname}}
 #'@author
 #'Jordan S. Read, Luke A. Winslow
 #'@examples
@@ -29,24 +29,43 @@ plot_var <- function(file, var_name, col_lim, reference = 'surface', num_cells =
   min_depth <- 0
   z_out <- seq(min_depth, max_depth,length.out = num_cells)
   variable_df <- get_var(file, reference = reference, z_out, var_name=var_name)
+
+  if (is.null(bar_title)){ 
+    bar_title <- sim_var_longname(file, var_name) 
+  }
+
+  if (is.character(fig_path)){
+    gen_default_fig(file_name = fig_path) 
+  }
+
   if (ncol(variable_df) == 2){
-    stop('plot_var() not yet supported for 1D output variables')
+    .plot_timeseries(variable_df, add, bar_title)
+  } else {
+    .plot_heatmap(variable_df, col_lim, reference, add, bar_title, z_out)
   }
+
+  if (is.character(fig_path)){
+    dev.off()
+  } else {
+    #layout(as.matrix(1))
+  }
+
+}
+
+.plot_heatmap <- function(variable_df, col_lim, reference, add, bar_title, z_out){
   palette <- colorRampPalette(c("violet","blue","cyan", "green3", "yellow", "orange", "red"), 
                               bias = 1, space = "rgb")
+
+  if (missing(col_lim)) col_lim <- range(variable_df[, -1], na.rm = TRUE)
   levels <- seq(col_lim[1], col_lim[2], by = diff(col_lim)/15)
-  #col_subs <- unique(floor(seq(col_lim[1], col_lim[2]-1, length.out = 15)))
   col_subs <- levels
   colors <- palette(n = length(levels)-1)
   dates <- variable_df[, 1]
   matrix_var <- data.matrix(variable_df[, -1])
   xaxis <- get_xaxis(dates)
   yaxis <- get_yaxis_2D(z_out, reference)
 
-  if (is.character(fig_path)){
-    gen_default_fig(file_name = fig_path) 
-  }
-
+
 
   plot_layout(xaxis, yaxis, add)
   .filled.contour(x = dates, y = z_out, z =matrix_var,
@@ -55,14 +74,11 @@ plot_var <- function(file, var_name, col_lim, reference = 'surface', num_cells =
 
   axis_layout(xaxis, yaxis) #doing this after heatmap so the axis are on top
 
-  if (is.null(bar_title)){
-    bar_title = var_name
-  }
   color_key(levels, colors, subs=col_subs, col_label = bar_title)
-  if (is.character(fig_path)){
-    dev.off()
-  } else {
-    #layout(as.matrix(1))
-  }
+
 }
 
+.plot_timeseries <- function(variable_df, add, bar_title){
+  if (add) par(new=TRUE)
+  plot(variable_df, ylab = bar_title)
+}

R/read_nml.R

@@ -56,7 +56,7 @@ read_nml  <-	function(nml_file = 'template'){
       #browser()
       if(substr(textLine,1,1)!='!'){
         # Add a check here, sometimes, if there is a hanging comma, 
-        #and only sumtimes that means add next row
+        #and only sometimes that means add next row
         if(substr(textLine,nchar(textLine), nchar(textLine)) == ',' && 
              j+1 <= length(fileLines) && !any(grep("=",fileLines[j+1])) && !any(grep("/",fileLines[j+1]))){
 
@@ -66,14 +66,17 @@ read_nml  <-	function(nml_file = 'template'){
           carryover = ''
         }
         # else, line is commented out
-        lineVal	<-	buildVal(textLine)
+        lineVal	<-	buildVal(textLine, lineNum=j, blckName)
         nml[[i]]	<-	c(nml[[i]],lineVal)
       }
     }
   }
-  return(.nml(nml))
+  nml <- .nml(nml)
+  .validate_nml(nml)
+  return(nml)
 }
 
+
 nml_path_norm <- function(nml_file){
   if (nml_file == "template"){
     nml_file <- nml_template_path()

R/sim_var_longname.R

@@ -0,0 +1,25 @@
+#'@title get long name of variable from a GLM simulation
+#'@param file a string with the path to the netcdf output from GLM
+#'@param var_name name of a valid variable from a simulation (see \code{\link{sim_vars}})
+#'@keywords methods
+#'@seealso \code{\link{sim_vars}}, \code{\link{sim_var_units}}
+#'@author
+#'Jordan S. Read
+#'@examples
+#'sim_folder <- run_example_sim(verbose = FALSE)
+#'nc_file <- file.path(sim_folder, 'output.nc')
+#'vars <- sim_vars(file = nc_file)
+#'sim_var_units(nc_file, vars[1])
+#'sim_var_units(nc_file, 'u_mean')
+#'@export
+sim_var_longname <- function(file, var_name){
+
+  glm_nc <- get_glm_nc(file)
+  longname <- glm_nc$var[[var_name]]$longname
+  close_glm_nc(glm_nc)
+  if (is.null(longname)){stop(var_name,' not found. Check variable name')}
+  return(longname)
+}
+
+
+

R/sim_var_units.R

@@ -0,0 +1,24 @@
+#'@title get units of variable from a GLM simulation
+#'@param file a string with the path to the netcdf output from GLM
+#'@param var_name name of a valid variable from a simulation (see \code{\link{sim_vars}})
+#'@keywords methods
+#'@seealso \code{\link{sim_vars}}, \code{\link{sim_var_longname}}
+#'@author
+#'Jordan S. Read
+#'@examples
+#'sim_folder <- run_example_sim(verbose = FALSE)
+#'nc_file <- file.path(sim_folder, 'output.nc')
+#'vars <- sim_vars(file = nc_file)
+#'sim_var_longname(nc_file, vars[1])
+#'sim_var_longname(nc_file, 'u_mean')
+#'@export
+sim_var_units <- function(file, var_name){
+
+  glm_nc <- get_glm_nc(file)
+  units <- glm_nc$var[[var_name]]$units
+  close_glm_nc(glm_nc)
+  if (is.null(units)){stop(var_name,' not found. Check variable name')}
+  return(units)
+}
+
+