What is rwrfhydro?

A community-contributed tool box for managing, analyzing, and visualizing WRF Hydro input and output files in R (everything but the model and the GIS).

Intentionally, “rwrfhydro” can be read as “our wrf hydro”. The purpose of this R package is to focus community development of tools for working with and analyzing data related to the WRF Hydro model. These tools are both free and open-source, just like R, which should help make them accessible and popular.

The git hub repository is found here: https://github.com/mccreigh/rwrfhydro/.

The README.Rmd provides instructions on installing, using, and contributing. Additional resouces for learning R are listed there as well.

Purpose

This vignette 1) Provides an a list of current vignettes, 2) Covers basic R installation and usage.

The ultimate goal is endocterination so that you will help contribute to the rwrfhydro source code.

Vignettes

R Basics [ html - R ]
rwrfhydro overview [ html - R ]
Domain visualization [ html - R ]
Streamflow evaluation [ html - R ]
Water balance [ html - R ]
GetMultiNcdf [ html - R ]
ET [ html - R ]
SNODAS retrieval [ html - R ]
-The following require optional libraries or compiled code.-
Regridding (devCompile branch) [ html - R ]
Geospatial Tools (rgdal) [ html - R ]
Precipitation evalation (rgdal) [ html - R ]
MODIS (modis) [ html - R ]

Installation Tips

The installation instructions require a minor detour for 2 reasons: 1) ncdf4 in a non-standard location, 2) there is no local R library yet. First we’ll install devtools.

In the terminal:

R
install.packages("devtools", repos="http://cran.at.r-project.org/")
q()

On a clean R install, the above will ask the user to create a new, writable Library path. This will be the first in the R_LIBS path (in R: .libPath()).

Next, we’ll return to the shell and install the ncdf4 package against the correct-for-R (gcc) build on the system.

For Windows, users can download the appropriate binary ncdf4 file from the following link: http://cirrus.ucsd.edu/~pierce/ncdf/. Then the following command, it will open a window for you to choose the downloaded zip file and will install it:

install.packages(file.choose(), repos=NULL, type = "binary")

For linux and OSX, in the terminal:

wget http://cran.r-project.org/src/contrib/ncdf4_1.13.tar.gz
R CMD INSTALL \\
--configure-args="--with-nc-config=/usr/local/netcdf-4.3.2-gcc/bin/nc-config" ncdf4_1.13.tar.gz

The path to the ncdf4 source can be found by googling “cran ncdf4” and using the information at the package’s home page. The config-args are specific to the machines in the lab. Note that if you wish to also install the rgdal package, you’ll also have to install gdal and proj4 and several other pieces of external software on your machine and then build rgdal against their locations in a similar way.

Now we will install rwrfhydro. The remainder of its dependencies install without issue. Again in the terminal:

R
library(ncdf4)  ## check if the install was successful.
devtools::install_github('mccreigh/rwrfhydro')  ## one time and for updates.
library(rwrfhydro) ## for each new R session where you want to use rwrfhydro.s

Several of the rwrfhydro vignettes depend on external testcase data to run. This data is external because WRF-Hydro output is voluminous! These test cases will be available separately on our website at some time inthe near future. They should be downloaded and unzipped in a folder ~/wrfHydroTestCases/, or the unzipped tar balls can be symlinked into this directory. For the examples included here we will need both ~/wrfHydroTestCases/Fourmile_Creek_testcase_v2.0 and ~/wrfHydroTestCases/usgsDB. The usgsDB directory is included in the class tar ball and can be symlinked by cd ~/wrfHydroTestCases ; ln -s ~/pathTo/rwrfhydro_class/usgsDB ..


R Basics

High-level View

The goal of this overview is to demistify R and help new users feel less confused when using R. The examples here are not deep at all (don’t believe that they are) but they give a view into some basic ways that R might be different than whatever languages you are used to. Once you absorb this, you can graduate to more sophisticated resources like Advanced R or R Packages with a solid foundation. Please see the rwrfhydro home page for more references and the R cheat sheet for a broad list of functionality.

One note is that R was developed as an open source project which did not apparently impose many coding style standards at the outset. Hence, there is really no standard code style (e.g. function.name or function_name or functionName or FunctionName or functionname might all be used for different functions). Dont read any other meaning into this. In contrast, we adopt Google’s coding style for rwrfhydro development with one modification. So, style is meaningful when you are reading rwrfhydro code and using it’s objects (functions and otherwise).

If you are used to including a library of functions in your path in another language, this notion is replaced by the “package” in R. This is a somewhat advanced way to use R but it is well worth learning the fundamentals. Contributing to rwfhydro can help learn some parts of package development, though we handle most of these. Notably, R possesses advanced and powerful documentation and markup features which are worth learning. Note that most of the course materials documents are provided in three formats generated from source rmarkdown (.Rmd) documents: .html are generated by running the code and the .R files turn the text into comments, leaving the code and not running it.

None of this is to mention the availablilty of packages and interfaces to other open-source software which extend the power of the R language. The Comprehensive R Archive Network (CRAN) is the (distributed) nexus for both the R software and community contributed packages which meet the CRAN standards. There are currently over 6500 contributed packages! It is useful to look at the homepage of packages on CRAN, e.g. that for the plyr package. Though rwfhydro is not on CRAN, we emulate this package overview at the top of our README. Imports describes which packages are required to run, Suggests describes optional packages for extended functionality. The Bug Reports URL may be the most important piece of information on the page. In the downloads section, installation is described, a pdf manual is offered, and the vignettes are listed. The pdf manual is simply a compilation of the help available within R. The vignettes provide working examples with annotation which also show the output and make the example self-contained.

Setup

While intefacing with R on command line is an option, using a more integrated editor will help you be more efficient. Rstudio provides a very good and free IDE (Integraged Development Environment) for R. The only competitor is ESS for Emacs. Both are highly recommended with RStudio having several advantages, particularly for package development.

When running R, you might benefit from setting options(warn=2) which turns all warnings into errors. It’s useful to stop execution and discover unintended mis-use of R as it starts (great for those new to R). Debugging in R can be turned on by options(error=utils::recover), for example. Debugging is a more advanced usage but good to be aware of, see this resource for more information.

My “startup” file contains both of the above suggestions. (In fact, these are the only things which remain of all the various things I’ve tried to date.) Here’s how that startup file is configured by use of the ~/.Renviron file.

james@orographic:~> more .Renviron 
R_LIBS=~/R/Libraries/R3.2/
R_PROFILE=/Users/james/R/startup_jlm.r

james@orographic:~> more /Users/james/R/startup_jlm.r 
options(warn=1)
options(error=utils::recover)

The first line of .Renviron specifies the R libraries path (R_LIBS), which is unix-like in searching for read and write. The second line specifies the R_PROFILE or startup file location. The contents of the R_PROFILE are R commands and my only commands are the options() mentioned above.

Functions

A basic R function looks like this:

BasicFunc <- function(x) {   ## define the function 
  y=x^2                      ## square the argument
  y                          ## return the square
}
xx <- 3
yy <- BasicFunc(xx)
print(yy)
## [1] 9
yy
## [1] 9

Note that the last line in the function is the return value. Also, the print method is invoked on an object when that object is entered by itself, as in the very last line.

Remember that nearly everything in R is a function object. Indeed, functions are “first-class”. A more complicated example illustrates passing a named function to another function. (In the scoping section below, we illustrate a function returning a function, which is then called a closure).

## Note named arguments. Args can be passed by name or position.
Function1 <- function(x=x,f=f) list(arg=x, result=f(x), func=f)
result1 <- Function1(xx, BasicFunc)
result2 <- Function1(f=BasicFunc, x=xx)
identical(result1,result2)
## [1] TRUE
result1
## $arg
## [1] 3
## 
## $result
## [1] 9
## 
## $func
## function (x) 
## {
##     y = x^2
##     y
## }
str(result1)
## List of 3
##  $ arg   : num 3
##  $ result: num 9
##  $ func  :function (x)  
##   ..- attr(*, "srcref")=Class 'srcref'  atomic [1:8] 1 14 4 1 14 1 1 4
##   .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7fc9303b66d8>

The result of this function is not a scalar or vector, it is a list object which contains a possibly arbitrary collection of things. The list object is the fundamental way to get more than a single object out of a function. The str() function reveals the structure of objects, including lists. It helps structure complicated, hierarchical items as we’ll see later. It also provides object type and class information.

Lists

Above we saw that lists are used to return multiple items from a function. Then, how do we get the contents out of a returned list? For simple lists, this can be done, by hand. Note that str() is wrapping many of the commands below to give a more informative view what the output actually is.

names(result1)          ## returns a character vector, hence the [1]
## [1] "arg"    "result" "func"
str(result1['arg'])     ## returns a sub-list
## List of 1
##  $ arg: num 3
str(result1[['arg']])   ## returns the item requested, a numeric scalar 
##  num 3
str(result1$arg)        ## dollar acts like the "[[" function.
##  num 3
str(result1$func(2))    ## function evaluation.
##  num 4
result1[['func']](2)    ## function evaluation, same as previous.
## [1] 4
## The easiest way to rename is by name using plyr::rename
renames <- paste0('names.',c("b","(c)"))  ## the new names are the vector entries
names(renames) <- c('result','func')      ## the old names are the names of the new names
## This kind of translation vector is very handy, note that
## value=rename[name] and name=names(rename)[which(rename == value)]
str(renames)
##  Named chr [1:2] "names.b" "names.(c)"
##  - attr(*, "names")= chr [1:2] "result" "func"
print(renames)  ## the top line is the names
##      result        func 
##   "names.b" "names.(c)"
result1 <- plyr::rename(result1, renames)
str(result1)
## List of 3
##  $ arg      : num 3
##  $ names.b  : num 9
##  $ names.(c):function (x)  
##   ..- attr(*, "srcref")=Class 'srcref'  atomic [1:8] 1 14 4 1 14 1 1 4
##   .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x7fc9303b66d8>
result1$names.b
## [1] 9
result1$`names.(c)`(2)   ## backquote can handle illegal names 
## [1] 4

This demonstrates a basic principle in R that you can forget about indices and call it by name. NO indices were used above, the number two is a value passed to a function.

Data frames (regular lists)

Before showing complicated lists, lets look at data frames. Data frames are special kinds of lists that are “regular”.

mtcars             ## data packaged with R typically comes in data frames.
mpg cyl disp hp drat wt qsec vs am gear carb
Mazda RX4 21.0 6 160.0 110 3.90 2.620 16.46 0 1 4 4
Mazda RX4 Wag 21.0 6 160.0 110 3.90 2.875 17.02 0 1 4 4
Datsun 710 22.8 4 108.0 93 3.85 2.320 18.61 1 1 4 1
Hornet 4 Drive 21.4 6 258.0 110 3.08 3.215 19.44 1 0 3 1
Hornet Sportabout 18.7 8 360.0 175 3.15 3.440 17.02 0 0 3 2
Valiant 18.1 6 225.0 105 2.76 3.460 20.22 1 0 3 1
Duster 360 14.3 8 360.0 245 3.21 3.570 15.84 0 0 3 4
Merc 240D 24.4 4 146.7 62 3.69 3.190 20.00 1 0 4 2
Merc 230 22.8 4 140.8 95 3.92 3.150 22.90 1 0 4 2
Merc 280 19.2 6 167.6 123 3.92 3.440 18.30 1 0 4 4
Merc 280C 17.8 6 167.6 123 3.92 3.440 18.90 1 0 4 4
Merc 450SE 16.4 8 275.8 180 3.07 4.070 17.40 0 0 3 3
Merc 450SL 17.3 8 275.8 180 3.07 3.730 17.60 0 0 3 3
Merc 450SLC 15.2 8 275.8 180 3.07 3.780 18.00 0 0 3 3
Cadillac Fleetwood 10.4 8 472.0 205 2.93 5.250 17.98 0 0 3 4
Lincoln Continental 10.4 8 460.0 215 3.00 5.424 17.82 0 0 3 4
Chrysler Imperial 14.7 8 440.0 230 3.23 5.345 17.42 0 0 3 4
Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1
Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2
Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1
Toyota Corona 21.5 4 120.1 97 3.70 2.465 20.01 1 0 3 1
Dodge Challenger 15.5 8 318.0 150 2.76 3.520 16.87 0 0 3 2
AMC Javelin 15.2 8 304.0 150 3.15 3.435 17.30 0 0 3 2
Camaro Z28 13.3 8 350.0 245 3.73 3.840 15.41 0 0 3 4
Pontiac Firebird 19.2 8 400.0 175 3.08 3.845 17.05 0 0 3 2
Fiat X1-9 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1
Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2
Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5 2
Ford Pantera L 15.8 8 351.0 264 4.22 3.170 14.50 0 1 5 4
Ferrari Dino 19.7 6 145.0 175 3.62 2.770 15.50 0 1 5 6
Maserati Bora 15.0 8 301.0 335 3.54 3.570 14.60 0 1 5 8
Volvo 142E 21.4 4 121.0 109 4.11 2.780 18.60 1 1 4 2
str(mtcars)         
## 'data.frame':    32 obs. of  11 variables:
##  $ mpg : num  21 21 22.8 21.4 18.7 18.1 14.3 24.4 22.8 19.2 ...
##  $ cyl : num  6 6 4 6 8 6 8 4 4 6 ...
##  $ disp: num  160 160 108 258 360 ...
##  $ hp  : num  110 110 93 110 175 105 245 62 95 123 ...
##  $ drat: num  3.9 3.9 3.85 3.08 3.15 2.76 3.21 3.69 3.92 3.92 ...
##  $ wt  : num  2.62 2.88 2.32 3.21 3.44 ...
##  $ qsec: num  16.5 17 18.6 19.4 17 ...
##  $ vs  : num  0 0 1 1 0 1 0 1 1 1 ...
##  $ am  : num  1 1 1 0 0 0 0 0 0 0 ...
##  $ gear: num  4 4 4 3 3 3 3 4 4 4 ...
##  $ carb: num  4 4 1 1 2 1 4 2 2 4 ...
rownames(mtcars)
##  [1] "Mazda RX4"           "Mazda RX4 Wag"       "Datsun 710"         
##  [4] "Hornet 4 Drive"      "Hornet Sportabout"   "Valiant"            
##  [7] "Duster 360"          "Merc 240D"           "Merc 230"           
## [10] "Merc 280"            "Merc 280C"           "Merc 450SE"         
## [13] "Merc 450SL"          "Merc 450SLC"         "Cadillac Fleetwood" 
## [16] "Lincoln Continental" "Chrysler Imperial"   "Fiat 128"           
## [19] "Honda Civic"         "Toyota Corolla"      "Toyota Corona"      
## [22] "Dodge Challenger"    "AMC Javelin"         "Camaro Z28"         
## [25] "Pontiac Firebird"    "Fiat X1-9"           "Porsche 914-2"      
## [28] "Lotus Europa"        "Ford Pantera L"      "Ferrari Dino"       
## [31] "Maserati Bora"       "Volvo 142E"
colnames(mtcars)
##  [1] "mpg"  "cyl"  "disp" "hp"   "drat" "wt"   "qsec" "vs"   "am"   "gear"
## [11] "carb"
?mtcars
mtcars R Documentation

Motor Trend Car Road Tests

Description

The data was extracted from the 1974 Motor Trend US magazine, and comprises fuel consumption and 10 aspects of automobile design and performance for 32 automobiles (1973–74 models).

Usage

mtcars

Format

A data frame with 32 observations on 11 variables.

[, 1] </td><td style="text-align: left;"> mpg  </td><td style="text-align: left;"> Miles/(US) gallon </td>
[, 2] </td><td style="text-align: left;"> cyl  </td><td style="text-align: left;"> Number of cylinders </td>
[, 3] </td><td style="text-align: left;"> disp </td><td style="text-align: left;"> Displacement (cu.in.) </td>
[, 4] </td><td style="text-align: left;"> hp   </td><td style="text-align: left;"> Gross horsepower </td>
[, 5] </td><td style="text-align: left;"> drat </td><td style="text-align: left;"> Rear axle ratio </td>
[, 6] </td><td style="text-align: left;"> wt   </td><td style="text-align: left;"> Weight (1000 lbs) </td>
[, 7] </td><td style="text-align: left;"> qsec </td><td style="text-align: left;"> 1/4 mile time </td>
[, 8] </td><td style="text-align: left;"> vs   </td><td style="text-align: left;"> V/S </td>
[, 9] </td><td style="text-align: left;"> am   </td><td style="text-align: left;"> Transmission (0 = automatic, 1 = manual) </td>
[,10] </td><td style="text-align: left;"> gear </td><td style="text-align: left;"> Number of forward gears </td>
[,11] </td><td style="text-align: left;"> carb </td><td style="text-align: left;"> Number of carburetors

Source

Henderson and Velleman (1981), Building multiple regression models interactively. Biometrics, 37, 391–411.

Examples

require(graphics)
pairs(mtcars, main = "mtcars data")
coplot(mpg ~ disp | as.factor(cyl), data = mtcars,
       panel = panel.smooth, rows = 1)
## subset is on rows
ecoCars<-subset(mtcars, mpg > 25)  ## non-standard evaluation of the column name
ecoCars      
mpg cyl disp hp drat wt qsec vs am gear carb
Fiat 128 32.4 4 78.7 66 4.08 2.200 19.47 1 1 4 1
Honda Civic 30.4 4 75.7 52 4.93 1.615 18.52 1 1 4 2
Toyota Corolla 33.9 4 71.1 65 4.22 1.835 19.90 1 1 4 1
Fiat X1-9 27.3 4 79.0 66 4.08 1.935 18.90 1 1 4 1
Porsche 914-2 26.0 4 120.3 91 4.43 2.140 16.70 0 1 5 2
Lotus Europa 30.4 4 95.1 113 3.77 1.513 16.90 1 1 5 2
ecoCars$hp    ## $ gives columns by name
## [1]  66  52  65  66  91 113
mtcars[mtcars$wt<3,c('wt','mpg','cyl','disp')]  ## rows and cols can be referenced 
wt mpg cyl disp
Mazda RX4 2.620 21.0 6 160.0
Mazda RX4 Wag 2.875 21.0 6 160.0
Datsun 710 2.320 22.8 4 108.0
Fiat 128 2.200 32.4 4 78.7
Honda Civic 1.615 30.4 4 75.7
Toyota Corolla 1.835 33.9 4 71.1
Toyota Corona 2.465 21.5 4 120.1
Fiat X1-9 1.935 27.3 4 79.0
Porsche 914-2 2.140 26.0 4 120.3
Lotus Europa 1.513 30.4 4 95.1
Ferrari Dino 2.770 19.7 6 145.0
Volvo 142E 2.780 21.4 4 121.0
mtcars$names <- rownames(mtcars)           ## new col with names, mixed types in df
mtcars$names <- NULL                       ## remove a column

The regular collation of data allows many special operations to be performed on data frames to summarize, subset, and etc the data. We dont have time to cover this important aspect directly.

Serious list example

One example of a very complicated list is all the netcdf meta data.

ncFile <- '~/wrfHydroTestCases/Fourmile_Creek_testcase_v2.0/run.FullRouting/201305160000.LDASOUT_DOMAIN1'
library(ncdf4)
ncid <- nc_open(ncFile)
(Click on the color-boxed section below to skip to its end.)

ncid
## File ~/wrfHydroTestCases/Fourmile_Creek_testcase_v2.0/run.FullRouting/201305160000.LDASOUT_DOMAIN1 (NC_FORMAT_CLASSIC):
## 
##      89 variables (excluding dimension variables):
##         int IVGTYP[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Dominant vegetation category
##             units: category
##         int ISLTYP[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Dominant soil category
##             units: category
##         float FVEG[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Green Vegetation Fraction
##             units: -
##         float LAI[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Leaf area index
##             units: -
##         float SAI[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Stem area index
##             units: -
##         float SWFORC[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Shortwave forcing
##             units: W m{-2}
##         float COSZ[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Cosine of zenith angle
##             units: W m{-2}
##         float LWFORC[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Longwave forcing
##             units: W m{-2}
##         float RAINRATE[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Precipitation rate
##             units: kg m{-2} s{-1}
##         float EMISS[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Grid emissivity
##             units: 
##         float FSA[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Total absorbed SW radiation
##             units: W m{-2}
##         float FIRA[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Total net LW radiation to atmosphere
##             units: W m{-2}
##         float GRDFLX[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Heat flux into the soil
##             units: W m{-2}
##         float HFX[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Total sensible heat to atmosphere
##             units: W m{-2}
##         float LH[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Total latent heat to atmosphere
##             units: W m{-2}
##         float ECAN[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Canopy water evaporation rate
##             units: kg m{-2} s{-1}
##         float EDIR[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Direct from soil evaporation rate
##             units: kg m{-2} s{-1}
##         float ALBEDO[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Surface albedo
##             units: -
##         float ETRAN[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Transpiration rate
##             units: kg m{-2} s{-1}
##         float UGDRNOFF[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Accumulated underground runoff
##             units: mm
##         float SFCRNOFF[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Accumulatetd surface runoff
##             units: mm
##         float CANLIQ[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Canopy liquid water content
##             units: mm
##         float CANICE[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Canopy ice water content
##             units: mm
##         float ZWT[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Depth to water table
##             units: m
##         float WA[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Water in aquifer
##             units: kg m{-2}
##         float WT[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Water in aquifer and saturated soil
##             units: kg m{-2}
##         float ACCPRCP[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Accumulated precip
##             units: mm
##         float ACCECAN[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Accumulated canopy evap
##             units: mm
##         float ACCEDIR[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Accumulated direct soil evap
##             units: mm
##         float ACCETRAN[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Accumulated transpiration
##             units: mm
##         float SAV[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Solar radiative heat flux absorbed by vegetation
##             units: W m{-2}
##         float TR[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Transpiration heat
##             units: W m{-2}
##         float EVC[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Canopy evap heat
##             units: W m{-2}
##         float IRC[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Canopy net LW rad
##             units: W m{-2}
##         float SHC[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Canopy sensible heat
##             units: W m{-2}
##         float IRG[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Ground net LW rad
##             units: W m{-2}
##         float SHG[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Ground sensible heat
##             units: W m{-2}
##         float EVG[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Ground evap heat
##             units: W m{-2}
##         float GHV[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Ground heat flux + to soil vegetated
##             units: W m{-2}
##         float SAG[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Solar radiative heat flux absorbed by ground
##             units: W m{-2}
##         float IRB[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Net LW rad to atm bare
##             units: W m{-2}
##         float SHB[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Sensible heat to atm bare
##             units: W m{-2}
##         float EVB[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Evaporation heat to atm bare
##             units: W m{-2}
##         float GHB[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Ground heat flux + to soil bare
##             units: W m{-2}
##         float TRAD[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Surface radiative temperature
##             units: K
##         float TG[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Ground temperature
##             units: K
##         float TV[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Vegetation temperature
##             units: K
##         float TAH[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Canopy air temperature
##             units: K
##         float TGV[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Ground surface Temp vegetated
##             units: K
##         float TGB[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Ground surface Temp bare
##             units: K
##         float T2MV[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: 2m Air Temp vegetated
##             units: K
##         float T2MB[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: 2m Air Temp bare
##             units: K
##         float Q2MV[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: 2m mixing ratio vegetated
##             units: kg/kg
##         float Q2MB[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: 2m mixing ratio bare
##             units: kg/kg
##         float EAH[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Canopy air vapor pressure
##             units: Pa
##         float FWET[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Wetted or snowed fraction of canopy
##             units: fraction
##         float ZSNSO_SN[west_east,snow_layers,south_north,time]   
##             MemoryOrder: XZY
##             description: Snow layer depths from snow surface
##             units: m
##         float SNICE[west_east,snow_layers,south_north,time]   
##             MemoryOrder: XZY
##             description: Snow layer ice
##             units: mm
##         float SNLIQ[west_east,snow_layers,south_north,time]   
##             MemoryOrder: XZY
##             description: Snow layer liquid water
##             units: mm
##         float SOIL_T[west_east,soil_layers_stag,south_north,time]   
##             MemoryOrder: XZY
##             description: soil temperature
##             units: K
##         float SOIL_W[west_east,soil_layers_stag,south_north,time]   
##             MemoryOrder: XZY
##             description: liquid volumetric soil moisture
##             units: m3 m-3
##         float SNOW_T[west_east,snow_layers,south_north,time]   
##             MemoryOrder: XZY
##             description: snow temperature
##             units: K
##         float SOIL_M[west_east,soil_layers_stag,south_north,time]   
##             MemoryOrder: XZY
##             description: volumetric soil moisture
##             units: m{3} m{-3}
##         float SNOWH[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Snow depth
##             units: m
##         float SNEQV[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Snow water equivalent
##             units: kg m{-2}
##         float QSNOW[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Snowfall rate
##             units: mm s{-1}
##         int ISNOW[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Number of snow layers
##             units: count
##         float FSNO[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Snow-cover fraction on the ground
##             units: 
##         float ACSNOW[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: accumulated snow fall
##             units: mm
##         float ACSNOM[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: accumulated melting water out of snow bottom
##             units: mm
##         float CM[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Momentum drag coefficient
##             units: 
##         float CH[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Sensible heat exchange coefficient
##             units: 
##         float CHV[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Exchange coefficient vegetated
##             units: m s{-1}
##         float CHB[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Exchange coefficient bare
##             units: m s{-1}
##         float CHLEAF[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Exchange coefficient leaf
##             units: m s{-1}
##         float CHUC[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Exchange coefficient bare
##             units: m s{-1}
##         float CHV2[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Exchange coefficient 2-meter vegetated
##             units: m s{-1}
##         float CHB2[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Exchange coefficient 2-meter bare
##             units: m s{-1}
##         float LFMASS[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Leaf mass
##             units: g m{-2}
##         float RTMASS[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Mass of fine roots
##             units: g m{-2}
##         float STMASS[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Stem mass
##             units: g m{-2}
##         float WOOD[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Mass of wood and woody roots
##             units: g m{-2}
##         float STBLCP[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Stable carbon in deep soil
##             units: g m{-2}
##         float FASTCP[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Short-lived carbon in shallow soil
##             units: g m{-2}
##         float NEE[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Net ecosystem exchange
##             units: g m{-2} s{-1} CO2
##         float GPP[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Net instantaneous assimilation
##             units: g m{-2} s{-1} C
##         float NPP[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Net primary productivity
##             units: g m{-2} s{-1} C
##         float PSN[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Total photosynthesis
##             units: umol CO@ m{-2} s{-1}
##         float APAR[west_east,south_north,time]   
##             MemoryOrder: XY
##             description: Photosynthesis active energy by canopy
##             units: W m{-2}
## 
##      5 dimensions:
##         time  Size:1   *** is unlimited ***
##             long_name: valid output time
##             units: seconds since 2012-10-01 00:00 UTC
##         west_east  Size:21
##         south_north  Size:7
##         soil_layers_stag  Size:4
##         snow_layers  Size:3
## 
##     4 global attributes:
##         TITLE: OUTPUT FROM HRLDAS v20150506
##         missing_value: -9.99999994495727e+32
##         model_initialization_time: 2012-10-01_00:00:00
##         model_output_valid_time: 2013-05-16_00:00:00


nc_close(ncid)

Note that the print method for ncid (which has class(ncid)=='ncdf4') does something like an ncdump - but you almost need to stand on your head. In rwrfhydro we modified this to look more like what you expect if you use ncdump on command line.

(Again, click on the color-boxed section below to skip to its end.)

rwrfhydro::ncdump(ncFile)  ## something more visually akin to unix ncdump
## File: ~/wrfHydroTestCases/Fourmile_Creek_testcase_v2.0/run.FullRouting/201305160000.LDASOUT_DOMAIN1
## ( NC_FORMAT_CLASSIC ):
## dimensions (5):
##     time = UNLIMITED ; // (1 currently)
##     west_east = 21 ; 
##     south_north = 7 ; 
##     soil_layers_stag = 4 ; 
##     snow_layers = 3 ; 
## variables (90):
##     integer time(time) ; 
##         time:long_name = "valid output time"
##         time:units = "seconds since 2012-10-01 00:00 UTC"
##     int IVGTYP(time,south_north,west_east)    ; 
##         IVGTYP:MemoryOrder = "XY" ;
##         IVGTYP:description = "Dominant vegetation category" ;
##         IVGTYP:units = "category" ;
##     int ISLTYP(time,south_north,west_east)    ; 
##         ISLTYP:MemoryOrder = "XY" ;
##         ISLTYP:description = "Dominant soil category" ;
##         ISLTYP:units = "category" ;
##     float FVEG(time,south_north,west_east)    ; 
##         FVEG:MemoryOrder = "XY" ;
##         FVEG:description = "Green Vegetation Fraction" ;
##         FVEG:units = "-" ;
##     float LAI(time,south_north,west_east)    ; 
##         LAI:MemoryOrder = "XY" ;
##         LAI:description = "Leaf area index" ;
##         LAI:units = "-" ;
##     float SAI(time,south_north,west_east)    ; 
##         SAI:MemoryOrder = "XY" ;
##         SAI:description = "Stem area index" ;
##         SAI:units = "-" ;
##     float SWFORC(time,south_north,west_east)    ; 
##         SWFORC:MemoryOrder = "XY" ;
##         SWFORC:description = "Shortwave forcing" ;
##         SWFORC:units = "W m{-2}" ;
##     float COSZ(time,south_north,west_east)    ; 
##         COSZ:MemoryOrder = "XY" ;
##         COSZ:description = "Cosine of zenith angle" ;
##         COSZ:units = "W m{-2}" ;
##     float LWFORC(time,south_north,west_east)    ; 
##         LWFORC:MemoryOrder = "XY" ;
##         LWFORC:description = "Longwave forcing" ;
##         LWFORC:units = "W m{-2}" ;
##     float RAINRATE(time,south_north,west_east)    ; 
##         RAINRATE:MemoryOrder = "XY" ;
##         RAINRATE:description = "Precipitation rate" ;
##         RAINRATE:units = "kg m{-2} s{-1}" ;
##     float EMISS(time,south_north,west_east)    ; 
##         EMISS:MemoryOrder = "XY" ;
##         EMISS:description = "Grid emissivity" ;
##         EMISS:units = "" ;
##     float FSA(time,south_north,west_east)    ; 
##         FSA:MemoryOrder = "XY" ;
##         FSA:description = "Total absorbed SW radiation" ;
##         FSA:units = "W m{-2}" ;
##     float FIRA(time,south_north,west_east)    ; 
##         FIRA:MemoryOrder = "XY" ;
##         FIRA:description = "Total net LW radiation to atmosphere" ;
##         FIRA:units = "W m{-2}" ;
##     float GRDFLX(time,south_north,west_east)    ; 
##         GRDFLX:MemoryOrder = "XY" ;
##         GRDFLX:description = "Heat flux into the soil" ;
##         GRDFLX:units = "W m{-2}" ;
##     float HFX(time,south_north,west_east)    ; 
##         HFX:MemoryOrder = "XY" ;
##         HFX:description = "Total sensible heat to atmosphere" ;
##         HFX:units = "W m{-2}" ;
##     float LH(time,south_north,west_east)    ; 
##         LH:MemoryOrder = "XY" ;
##         LH:description = "Total latent heat to atmosphere" ;
##         LH:units = "W m{-2}" ;
##     float ECAN(time,south_north,west_east)    ; 
##         ECAN:MemoryOrder = "XY" ;
##         ECAN:description = "Canopy water evaporation rate" ;
##         ECAN:units = "kg m{-2} s{-1}" ;
##     float EDIR(time,south_north,west_east)    ; 
##         EDIR:MemoryOrder = "XY" ;
##         EDIR:description = "Direct from soil evaporation rate" ;
##         EDIR:units = "kg m{-2} s{-1}" ;
##     float ALBEDO(time,south_north,west_east)    ; 
##         ALBEDO:MemoryOrder = "XY" ;
##         ALBEDO:description = "Surface albedo" ;
##         ALBEDO:units = "-" ;
##     float ETRAN(time,south_north,west_east)    ; 
##         ETRAN:MemoryOrder = "XY" ;
##         ETRAN:description = "Transpiration rate" ;
##         ETRAN:units = "kg m{-2} s{-1}" ;
##     float UGDRNOFF(time,south_north,west_east)    ; 
##         UGDRNOFF:MemoryOrder = "XY" ;
##         UGDRNOFF:description = "Accumulated underground runoff" ;
##         UGDRNOFF:units = "mm" ;
##     float SFCRNOFF(time,south_north,west_east)    ; 
##         SFCRNOFF:MemoryOrder = "XY" ;
##         SFCRNOFF:description = "Accumulatetd surface runoff" ;
##         SFCRNOFF:units = "mm" ;
##     float CANLIQ(time,south_north,west_east)    ; 
##         CANLIQ:MemoryOrder = "XY" ;
##         CANLIQ:description = "Canopy liquid water content" ;
##         CANLIQ:units = "mm" ;
##     float CANICE(time,south_north,west_east)    ; 
##         CANICE:MemoryOrder = "XY" ;
##         CANICE:description = "Canopy ice water content" ;
##         CANICE:units = "mm" ;
##     float ZWT(time,south_north,west_east)    ; 
##         ZWT:MemoryOrder = "XY" ;
##         ZWT:description = "Depth to water table" ;
##         ZWT:units = "m" ;
##     float WA(time,south_north,west_east)    ; 
##         WA:MemoryOrder = "XY" ;
##         WA:description = "Water in aquifer" ;
##         WA:units = "kg m{-2}" ;
##     float WT(time,south_north,west_east)    ; 
##         WT:MemoryOrder = "XY" ;
##         WT:description = "Water in aquifer and saturated soil" ;
##         WT:units = "kg m{-2}" ;
##     float ACCPRCP(time,south_north,west_east)    ; 
##         ACCPRCP:MemoryOrder = "XY" ;
##         ACCPRCP:description = "Accumulated precip" ;
##         ACCPRCP:units = "mm" ;
##     float ACCECAN(time,south_north,west_east)    ; 
##         ACCECAN:MemoryOrder = "XY" ;
##         ACCECAN:description = "Accumulated canopy evap" ;
##         ACCECAN:units = "mm" ;
##     float ACCEDIR(time,south_north,west_east)    ; 
##         ACCEDIR:MemoryOrder = "XY" ;
##         ACCEDIR:description = "Accumulated direct soil evap" ;
##         ACCEDIR:units = "mm" ;
##     float ACCETRAN(time,south_north,west_east)    ; 
##         ACCETRAN:MemoryOrder = "XY" ;
##         ACCETRAN:description = "Accumulated transpiration" ;
##         ACCETRAN:units = "mm" ;
##     float SAV(time,south_north,west_east)    ; 
##         SAV:MemoryOrder = "XY" ;
##         SAV:description = "Solar radiative heat flux absorbed by vegetation" ;
##         SAV:units = "W m{-2}" ;
##     float TR(time,south_north,west_east)    ; 
##         TR:MemoryOrder = "XY" ;
##         TR:description = "Transpiration heat" ;
##         TR:units = "W m{-2}" ;
##     float EVC(time,south_north,west_east)    ; 
##         EVC:MemoryOrder = "XY" ;
##         EVC:description = "Canopy evap heat" ;
##         EVC:units = "W m{-2}" ;
##     float IRC(time,south_north,west_east)    ; 
##         IRC:MemoryOrder = "XY" ;
##         IRC:description = "Canopy net LW rad" ;
##         IRC:units = "W m{-2}" ;
##     float SHC(time,south_north,west_east)    ; 
##         SHC:MemoryOrder = "XY" ;
##         SHC:description = "Canopy sensible heat" ;
##         SHC:units = "W m{-2}" ;
##     float IRG(time,south_north,west_east)    ; 
##         IRG:MemoryOrder = "XY" ;
##         IRG:description = "Ground net LW rad" ;
##         IRG:units = "W m{-2}" ;
##     float SHG(time,south_north,west_east)    ; 
##         SHG:MemoryOrder = "XY" ;
##         SHG:description = "Ground sensible heat" ;
##         SHG:units = "W m{-2}" ;
##     float EVG(time,south_north,west_east)    ; 
##         EVG:MemoryOrder = "XY" ;
##         EVG:description = "Ground evap heat" ;
##         EVG:units = "W m{-2}" ;
##     float GHV(time,south_north,west_east)    ; 
##         GHV:MemoryOrder = "XY" ;
##         GHV:description = "Ground heat flux + to soil vegetated" ;
##         GHV:units = "W m{-2}" ;
##     float SAG(time,south_north,west_east)    ; 
##         SAG:MemoryOrder = "XY" ;
##         SAG:description = "Solar radiative heat flux absorbed by ground" ;
##         SAG:units = "W m{-2}" ;
##     float IRB(time,south_north,west_east)    ; 
##         IRB:MemoryOrder = "XY" ;
##         IRB:description = "Net LW rad to atm bare" ;
##         IRB:units = "W m{-2}" ;
##     float SHB(time,south_north,west_east)    ; 
##         SHB:MemoryOrder = "XY" ;
##         SHB:description = "Sensible heat to atm bare" ;
##         SHB:units = "W m{-2}" ;
##     float EVB(time,south_north,west_east)    ; 
##         EVB:MemoryOrder = "XY" ;
##         EVB:description = "Evaporation heat to atm bare" ;
##         EVB:units = "W m{-2}" ;
##     float GHB(time,south_north,west_east)    ; 
##         GHB:MemoryOrder = "XY" ;
##         GHB:description = "Ground heat flux + to soil bare" ;
##         GHB:units = "W m{-2}" ;
##     float TRAD(time,south_north,west_east)    ; 
##         TRAD:MemoryOrder = "XY" ;
##         TRAD:description = "Surface radiative temperature" ;
##         TRAD:units = "K" ;
##     float TG(time,south_north,west_east)    ; 
##         TG:MemoryOrder = "XY" ;
##         TG:description = "Ground temperature" ;
##         TG:units = "K" ;
##     float TV(time,south_north,west_east)    ; 
##         TV:MemoryOrder = "XY" ;
##         TV:description = "Vegetation temperature" ;
##         TV:units = "K" ;
##     float TAH(time,south_north,west_east)    ; 
##         TAH:MemoryOrder = "XY" ;
##         TAH:description = "Canopy air temperature" ;
##         TAH:units = "K" ;
##     float TGV(time,south_north,west_east)    ; 
##         TGV:MemoryOrder = "XY" ;
##         TGV:description = "Ground surface Temp vegetated" ;
##         TGV:units = "K" ;
##     float TGB(time,south_north,west_east)    ; 
##         TGB:MemoryOrder = "XY" ;
##         TGB:description = "Ground surface Temp bare" ;
##         TGB:units = "K" ;
##     float T2MV(time,south_north,west_east)    ; 
##         T2MV:MemoryOrder = "XY" ;
##         T2MV:description = "2m Air Temp vegetated" ;
##         T2MV:units = "K" ;
##     float T2MB(time,south_north,west_east)    ; 
##         T2MB:MemoryOrder = "XY" ;
##         T2MB:description = "2m Air Temp bare" ;
##         T2MB:units = "K" ;
##     float Q2MV(time,south_north,west_east)    ; 
##         Q2MV:MemoryOrder = "XY" ;
##         Q2MV:description = "2m mixing ratio vegetated" ;
##         Q2MV:units = "kg/kg" ;
##     float Q2MB(time,south_north,west_east)    ; 
##         Q2MB:MemoryOrder = "XY" ;
##         Q2MB:description = "2m mixing ratio bare" ;
##         Q2MB:units = "kg/kg" ;
##     float EAH(time,south_north,west_east)    ; 
##         EAH:MemoryOrder = "XY" ;
##         EAH:description = "Canopy air vapor pressure" ;
##         EAH:units = "Pa" ;
##     float FWET(time,south_north,west_east)    ; 
##         FWET:MemoryOrder = "XY" ;
##         FWET:description = "Wetted or snowed fraction of canopy" ;
##         FWET:units = "fraction" ;
##     float ZSNSO_SN(time,south_north,snow_layers,west_east)    ; 
##         ZSNSO_SN:MemoryOrder = "XZY" ;
##         ZSNSO_SN:description = "Snow layer depths from snow surface" ;
##         ZSNSO_SN:units = "m" ;
##     float SNICE(time,south_north,snow_layers,west_east)    ; 
##         SNICE:MemoryOrder = "XZY" ;
##         SNICE:description = "Snow layer ice" ;
##         SNICE:units = "mm" ;
##     float SNLIQ(time,south_north,snow_layers,west_east)    ; 
##         SNLIQ:MemoryOrder = "XZY" ;
##         SNLIQ:description = "Snow layer liquid water" ;
##         SNLIQ:units = "mm" ;
##     float SOIL_T(time,south_north,soil_layers_stag,west_east)    ; 
##         SOIL_T:MemoryOrder = "XZY" ;
##         SOIL_T:description = "soil temperature" ;
##         SOIL_T:units = "K" ;
##     float SOIL_W(time,south_north,soil_layers_stag,west_east)    ; 
##         SOIL_W:MemoryOrder = "XZY" ;
##         SOIL_W:description = "liquid volumetric soil moisture" ;
##         SOIL_W:units = "m3 m-3" ;
##     float SNOW_T(time,south_north,snow_layers,west_east)    ; 
##         SNOW_T:MemoryOrder = "XZY" ;
##         SNOW_T:description = "snow temperature" ;
##         SNOW_T:units = "K" ;
##     float SOIL_M(time,south_north,soil_layers_stag,west_east)    ; 
##         SOIL_M:MemoryOrder = "XZY" ;
##         SOIL_M:description = "volumetric soil moisture" ;
##         SOIL_M:units = "m{3} m{-3}" ;
##     float SNOWH(time,south_north,west_east)    ; 
##         SNOWH:MemoryOrder = "XY" ;
##         SNOWH:description = "Snow depth" ;
##         SNOWH:units = "m" ;
##     float SNEQV(time,south_north,west_east)    ; 
##         SNEQV:MemoryOrder = "XY" ;
##         SNEQV:description = "Snow water equivalent" ;
##         SNEQV:units = "kg m{-2}" ;
##     float QSNOW(time,south_north,west_east)    ; 
##         QSNOW:MemoryOrder = "XY" ;
##         QSNOW:description = "Snowfall rate" ;
##         QSNOW:units = "mm s{-1}" ;
##     int ISNOW(time,south_north,west_east)    ; 
##         ISNOW:MemoryOrder = "XY" ;
##         ISNOW:description = "Number of snow layers" ;
##         ISNOW:units = "count" ;
##     float FSNO(time,south_north,west_east)    ; 
##         FSNO:MemoryOrder = "XY" ;
##         FSNO:description = "Snow-cover fraction on the ground" ;
##         FSNO:units = "" ;
##     float ACSNOW(time,south_north,west_east)    ; 
##         ACSNOW:MemoryOrder = "XY" ;
##         ACSNOW:description = "accumulated snow fall" ;
##         ACSNOW:units = "mm" ;
##     float ACSNOM(time,south_north,west_east)    ; 
##         ACSNOM:MemoryOrder = "XY" ;
##         ACSNOM:description = "accumulated melting water out of snow bottom" ;
##         ACSNOM:units = "mm" ;
##     float CM(time,south_north,west_east)    ; 
##         CM:MemoryOrder = "XY" ;
##         CM:description = "Momentum drag coefficient" ;
##         CM:units = "" ;
##     float CH(time,south_north,west_east)    ; 
##         CH:MemoryOrder = "XY" ;
##         CH:description = "Sensible heat exchange coefficient" ;
##         CH:units = "" ;
##     float CHV(time,south_north,west_east)    ; 
##         CHV:MemoryOrder = "XY" ;
##         CHV:description = "Exchange coefficient vegetated" ;
##         CHV:units = "m s{-1}" ;
##     float CHB(time,south_north,west_east)    ; 
##         CHB:MemoryOrder = "XY" ;
##         CHB:description = "Exchange coefficient bare" ;
##         CHB:units = "m s{-1}" ;
##     float CHLEAF(time,south_north,west_east)    ; 
##         CHLEAF:MemoryOrder = "XY" ;
##         CHLEAF:description = "Exchange coefficient leaf" ;
##         CHLEAF:units = "m s{-1}" ;
##     float CHUC(time,south_north,west_east)    ; 
##         CHUC:MemoryOrder = "XY" ;
##         CHUC:description = "Exchange coefficient bare" ;
##         CHUC:units = "m s{-1}" ;
##     float CHV2(time,south_north,west_east)    ; 
##         CHV2:MemoryOrder = "XY" ;
##         CHV2:description = "Exchange coefficient 2-meter vegetated" ;
##         CHV2:units = "m s{-1}" ;
##     float CHB2(time,south_north,west_east)    ; 
##         CHB2:MemoryOrder = "XY" ;
##         CHB2:description = "Exchange coefficient 2-meter bare" ;
##         CHB2:units = "m s{-1}" ;
##     float LFMASS(time,south_north,west_east)    ; 
##         LFMASS:MemoryOrder = "XY" ;
##         LFMASS:description = "Leaf mass" ;
##         LFMASS:units = "g m{-2}" ;
##     float RTMASS(time,south_north,west_east)    ; 
##         RTMASS:MemoryOrder = "XY" ;
##         RTMASS:description = "Mass of fine roots" ;
##         RTMASS:units = "g m{-2}" ;
##     float STMASS(time,south_north,west_east)    ; 
##         STMASS:MemoryOrder = "XY" ;
##         STMASS:description = "Stem mass" ;
##         STMASS:units = "g m{-2}" ;
##     float WOOD(time,south_north,west_east)    ; 
##         WOOD:MemoryOrder = "XY" ;
##         WOOD:description = "Mass of wood and woody roots" ;
##         WOOD:units = "g m{-2}" ;
##     float STBLCP(time,south_north,west_east)    ; 
##         STBLCP:MemoryOrder = "XY" ;
##         STBLCP:description = "Stable carbon in deep soil" ;
##         STBLCP:units = "g m{-2}" ;
##     float FASTCP(time,south_north,west_east)    ; 
##         FASTCP:MemoryOrder = "XY" ;
##         FASTCP:description = "Short-lived carbon in shallow soil" ;
##         FASTCP:units = "g m{-2}" ;
##     float NEE(time,south_north,west_east)    ; 
##         NEE:MemoryOrder = "XY" ;
##         NEE:description = "Net ecosystem exchange" ;
##         NEE:units = "g m{-2} s{-1} CO2" ;
##     float GPP(time,south_north,west_east)    ; 
##         GPP:MemoryOrder = "XY" ;
##         GPP:description = "Net instantaneous assimilation" ;
##         GPP:units = "g m{-2} s{-1} C" ;
##     float NPP(time,south_north,west_east)    ; 
##         NPP:MemoryOrder = "XY" ;
##         NPP:description = "Net primary productivity" ;
##         NPP:units = "g m{-2} s{-1} C" ;
##     float PSN(time,south_north,west_east)    ; 
##         PSN:MemoryOrder = "XY" ;
##         PSN:description = "Total photosynthesis" ;
##         PSN:units = "umol CO@ m{-2} s{-1}" ;
##     float APAR(time,south_north,west_east)    ; 
##         APAR:MemoryOrder = "XY" ;
##         APAR:description = "Photosynthesis active energy by canopy" ;
##         APAR:units = "W m{-2}" ;
## 
## // global attributes (4):
##     :TITLE = "OUTPUT FROM HRLDAS v20150506"
##     :missing_value = "-9.99999994495727e+32"
##     :model_initialization_time = "2012-10-01_00:00:00"
##     :model_output_valid_time = "2013-05-16_00:00:00"


Detailed inspection of the ncid object makes it obvious that automating information extraction is going to be key.

(Again, click on the color-boxed section below to skip to its end.)

str(ncid)
## List of 14
##  $ filename   : chr "~/wrfHydroTestCases/Fourmile_Creek_testcase_v2.0/run.FullRouting/201305160000.LDASOUT_DOMAIN1"
##  $ writable   : logi FALSE
##  $ id         : int 65536
##  $ safemode   : logi FALSE
##  $ format     : chr "NC_FORMAT_CLASSIC"
##  $ is_GMT     : logi FALSE
##  $ groups     :List of 1
##   ..$ :List of 7
##   .. ..$ id   : int 65536
##   .. ..$ name : chr ""
##   .. ..$ ndims: int 5
##   .. ..$ nvars: int 90
##   .. ..$ natts: int 4
##   .. ..$ dimid: int [1:5(1d)] 0 1 2 3 4
##   .. ..$ fqgn : chr ""
##   .. ..- attr(*, "class")= chr "ncgroup4"
##  $ fqgn2Rindex:List of 1
##   ..$ : int 1
##  $ ndims      : num 5
##  $ natts      : num 4
##  $ dim        :List of 5
##   ..$ time            :List of 10
##   .. ..$ name         : chr "time"
##   .. ..$ len          : int 1
##   .. ..$ unlim        : logi TRUE
##   .. ..$ group_index  : int 1
##   .. ..$ group_id     : int 65536
##   .. ..$ id           : int 0
##   .. ..$ dimvarid     :List of 5
##   .. .. ..$ id         : int 0
##   .. .. ..$ group_index: int 1
##   .. .. ..$ group_id   : int 65536
##   .. .. ..$ list_index : num -1
##   .. .. ..$ isdimvar   : logi TRUE
##   .. .. ..- attr(*, "class")= chr "ncid4"
##   .. ..$ units        : chr "seconds since 2012-10-01 00:00 UTC"
##   .. ..$ vals         : int [1(1d)] 19612800
##   .. ..$ create_dimvar: logi TRUE
##   .. ..- attr(*, "class")= chr "ncdim4"
##   ..$ west_east       :List of 10
##   .. ..$ name         : chr "west_east"
##   .. ..$ len          : int 21
##   .. ..$ unlim        : logi FALSE
##   .. ..$ group_index  : int 1
##   .. ..$ group_id     : int 65536
##   .. ..$ id           : int 1
##   .. ..$ dimvarid     :List of 5
##   .. .. ..$ id         : int -1
##   .. .. ..$ group_index: int 1
##   .. .. ..$ group_id   : int 65536
##   .. .. ..$ list_index : num -1
##   .. .. ..$ isdimvar   : logi TRUE
##   .. .. ..- attr(*, "class")= chr "ncid4"
##   .. ..$ vals         : int [1:21] 1 2 3 4 5 6 7 8 9 10 ...
##   .. ..$ units        : chr ""
##   .. ..$ create_dimvar: logi FALSE
##   .. ..- attr(*, "class")= chr "ncdim4"
##   ..$ south_north     :List of 10
##   .. ..$ name         : chr "south_north"
##   .. ..$ len          : int 7
##   .. ..$ unlim        : logi FALSE
##   .. ..$ group_index  : int 1
##   .. ..$ group_id     : int 65536
##   .. ..$ id           : int 2
##   .. ..$ dimvarid     :List of 5
##   .. .. ..$ id         : int -1
##   .. .. ..$ group_index: int 1
##   .. .. ..$ group_id   : int 65536
##   .. .. ..$ list_index : num -1
##   .. .. ..$ isdimvar   : logi TRUE
##   .. .. ..- attr(*, "class")= chr "ncid4"
##   .. ..$ vals         : int [1:7] 1 2 3 4 5 6 7
##   .. ..$ units        : chr ""
##   .. ..$ create_dimvar: logi FALSE
##   .. ..- attr(*, "class")= chr "ncdim4"
##   ..$ soil_layers_stag:List of 10
##   .. ..$ name         : chr "soil_layers_stag"
##   .. ..$ len          : int 4
##   .. ..$ unlim        : logi FALSE
##   .. ..$ group_index  : int 1
##   .. ..$ group_id     : int 65536
##   .. ..$ id           : int 3
##   .. ..$ dimvarid     :List of 5
##   .. .. ..$ id         : int -1
##   .. .. ..$ group_index: int 1
##   .. .. ..$ group_id   : int 65536
##   .. .. ..$ list_index : num -1
##   .. .. ..$ isdimvar   : logi TRUE
##   .. .. ..- attr(*, "class")= chr "ncid4"
##   .. ..$ vals         : int [1:4] 1 2 3 4
##   .. ..$ units        : chr ""
##   .. ..$ create_dimvar: logi FALSE
##   .. ..- attr(*, "class")= chr "ncdim4"
##   ..$ snow_layers     :List of 10
##   .. ..$ name         : chr "snow_layers"
##   .. ..$ len          : int 3
##   .. ..$ unlim        : logi FALSE
##   .. ..$ group_index  : int 1
##   .. ..$ group_id     : int 65536
##   .. ..$ id           : int 4
##   .. ..$ dimvarid     :List of 5
##   .. .. ..$ id         : int -1
##   .. .. ..$ group_index: int 1
##   .. .. ..$ group_id   : int 65536
##   .. .. ..$ list_index : num -1
##   .. .. ..$ isdimvar   : logi TRUE
##   .. .. ..- attr(*, "class")= chr "ncid4"
##   .. ..$ vals         : int [1:3] 1 2 3
##   .. ..$ units        : chr ""
##   .. ..$ create_dimvar: logi FALSE
##   .. ..- attr(*, "class")= chr "ncdim4"
##  $ unlimdimid : num 1
##  $ nvars      : num 89
##  $ var        :List of 89
##   ..$ IVGTYP  :List of 22
##   .. ..$ id                :List of 5
##   .. .. ..$ id         : num 1
##   .. .. ..$ group_index: num -1
##   .. .. ..$ group_id   : int 65536
##   .. .. ..$ list_index : num 1
##   .. .. ..$ isdimvar   : logi FALSE
##   .. .. ..- attr(*, "class")= chr "ncid4"
##   .. ..$ name              : chr "IVGTYP"
##   .. ..$ ndims             : int 3
##   .. ..$ natts             : int 3
##   .. ..$ size              : int [1:3] 21 7 1
##   .. ..$ dimids            : int [1:3] 1 2 0
##   .. ..$ prec              : chr "int"
##   .. ..$ units             : chr "category"
##   .. ..$ longname          : chr "IVGTYP"
##   .. ..$ group_index       : int 1
##   .. ..$ chunksizes        : logi NA
##   .. ..$ storage           : num 2
##   .. ..$ shuffle           : logi FALSE
##   .. ..$ compression       : logi NA
##   .. ..$ dims              : list()
##   .. ..$ dim               :List of 3
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "west_east"
##   .. .. .. ..$ len          : int 21
##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 1
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int -1
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:21] 1 2 3 4 5 6 7 8 9 10 ...
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "south_north"
##   .. .. .. ..$ len          : int 7
##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 2
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int -1
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:7] 1 2 3 4 5 6 7
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "time"
##   .. .. .. ..$ len          : int 1
##   .. .. .. ..$ unlim        : logi TRUE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 0
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int 0
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ units        : chr "seconds since 2012-10-01 00:00 UTC"
##   .. .. .. ..$ vals         : int [1(1d)] 19612800
##   .. .. .. ..$ create_dimvar: logi TRUE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. ..$ varsize           : int [1:3] 21 7 1
##   .. ..$ unlim             : logi TRUE
##   .. ..$ make_missing_value: logi FALSE
##   .. ..$ missval           : logi NA
##   .. ..$ hasAddOffset      : logi FALSE
##   .. ..$ hasScaleFact      : logi FALSE
##   .. ..- attr(*, "class")= chr "ncvar4"
##   ..$ ISLTYP  :List of 22
##   .. ..$ id                :List of 5
##   .. .. ..$ id         : num 2
##   .. .. ..$ group_index: num -1
##   .. .. ..$ group_id   : int 65536
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##   .. .. ..$ isdimvar   : logi FALSE
##   .. .. ..- attr(*, "class")= chr "ncid4"
##   .. ..$ name              : chr "ISLTYP"
##   .. ..$ ndims             : int 3
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##   .. ..$ size              : int [1:3] 21 7 1
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##   .. ..$ prec              : chr "int"
##   .. ..$ units             : chr "category"
##   .. ..$ longname          : chr "ISLTYP"
##   .. ..$ group_index       : int 1
##   .. ..$ chunksizes        : logi NA
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##   .. ..$ dims              : list()
##   .. ..$ dim               :List of 3
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "west_east"
##   .. .. .. ..$ len          : int 21
##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 1
##   .. .. .. ..$ dimvarid     :List of 5
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##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:21] 1 2 3 4 5 6 7 8 9 10 ...
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "south_north"
##   .. .. .. ..$ len          : int 7
##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 2
##   .. .. .. ..$ dimvarid     :List of 5
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##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:7] 1 2 3 4 5 6 7
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "time"
##   .. .. .. ..$ len          : int 1
##   .. .. .. ..$ unlim        : logi TRUE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 0
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int 0
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ units        : chr "seconds since 2012-10-01 00:00 UTC"
##   .. .. .. ..$ vals         : int [1(1d)] 19612800
##   .. .. .. ..$ create_dimvar: logi TRUE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. ..$ varsize           : int [1:3] 21 7 1
##   .. ..$ unlim             : logi TRUE
##   .. ..$ make_missing_value: logi FALSE
##   .. ..$ missval           : logi NA
##   .. ..$ hasAddOffset      : logi FALSE
##   .. ..$ hasScaleFact      : logi FALSE
##   .. ..- attr(*, "class")= chr "ncvar4"
##   ..$ FVEG    :List of 22
##   .. ..$ id                :List of 5
##   .. .. ..$ id         : num 3
##   .. .. ..$ group_index: num -1
##   .. .. ..$ group_id   : int 65536
##   .. .. ..$ list_index : num 3
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##   .. .. ..- attr(*, "class")= chr "ncid4"
##   .. ..$ name              : chr "FVEG"
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##   .. ..$ natts             : int 3
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##   .. ..$ prec              : chr "float"
##   .. ..$ units             : chr "-"
##   .. ..$ longname          : chr "FVEG"
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##   .. ..$ chunksizes        : logi NA
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##   .. ..$ shuffle           : logi FALSE
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##   .. ..$ dims              : list()
##   .. ..$ dim               :List of 3
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "west_east"
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##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
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##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:21] 1 2 3 4 5 6 7 8 9 10 ...
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "south_north"
##   .. .. .. ..$ len          : int 7
##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 2
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int -1
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:7] 1 2 3 4 5 6 7
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "time"
##   .. .. .. ..$ len          : int 1
##   .. .. .. ..$ unlim        : logi TRUE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 0
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int 0
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
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##   .. .. .. ..$ vals         : int [1(1d)] 19612800
##   .. .. .. ..$ create_dimvar: logi TRUE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. ..$ varsize           : int [1:3] 21 7 1
##   .. ..$ unlim             : logi TRUE
##   .. ..$ make_missing_value: logi FALSE
##   .. ..$ missval           : num 1e+30
##   .. ..$ hasAddOffset      : logi FALSE
##   .. ..$ hasScaleFact      : logi FALSE
##   .. ..- attr(*, "class")= chr "ncvar4"
##   ..$ LAI     :List of 22
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##   .. .. ..$ group_index: num -1
##   .. .. ..$ group_id   : int 65536
##   .. .. ..$ list_index : num 4
##   .. .. ..$ isdimvar   : logi FALSE
##   .. .. ..- attr(*, "class")= chr "ncid4"
##   .. ..$ name              : chr "LAI"
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##   .. ..$ natts             : int 3
##   .. ..$ size              : int [1:3] 21 7 1
##   .. ..$ dimids            : int [1:3] 1 2 0
##   .. ..$ prec              : chr "float"
##   .. ..$ units             : chr "-"
##   .. ..$ longname          : chr "LAI"
##   .. ..$ group_index       : int 1
##   .. ..$ chunksizes        : logi NA
##   .. ..$ storage           : num 2
##   .. ..$ shuffle           : logi FALSE
##   .. ..$ compression       : logi NA
##   .. ..$ dims              : list()
##   .. ..$ dim               :List of 3
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "west_east"
##   .. .. .. ..$ len          : int 21
##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 1
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int -1
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:21] 1 2 3 4 5 6 7 8 9 10 ...
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "south_north"
##   .. .. .. ..$ len          : int 7
##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 2
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int -1
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:7] 1 2 3 4 5 6 7
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "time"
##   .. .. .. ..$ len          : int 1
##   .. .. .. ..$ unlim        : logi TRUE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 0
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int 0
##   .. .. .. .. ..$ group_index: int 1
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##   .. .. .. .. ..$ id         : int -1
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:7] 1 2 3 4 5 6 7
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "time"
##   .. .. .. ..$ len          : int 1
##   .. .. .. ..$ unlim        : logi TRUE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 0
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int 0
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ units        : chr "seconds since 2012-10-01 00:00 UTC"
##   .. .. .. ..$ vals         : int [1(1d)] 19612800
##   .. .. .. ..$ create_dimvar: logi TRUE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. ..$ varsize           : int [1:3] 21 7 1
##   .. ..$ unlim             : logi TRUE
##   .. ..$ make_missing_value: logi FALSE
##   .. ..$ missval           : num 1e+30
##   .. ..$ hasAddOffset      : logi FALSE
##   .. ..$ hasScaleFact      : logi FALSE
##   .. ..- attr(*, "class")= chr "ncvar4"
##   ..$ NEE     :List of 22
##   .. ..$ id                :List of 5
##   .. .. ..$ id         : num 85
##   .. .. ..$ group_index: num -1
##   .. .. ..$ group_id   : int 65536
##   .. .. ..$ list_index : num 85
##   .. .. ..$ isdimvar   : logi FALSE
##   .. .. ..- attr(*, "class")= chr "ncid4"
##   .. ..$ name              : chr "NEE"
##   .. ..$ ndims             : int 3
##   .. ..$ natts             : int 3
##   .. ..$ size              : int [1:3] 21 7 1
##   .. ..$ dimids            : int [1:3] 1 2 0
##   .. ..$ prec              : chr "float"
##   .. ..$ units             : chr "g m{-2} s{-1} CO2"
##   .. ..$ longname          : chr "NEE"
##   .. ..$ group_index       : int 1
##   .. ..$ chunksizes        : logi NA
##   .. ..$ storage           : num 2
##   .. ..$ shuffle           : logi FALSE
##   .. ..$ compression       : logi NA
##   .. ..$ dims              : list()
##   .. ..$ dim               :List of 3
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "west_east"
##   .. .. .. ..$ len          : int 21
##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 1
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int -1
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:21] 1 2 3 4 5 6 7 8 9 10 ...
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "south_north"
##   .. .. .. ..$ len          : int 7
##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 2
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int -1
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:7] 1 2 3 4 5 6 7
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "time"
##   .. .. .. ..$ len          : int 1
##   .. .. .. ..$ unlim        : logi TRUE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 0
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int 0
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ units        : chr "seconds since 2012-10-01 00:00 UTC"
##   .. .. .. ..$ vals         : int [1(1d)] 19612800
##   .. .. .. ..$ create_dimvar: logi TRUE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. ..$ varsize           : int [1:3] 21 7 1
##   .. ..$ unlim             : logi TRUE
##   .. ..$ make_missing_value: logi FALSE
##   .. ..$ missval           : num 1e+30
##   .. ..$ hasAddOffset      : logi FALSE
##   .. ..$ hasScaleFact      : logi FALSE
##   .. ..- attr(*, "class")= chr "ncvar4"
##   ..$ GPP     :List of 22
##   .. ..$ id                :List of 5
##   .. .. ..$ id         : num 86
##   .. .. ..$ group_index: num -1
##   .. .. ..$ group_id   : int 65536
##   .. .. ..$ list_index : num 86
##   .. .. ..$ isdimvar   : logi FALSE
##   .. .. ..- attr(*, "class")= chr "ncid4"
##   .. ..$ name              : chr "GPP"
##   .. ..$ ndims             : int 3
##   .. ..$ natts             : int 3
##   .. ..$ size              : int [1:3] 21 7 1
##   .. ..$ dimids            : int [1:3] 1 2 0
##   .. ..$ prec              : chr "float"
##   .. ..$ units             : chr "g m{-2} s{-1} C"
##   .. ..$ longname          : chr "GPP"
##   .. ..$ group_index       : int 1
##   .. ..$ chunksizes        : logi NA
##   .. ..$ storage           : num 2
##   .. ..$ shuffle           : logi FALSE
##   .. ..$ compression       : logi NA
##   .. ..$ dims              : list()
##   .. ..$ dim               :List of 3
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "west_east"
##   .. .. .. ..$ len          : int 21
##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 1
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int -1
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:21] 1 2 3 4 5 6 7 8 9 10 ...
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "south_north"
##   .. .. .. ..$ len          : int 7
##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 2
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int -1
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:7] 1 2 3 4 5 6 7
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "time"
##   .. .. .. ..$ len          : int 1
##   .. .. .. ..$ unlim        : logi TRUE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 0
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int 0
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ units        : chr "seconds since 2012-10-01 00:00 UTC"
##   .. .. .. ..$ vals         : int [1(1d)] 19612800
##   .. .. .. ..$ create_dimvar: logi TRUE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. ..$ varsize           : int [1:3] 21 7 1
##   .. ..$ unlim             : logi TRUE
##   .. ..$ make_missing_value: logi FALSE
##   .. ..$ missval           : num 1e+30
##   .. ..$ hasAddOffset      : logi FALSE
##   .. ..$ hasScaleFact      : logi FALSE
##   .. ..- attr(*, "class")= chr "ncvar4"
##   ..$ NPP     :List of 22
##   .. ..$ id                :List of 5
##   .. .. ..$ id         : num 87
##   .. .. ..$ group_index: num -1
##   .. .. ..$ group_id   : int 65536
##   .. .. ..$ list_index : num 87
##   .. .. ..$ isdimvar   : logi FALSE
##   .. .. ..- attr(*, "class")= chr "ncid4"
##   .. ..$ name              : chr "NPP"
##   .. ..$ ndims             : int 3
##   .. ..$ natts             : int 3
##   .. ..$ size              : int [1:3] 21 7 1
##   .. ..$ dimids            : int [1:3] 1 2 0
##   .. ..$ prec              : chr "float"
##   .. ..$ units             : chr "g m{-2} s{-1} C"
##   .. ..$ longname          : chr "NPP"
##   .. ..$ group_index       : int 1
##   .. ..$ chunksizes        : logi NA
##   .. ..$ storage           : num 2
##   .. ..$ shuffle           : logi FALSE
##   .. ..$ compression       : logi NA
##   .. ..$ dims              : list()
##   .. ..$ dim               :List of 3
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "west_east"
##   .. .. .. ..$ len          : int 21
##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 1
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int -1
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:21] 1 2 3 4 5 6 7 8 9 10 ...
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "south_north"
##   .. .. .. ..$ len          : int 7
##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 2
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int -1
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:7] 1 2 3 4 5 6 7
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "time"
##   .. .. .. ..$ len          : int 1
##   .. .. .. ..$ unlim        : logi TRUE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 0
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int 0
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ units        : chr "seconds since 2012-10-01 00:00 UTC"
##   .. .. .. ..$ vals         : int [1(1d)] 19612800
##   .. .. .. ..$ create_dimvar: logi TRUE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. ..$ varsize           : int [1:3] 21 7 1
##   .. ..$ unlim             : logi TRUE
##   .. ..$ make_missing_value: logi FALSE
##   .. ..$ missval           : num 1e+30
##   .. ..$ hasAddOffset      : logi FALSE
##   .. ..$ hasScaleFact      : logi FALSE
##   .. ..- attr(*, "class")= chr "ncvar4"
##   ..$ PSN     :List of 22
##   .. ..$ id                :List of 5
##   .. .. ..$ id         : num 88
##   .. .. ..$ group_index: num -1
##   .. .. ..$ group_id   : int 65536
##   .. .. ..$ list_index : num 88
##   .. .. ..$ isdimvar   : logi FALSE
##   .. .. ..- attr(*, "class")= chr "ncid4"
##   .. ..$ name              : chr "PSN"
##   .. ..$ ndims             : int 3
##   .. ..$ natts             : int 3
##   .. ..$ size              : int [1:3] 21 7 1
##   .. ..$ dimids            : int [1:3] 1 2 0
##   .. ..$ prec              : chr "float"
##   .. ..$ units             : chr "umol CO@ m{-2} s{-1}"
##   .. ..$ longname          : chr "PSN"
##   .. ..$ group_index       : int 1
##   .. ..$ chunksizes        : logi NA
##   .. ..$ storage           : num 2
##   .. ..$ shuffle           : logi FALSE
##   .. ..$ compression       : logi NA
##   .. ..$ dims              : list()
##   .. ..$ dim               :List of 3
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "west_east"
##   .. .. .. ..$ len          : int 21
##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 1
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int -1
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:21] 1 2 3 4 5 6 7 8 9 10 ...
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "south_north"
##   .. .. .. ..$ len          : int 7
##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 2
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int -1
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:7] 1 2 3 4 5 6 7
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "time"
##   .. .. .. ..$ len          : int 1
##   .. .. .. ..$ unlim        : logi TRUE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 0
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int 0
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ units        : chr "seconds since 2012-10-01 00:00 UTC"
##   .. .. .. ..$ vals         : int [1(1d)] 19612800
##   .. .. .. ..$ create_dimvar: logi TRUE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. ..$ varsize           : int [1:3] 21 7 1
##   .. ..$ unlim             : logi TRUE
##   .. ..$ make_missing_value: logi FALSE
##   .. ..$ missval           : num 1e+30
##   .. ..$ hasAddOffset      : logi FALSE
##   .. ..$ hasScaleFact      : logi FALSE
##   .. ..- attr(*, "class")= chr "ncvar4"
##   ..$ APAR    :List of 22
##   .. ..$ id                :List of 5
##   .. .. ..$ id         : num 89
##   .. .. ..$ group_index: num -1
##   .. .. ..$ group_id   : int 65536
##   .. .. ..$ list_index : num 89
##   .. .. ..$ isdimvar   : logi FALSE
##   .. .. ..- attr(*, "class")= chr "ncid4"
##   .. ..$ name              : chr "APAR"
##   .. ..$ ndims             : int 3
##   .. ..$ natts             : int 3
##   .. ..$ size              : int [1:3] 21 7 1
##   .. ..$ dimids            : int [1:3] 1 2 0
##   .. ..$ prec              : chr "float"
##   .. ..$ units             : chr "W m{-2}"
##   .. ..$ longname          : chr "APAR"
##   .. ..$ group_index       : int 1
##   .. ..$ chunksizes        : logi NA
##   .. ..$ storage           : num 2
##   .. ..$ shuffle           : logi FALSE
##   .. ..$ compression       : logi NA
##   .. ..$ dims              : list()
##   .. ..$ dim               :List of 3
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "west_east"
##   .. .. .. ..$ len          : int 21
##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 1
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int -1
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:21] 1 2 3 4 5 6 7 8 9 10 ...
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "south_north"
##   .. .. .. ..$ len          : int 7
##   .. .. .. ..$ unlim        : logi FALSE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 2
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int -1
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ vals         : int [1:7] 1 2 3 4 5 6 7
##   .. .. .. ..$ units        : chr ""
##   .. .. .. ..$ create_dimvar: logi FALSE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. .. ..$ :List of 10
##   .. .. .. ..$ name         : chr "time"
##   .. .. .. ..$ len          : int 1
##   .. .. .. ..$ unlim        : logi TRUE
##   .. .. .. ..$ group_index  : int 1
##   .. .. .. ..$ group_id     : int 65536
##   .. .. .. ..$ id           : int 0
##   .. .. .. ..$ dimvarid     :List of 5
##   .. .. .. .. ..$ id         : int 0
##   .. .. .. .. ..$ group_index: int 1
##   .. .. .. .. ..$ group_id   : int 65536
##   .. .. .. .. ..$ list_index : num -1
##   .. .. .. .. ..$ isdimvar   : logi TRUE
##   .. .. .. .. ..- attr(*, "class")= chr "ncid4"
##   .. .. .. ..$ units        : chr "seconds since 2012-10-01 00:00 UTC"
##   .. .. .. ..$ vals         : int [1(1d)] 19612800
##   .. .. .. ..$ create_dimvar: logi TRUE
##   .. .. .. ..- attr(*, "class")= chr "ncdim4"
##   .. ..$ varsize           : int [1:3] 21 7 1
##   .. ..$ unlim             : logi TRUE
##   .. ..$ make_missing_value: logi FALSE
##   .. ..$ missval           : num 1e+30
##   .. ..$ hasAddOffset      : logi FALSE
##   .. ..$ hasScaleFact      : logi FALSE
##   .. ..- attr(*, "class")= chr "ncvar4"
##  - attr(*, "class")= chr "ncdf4"


Whoa!! How in the world would you, for example, get the dimensions of each variable?

## drill down by name into the object, var looks like it describes variables.
names(ncid) 
##  [1] "filename"    "writable"    "id"          "safemode"    "format"     
##  [6] "is_GMT"      "groups"      "fqgn2Rindex" "ndims"       "natts"      
## [11] "dim"         "unlimdimid"  "nvars"       "var"
## what are the objects named contained in ncid$var?
names(ncid$var)  
##  [1] "IVGTYP"   "ISLTYP"   "FVEG"     "LAI"      "SAI"      "SWFORC"  
##  [7] "COSZ"     "LWFORC"   "RAINRATE" "EMISS"    "FSA"      "FIRA"    
## [13] "GRDFLX"   "HFX"      "LH"       "ECAN"     "EDIR"     "ALBEDO"  
## [19] "ETRAN"    "UGDRNOFF" "SFCRNOFF" "CANLIQ"   "CANICE"   "ZWT"     
## [25] "WA"       "WT"       "ACCPRCP"  "ACCECAN"  "ACCEDIR"  "ACCETRAN"
## [31] "SAV"      "TR"       "EVC"      "IRC"      "SHC"      "IRG"     
## [37] "SHG"      "EVG"      "GHV"      "SAG"      "IRB"      "SHB"     
## [43] "EVB"      "GHB"      "TRAD"     "TG"       "TV"       "TAH"     
## [49] "TGV"      "TGB"      "T2MV"     "T2MB"     "Q2MV"     "Q2MB"    
## [55] "EAH"      "FWET"     "ZSNSO_SN" "SNICE"    "SNLIQ"    "SOIL_T"  
## [61] "SOIL_W"   "SNOW_T"   "SOIL_M"   "SNOWH"    "SNEQV"    "QSNOW"   
## [67] "ISNOW"    "FSNO"     "ACSNOW"   "ACSNOM"   "CM"       "CH"      
## [73] "CHV"      "CHB"      "CHLEAF"   "CHUC"     "CHV2"     "CHB2"    
## [79] "LFMASS"   "RTMASS"   "STMASS"   "WOOD"     "STBLCP"   "FASTCP"  
## [85] "NEE"      "GPP"      "NPP"      "PSN"      "APAR"
## each variables has these named objects
names(ncid$var$SOIL_M)  
##  [1] "id"                 "name"               "ndims"             
##  [4] "natts"              "size"               "dimids"            
##  [7] "prec"               "units"              "longname"          
## [10] "group_index"        "chunksizes"         "storage"           
## [13] "shuffle"            "compression"        "dims"              
## [16] "dim"                "varsize"            "unlim"             
## [19] "make_missing_value" "missval"            "hasAddOffset"      
## [22] "hasScaleFact"
## NamedList simply names a list named by its entries
varList <- rwrfhydro::NamedList(names(ncid$var))  
varList   
## $IVGTYP
## [1] "IVGTYP"
## 
## $ISLTYP
## [1] "ISLTYP"
## 
## $FVEG
## [1] "FVEG"
## 
## $LAI
## [1] "LAI"
## 
## $SAI
## [1] "SAI"
## 
## $SWFORC
## [1] "SWFORC"
## 
## $COSZ
## [1] "COSZ"
## 
## $LWFORC
## [1] "LWFORC"
## 
## $RAINRATE
## [1] "RAINRATE"
## 
## $EMISS
## [1] "EMISS"
## 
## $FSA
## [1] "FSA"
## 
## $FIRA
## [1] "FIRA"
## 
## $GRDFLX
## [1] "GRDFLX"
## 
## $HFX
## [1] "HFX"
## 
## $LH
## [1] "LH"
## 
## $ECAN
## [1] "ECAN"
## 
## $EDIR
## [1] "EDIR"
## 
## $ALBEDO
## [1] "ALBEDO"
## 
## $ETRAN
## [1] "ETRAN"
## 
## $UGDRNOFF
## [1] "UGDRNOFF"
## 
## $SFCRNOFF
## [1] "SFCRNOFF"
## 
## $CANLIQ
## [1] "CANLIQ"
## 
## $CANICE
## [1] "CANICE"
## 
## $ZWT
## [1] "ZWT"
## 
## $WA
## [1] "WA"
## 
## $WT
## [1] "WT"
## 
## $ACCPRCP
## [1] "ACCPRCP"
## 
## $ACCECAN
## [1] "ACCECAN"
## 
## $ACCEDIR
## [1] "ACCEDIR"
## 
## $ACCETRAN
## [1] "ACCETRAN"
## 
## $SAV
## [1] "SAV"
## 
## $TR
## [1] "TR"
## 
## $EVC
## [1] "EVC"
## 
## $IRC
## [1] "IRC"
## 
## $SHC
## [1] "SHC"
## 
## $IRG
## [1] "IRG"
## 
## $SHG
## [1] "SHG"
## 
## $EVG
## [1] "EVG"
## 
## $GHV
## [1] "GHV"
## 
## $SAG
## [1] "SAG"
## 
## $IRB
## [1] "IRB"
## 
## $SHB
## [1] "SHB"
## 
## $EVB
## [1] "EVB"
## 
## $GHB
## [1] "GHB"
## 
## $TRAD
## [1] "TRAD"
## 
## $TG
## [1] "TG"
## 
## $TV
## [1] "TV"
## 
## $TAH
## [1] "TAH"
## 
## $TGV
## [1] "TGV"
## 
## $TGB
## [1] "TGB"
## 
## $T2MV
## [1] "T2MV"
## 
## $T2MB
## [1] "T2MB"
## 
## $Q2MV
## [1] "Q2MV"
## 
## $Q2MB
## [1] "Q2MB"
## 
## $EAH
## [1] "EAH"
## 
## $FWET
## [1] "FWET"
## 
## $ZSNSO_SN
## [1] "ZSNSO_SN"
## 
## $SNICE
## [1] "SNICE"
## 
## $SNLIQ
## [1] "SNLIQ"
## 
## $SOIL_T
## [1] "SOIL_T"
## 
## $SOIL_W
## [1] "SOIL_W"
## 
## $SNOW_T
## [1] "SNOW_T"
## 
## $SOIL_M
## [1] "SOIL_M"
## 
## $SNOWH
## [1] "SNOWH"
## 
## $SNEQV
## [1] "SNEQV"
## 
## $QSNOW
## [1] "QSNOW"
## 
## $ISNOW
## [1] "ISNOW"
## 
## $FSNO
## [1] "FSNO"
## 
## $ACSNOW
## [1] "ACSNOW"
## 
## $ACSNOM
## [1] "ACSNOM"
## 
## $CM
## [1] "CM"
## 
## $CH
## [1] "CH"
## 
## $CHV
## [1] "CHV"
## 
## $CHB
## [1] "CHB"
## 
## $CHLEAF
## [1] "CHLEAF"
## 
## $CHUC
## [1] "CHUC"
## 
## $CHV2
## [1] "CHV2"
## 
## $CHB2
## [1] "CHB2"
## 
## $LFMASS
## [1] "LFMASS"
## 
## $RTMASS
## [1] "RTMASS"
## 
## $STMASS
## [1] "STMASS"
## 
## $WOOD
## [1] "WOOD"
## 
## $STBLCP
## [1] "STBLCP"
## 
## $FASTCP
## [1] "FASTCP"
## 
## $NEE
## [1] "NEE"
## 
## $GPP
## [1] "GPP"
## 
## $NPP
## [1] "NPP"
## 
## $PSN
## [1] "PSN"
## 
## $APAR
## [1] "APAR"
## Pass all the variable names to the function which then
## looks up the size information for that variable.
str(plyr::llply(varList, function(vv) ncid$var[[vv]]$size )) 
## List of 89
##  $ IVGTYP  : int [1:3] 21 7 1
##  $ ISLTYP  : int [1:3] 21 7 1
##  $ FVEG    : int [1:3] 21 7 1
##  $ LAI     : int [1:3] 21 7 1
##  $ SAI     : int [1:3] 21 7 1
##  $ SWFORC  : int [1:3] 21 7 1
##  $ COSZ    : int [1:3] 21 7 1
##  $ LWFORC  : int [1:3] 21 7 1
##  $ RAINRATE: int [1:3] 21 7 1
##  $ EMISS   : int [1:3] 21 7 1
##  $ FSA     : int [1:3] 21 7 1
##  $ FIRA    : int [1:3] 21 7 1
##  $ GRDFLX  : int [1:3] 21 7 1
##  $ HFX     : int [1:3] 21 7 1
##  $ LH      : int [1:3] 21 7 1
##  $ ECAN    : int [1:3] 21 7 1
##  $ EDIR    : int [1:3] 21 7 1
##  $ ALBEDO  : int [1:3] 21 7 1
##  $ ETRAN   : int [1:3] 21 7 1
##  $ UGDRNOFF: int [1:3] 21 7 1
##  $ SFCRNOFF: int [1:3] 21 7 1
##  $ CANLIQ  : int [1:3] 21 7 1
##  $ CANICE  : int [1:3] 21 7 1
##  $ ZWT     : int [1:3] 21 7 1
##  $ WA      : int [1:3] 21 7 1
##  $ WT      : int [1:3] 21 7 1
##  $ ACCPRCP : int [1:3] 21 7 1
##  $ ACCECAN : int [1:3] 21 7 1
##  $ ACCEDIR : int [1:3] 21 7 1
##  $ ACCETRAN: int [1:3] 21 7 1
##  $ SAV     : int [1:3] 21 7 1
##  $ TR      : int [1:3] 21 7 1
##  $ EVC     : int [1:3] 21 7 1
##  $ IRC     : int [1:3] 21 7 1
##  $ SHC     : int [1:3] 21 7 1
##  $ IRG     : int [1:3] 21 7 1
##  $ SHG     : int [1:3] 21 7 1
##  $ EVG     : int [1:3] 21 7 1
##  $ GHV     : int [1:3] 21 7 1
##  $ SAG     : int [1:3] 21 7 1
##  $ IRB     : int [1:3] 21 7 1
##  $ SHB     : int [1:3] 21 7 1
##  $ EVB     : int [1:3] 21 7 1
##  $ GHB     : int [1:3] 21 7 1
##  $ TRAD    : int [1:3] 21 7 1
##  $ TG      : int [1:3] 21 7 1
##  $ TV      : int [1:3] 21 7 1
##  $ TAH     : int [1:3] 21 7 1
##  $ TGV     : int [1:3] 21 7 1
##  $ TGB     : int [1:3] 21 7 1
##  $ T2MV    : int [1:3] 21 7 1
##  $ T2MB    : int [1:3] 21 7 1
##  $ Q2MV    : int [1:3] 21 7 1
##  $ Q2MB    : int [1:3] 21 7 1
##  $ EAH     : int [1:3] 21 7 1
##  $ FWET    : int [1:3] 21 7 1
##  $ ZSNSO_SN: int [1:4] 21 3 7 1
##  $ SNICE   : int [1:4] 21 3 7 1
##  $ SNLIQ   : int [1:4] 21 3 7 1
##  $ SOIL_T  : int [1:4] 21 4 7 1
##  $ SOIL_W  : int [1:4] 21 4 7 1
##  $ SNOW_T  : int [1:4] 21 3 7 1
##  $ SOIL_M  : int [1:4] 21 4 7 1
##  $ SNOWH   : int [1:3] 21 7 1
##  $ SNEQV   : int [1:3] 21 7 1
##  $ QSNOW   : int [1:3] 21 7 1
##  $ ISNOW   : int [1:3] 21 7 1
##  $ FSNO    : int [1:3] 21 7 1
##  $ ACSNOW  : int [1:3] 21 7 1
##  $ ACSNOM  : int [1:3] 21 7 1
##  $ CM      : int [1:3] 21 7 1
##  $ CH      : int [1:3] 21 7 1
##  $ CHV     : int [1:3] 21 7 1
##  $ CHB     : int [1:3] 21 7 1
##  $ CHLEAF  : int [1:3] 21 7 1
##  $ CHUC    : int [1:3] 21 7 1
##  $ CHV2    : int [1:3] 21 7 1
##  $ CHB2    : int [1:3] 21 7 1
##  $ LFMASS  : int [1:3] 21 7 1
##  $ RTMASS  : int [1:3] 21 7 1
##  $ STMASS  : int [1:3] 21 7 1
##  $ WOOD    : int [1:3] 21 7 1
##  $ STBLCP  : int [1:3] 21 7 1
##  $ FASTCP  : int [1:3] 21 7 1
##  $ NEE     : int [1:3] 21 7 1
##  $ GPP     : int [1:3] 21 7 1
##  $ NPP     : int [1:3] 21 7 1
##  $ PSN     : int [1:3] 21 7 1
##  $ APAR    : int [1:3] 21 7 1
## or if you want the units
str(plyr::llply(varList, function(vv) ncid$var[[vv]]$units )) 
## List of 89
##  $ IVGTYP  : chr "category"
##  $ ISLTYP  : chr "category"
##  $ FVEG    : chr "-"
##  $ LAI     : chr "-"
##  $ SAI     : chr "-"
##  $ SWFORC  : chr "W m{-2}"
##  $ COSZ    : chr "W m{-2}"
##  $ LWFORC  : chr "W m{-2}"
##  $ RAINRATE: chr "kg m{-2} s{-1}"
##  $ EMISS   : chr ""
##  $ FSA     : chr "W m{-2}"
##  $ FIRA    : chr "W m{-2}"
##  $ GRDFLX  : chr "W m{-2}"
##  $ HFX     : chr "W m{-2}"
##  $ LH      : chr "W m{-2}"
##  $ ECAN    : chr "kg m{-2} s{-1}"
##  $ EDIR    : chr "kg m{-2} s{-1}"
##  $ ALBEDO  : chr "-"
##  $ ETRAN   : chr "kg m{-2} s{-1}"
##  $ UGDRNOFF: chr "mm"
##  $ SFCRNOFF: chr "mm"
##  $ CANLIQ  : chr "mm"
##  $ CANICE  : chr "mm"
##  $ ZWT     : chr "m"
##  $ WA      : chr "kg m{-2}"
##  $ WT      : chr "kg m{-2}"
##  $ ACCPRCP : chr "mm"
##  $ ACCECAN : chr "mm"
##  $ ACCEDIR : chr "mm"
##  $ ACCETRAN: chr "mm"
##  $ SAV     : chr "W m{-2}"
##  $ TR      : chr "W m{-2}"
##  $ EVC     : chr "W m{-2}"
##  $ IRC     : chr "W m{-2}"
##  $ SHC     : chr "W m{-2}"
##  $ IRG     : chr "W m{-2}"
##  $ SHG     : chr "W m{-2}"
##  $ EVG     : chr "W m{-2}"
##  $ GHV     : chr "W m{-2}"
##  $ SAG     : chr "W m{-2}"
##  $ IRB     : chr "W m{-2}"
##  $ SHB     : chr "W m{-2}"
##  $ EVB     : chr "W m{-2}"
##  $ GHB     : chr "W m{-2}"
##  $ TRAD    : chr "K"
##  $ TG      : chr "K"
##  $ TV      : chr "K"
##  $ TAH     : chr "K"
##  $ TGV     : chr "K"
##  $ TGB     : chr "K"
##  $ T2MV    : chr "K"
##  $ T2MB    : chr "K"
##  $ Q2MV    : chr "kg/kg"
##  $ Q2MB    : chr "kg/kg"
##  $ EAH     : chr "Pa"
##  $ FWET    : chr "fraction"
##  $ ZSNSO_SN: chr "m"
##  $ SNICE   : chr "mm"
##  $ SNLIQ   : chr "mm"
##  $ SOIL_T  : chr "K"
##  $ SOIL_W  : chr "m3 m-3"
##  $ SNOW_T  : chr "K"
##  $ SOIL_M  : chr "m{3} m{-3}"
##  $ SNOWH   : chr "m"
##  $ SNEQV   : chr "kg m{-2}"
##  $ QSNOW   : chr "mm s{-1}"
##  $ ISNOW   : chr "count"
##  $ FSNO    : chr ""
##  $ ACSNOW  : chr "mm"
##  $ ACSNOM  : chr "mm"
##  $ CM      : chr ""
##  $ CH      : chr ""
##  $ CHV     : chr "m s{-1}"
##  $ CHB     : chr "m s{-1}"
##  $ CHLEAF  : chr "m s{-1}"
##  $ CHUC    : chr "m s{-1}"
##  $ CHV2    : chr "m s{-1}"
##  $ CHB2    : chr "m s{-1}"
##  $ LFMASS  : chr "g m{-2}"
##  $ RTMASS  : chr "g m{-2}"
##  $ STMASS  : chr "g m{-2}"
##  $ WOOD    : chr "g m{-2}"
##  $ STBLCP  : chr "g m{-2}"
##  $ FASTCP  : chr "g m{-2}"
##  $ NEE     : chr "g m{-2} s{-1} CO2"
##  $ GPP     : chr "g m{-2} s{-1} C"
##  $ NPP     : chr "g m{-2} s{-1} C"
##  $ PSN     : chr "umol CO@ m{-2} s{-1}"
##  $ APAR    : chr "W m{-2}"

In the above, the llply function from the plyr package applies a function (anonymously specified in-line) to a list (varList) and returns a list. The characters in VarList are passed to the function as vv and these characters are used to select the variable from ncid$var. Note that the names on the returned list are the names on the list which were iterated over. To illustrate this,

names(varList) <- NULL
str(plyr::llply(varList, function(vv) ncid$var[[vv]]$size )) 
## List of 89
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:4] 21 3 7 1
##  $ : int [1:4] 21 3 7 1
##  $ : int [1:4] 21 3 7 1
##  $ : int [1:4] 21 4 7 1
##  $ : int [1:4] 21 4 7 1
##  $ : int [1:4] 21 3 7 1
##  $ : int [1:4] 21 4 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1
##  $ : int [1:3] 21 7 1

That’s fairly useless. So it’s important to understand that the result is collated against the name of the input list and the value of that list object is what is passed to the function. They just happen to be identical in this case.

Methods and classes

It’s also good to have a basic awareness of methods and classes in R, this can be particularly mystifying to new users. This is how the same generic function can appear to give a variety of different behaviors, these are methods conditioned on the class of the input. It’s also worth noting that the common S3 object system used in R is very “lightweight” (e.g. see setting the class below) and easy to use. For those who shudder at such an informal system there are other object approaches in R.

class(mtcars)
## [1] "data.frame"
print(head(mtcars))
##                    mpg cyl disp  hp drat    wt  qsec vs am gear carb
## Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
## Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
## Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1    4    1
## Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
## Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2
## Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1
print.data.frame(head(mtcars))
##                    mpg cyl disp  hp drat    wt  qsec vs am gear carb
## Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
## Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
## Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1    4    1
## Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
## Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2
## Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1
print.default(head(mtcars))
## $mpg
## [1] 21.0 21.0 22.8 21.4 18.7 18.1
## 
## $cyl
## [1] 6 6 4 6 8 6
## 
## $disp
## [1] 160 160 108 258 360 225
## 
## $hp
## [1] 110 110  93 110 175 105
## 
## $drat
## [1] 3.90 3.90 3.85 3.08 3.15 2.76
## 
## $wt
## [1] 2.620 2.875 2.320 3.215 3.440 3.460
## 
## $qsec
## [1] 16.46 17.02 18.61 19.44 17.02 20.22
## 
## $vs
## [1] 0 0 1 1 0 1
## 
## $am
## [1] 1 1 1 0 0 0
## 
## $gear
## [1] 4 4 4 3 3 3
## 
## $carb
## [1] 4 4 1 1 2 1
## 
## attr(,"class")
## [1] "data.frame"
print.foo <- function(x){
  print(names(x))
  print('foo!!!!!!!!!!!')  ## really not helpful!
}
class(mtcars) <- append('foo',class(mtcars))
print(mtcars)
##  [1] "mpg"  "cyl"  "disp" "hp"   "drat" "wt"   "qsec" "vs"   "am"   "gear"
## [11] "carb"
## [1] "foo!!!!!!!!!!!"

Scoping

Scoping: what variables are available where? R has Lexical scoping: variables in enclosing environments/functions are available to a given environment/function. For assignment: when assigning to a name the name is searched for in enclosing functions until it is found, if not found in the global environment it is created there. Lastly, functions can be returned with their own environment, these are called closures. Here are some examples.

The variable a is in the global environment and is found by the function f because f is enclosed in the global environment.

a <- 10  
f <- function(x) a*x   
f(2)
## [1] 20

Now g contains a variable b which f2 cannot find because g does not enclose f2. I wrap failing evaluations in print(try()) so that this document compiles. Note that try() is a very vaulable function for fault tolerance. Also, examination of try() shows that it returns it’s agument wrapped in invisible(), to see that object print() has to be explicitly called on try().

options(warn=1)
g <- function(x) {b <- 10; 1/x}   
f2 <- function(x)  b*x 
print(try(f2(.1)))
## [1] "Error in f2(0.1) : object 'b' not found\n"
## attr(,"class")
## [1] "try-error"
## attr(,"condition")
## <simpleError in f2(0.1): object 'b' not found>
## the following lexical assignment is frowned upon by most guRus.
g2 <- function(x) {b <<- 100; 1/x}   
print(try(b)) # whoa, isnt it supposed to be assigned?
## [1] "Error in try(b) : object 'b' not found\n"
## attr(,"class")
## [1] "try-error"
## attr(,"condition")
## <simpleError in doTryCatch(return(expr), name, parentenv, handler): object 'b' not found>
g2(2)
## [1] 0.5
b # R is lazy, so b isnt assigned until the function is called.
## [1] 100
f2(.1)
## [1] 10

A closure is a function with data, that data is arbitrary.

fOuter <- function(x) {qqq <- 2*x; function() qqq }
fInner <- fOuter(4)
fInner()
## [1] 8
print(try(qqq))
## [1] "Error in try(qqq) : object 'qqq' not found\n"
## attr(,"class")
## [1] "try-error"
## attr(,"condition")
## <simpleError in doTryCatch(return(expr), name, parentenv, handler): object 'qqq' not found>
get('qqq',envir = environment(fInner))
## [1] 8

Or maybe more informatively:

vvv <- 123
gOuter <- function(x) {
  ttt <- 2*x
  junk <- rwrfhydro::NamedList(letters[1:4])
  function(getVar) get(getVar) 
}
gInner <- gOuter(4)
print(try(ttt))
## [1] "Error in try(ttt) : object 'ttt' not found\n"
## attr(,"class")
## [1] "try-error"
## attr(,"condition")
## <simpleError in doTryCatch(return(expr), name, parentenv, handler): object 'ttt' not found>
gInner('junk')
## $a
## [1] "a"
## 
## $b
## [1] "b"
## 
## $c
## [1] "c"
## 
## $d
## [1] "d"
gOuter(c(1,2,4))('ttt')
## [1] 2 4 8
gInner('vvv')
## [1] 123

The caveat emptor with scoping is that, while functions which reference variables in enclosing envrionments are plug-and-play, unintended changes to variables in enclosing environments are vunerabilities/liabilities to function accuracy! Be careful and declare all variables in a function when saftey is needed.

Getting help

Getting information on functions is key. Getting the source code of a function is as easy as calling a function without parentheses (i.e., invoking the print method on the function!) and reading functions is a great way to pickup R programming tips:

lm
## function (formula, data, subset, weights, na.action, method = "qr", 
##     model = TRUE, x = FALSE, y = FALSE, qr = TRUE, singular.ok = TRUE, 
##     contrasts = NULL, offset, ...) 
## {
##     ret.x <- x
##     ret.y <- y
##     cl <- match.call()
##     mf <- match.call(expand.dots = FALSE)
##     m <- match(c("formula", "data", "subset", "weights", "na.action", 
##         "offset"), names(mf), 0L)
##     mf <- mf[c(1L, m)]
##     mf$drop.unused.levels <- TRUE
##     mf[[1L]] <- quote(stats::model.frame)
##     mf <- eval(mf, parent.frame())
##     if (method == "model.frame") 
##         return(mf)
##     else if (method != "qr") 
##         warning(gettextf("method = '%s' is not supported. Using 'qr'", 
##             method), domain = NA)
##     mt <- attr(mf, "terms")
##     y <- model.response(mf, "numeric")
##     w <- as.vector(model.weights(mf))
##     if (!is.null(w) && !is.numeric(w)) 
##         stop("'weights' must be a numeric vector")
##     offset <- as.vector(model.offset(mf))
##     if (!is.null(offset)) {
##         if (length(offset) != NROW(y)) 
##             stop(gettextf("number of offsets is %d, should equal %d (number of observations)", 
##                 length(offset), NROW(y)), domain = NA)
##     }
##     if (is.empty.model(mt)) {
##         x <- NULL
##         z <- list(coefficients = if (is.matrix(y)) matrix(, 0, 
##             3) else numeric(), residuals = y, fitted.values = 0 * 
##             y, weights = w, rank = 0L, df.residual = if (!is.null(w)) sum(w != 
##             0) else if (is.matrix(y)) nrow(y) else length(y))
##         if (!is.null(offset)) {
##             z$fitted.values <- offset
##             z$residuals <- y - offset
##         }
##     }
##     else {
##         x <- model.matrix(mt, mf, contrasts)
##         z <- if (is.null(w)) 
##             lm.fit(x, y, offset = offset, singular.ok = singular.ok, 
##                 ...)
##         else lm.wfit(x, y, w, offset = offset, singular.ok = singular.ok, 
##             ...)
##     }
##     class(z) <- c(if (is.matrix(y)) "mlm", "lm")
##     z$na.action <- attr(mf, "na.action")
##     z$offset <- offset
##     z$contrasts <- attr(x, "contrasts")
##     z$xlevels <- .getXlevels(mt, mf)
##     z$call <- cl
##     z$terms <- mt
##     if (model) 
##         z$model <- mf
##     if (ret.x) 
##         z$x <- x
##     if (ret.y) 
##         z$y <- y
##     if (!qr) 
##         z$qr <- NULL
##     z
## }
## <bytecode: 0x7fc92db4a5c8>
## <environment: namespace:stats>

Beyond reading the body of the text, note that the arguments are listed at the top with default values following =. The ... argument is for passing arguments to “low-level” regression functions (described in ?lm). We also see that the function belongs to the stats namespace.

See also (not run here):

formals(lm)
?lm
?'%in%'
?'['
## the following are help on help
?help
?`?`
?`??`

Packages and namespaces

R packages are like toolboxes for specific purposes.Namespaces for packages make their functions available and managing namespaces is how one can open an entire toolbox or just pull a specific tool out of a specific toolbox. Namespaces can be made entirely available by attaching a package using library(), e.g. the whole toolbox is available in the global environment:

sessionInfo()
## R version 3.3.2 (2016-10-31)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: macOS Sierra 10.12.4
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] parallel  stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
## [1] printr_0.0.6       scales_0.4.1       doMC_1.3.4        
## [4] iterators_1.0.8    foreach_1.4.3      ncdf4_1.15        
## [7] ggplot2_2.2.0      rwrfhydro_1.0.9000
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.10      highr_0.6         plyr_1.8.4       
##  [4] bitops_1.0-6      tools_3.3.2       digest_0.6.12    
##  [7] evaluate_0.10     tibble_1.3.0      gtable_0.2.0     
## [10] lattice_0.20-34   png_0.1-7         DBI_0.5-1        
## [13] mapproj_1.2-4     yaml_2.1.14       rgdal_1.2-7      
## [16] proto_1.0.0       raster_2.5-8      stringr_1.1.0    
## [19] dplyr_0.5.0       knitr_1.15.1      RgoogleMaps_1.4.1
## [22] maps_3.1.1        rprojroot_1.2     grid_3.3.2       
## [25] data.table_1.10.0 R6_2.2.0          jpeg_0.1-8       
## [28] rmarkdown_1.5     sp_1.2-3          ggmap_2.7        
## [31] reshape2_1.4.2    magrittr_1.5      codetools_0.2-15 
## [34] backports_1.0.5   htmltools_0.3.5   assertthat_0.1   
## [37] colorspace_1.3-1  geosphere_1.5-5   labeling_0.3     
## [40] stringi_1.1.2     lazyeval_0.2.0    munsell_0.4.3    
## [43] rjson_0.2.15
library(rwrfhydro)  ## this adds rwrfhydro to the 'other attached packages' list
sessionInfo()
## R version 3.3.2 (2016-10-31)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: macOS Sierra 10.12.4
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] parallel  stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
## [1] printr_0.0.6       scales_0.4.1       doMC_1.3.4        
## [4] iterators_1.0.8    foreach_1.4.3      ncdf4_1.15        
## [7] ggplot2_2.2.0      rwrfhydro_1.0.9000
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.10      highr_0.6         plyr_1.8.4       
##  [4] bitops_1.0-6      tools_3.3.2       digest_0.6.12    
##  [7] evaluate_0.10     tibble_1.3.0      gtable_0.2.0     
## [10] lattice_0.20-34   png_0.1-7         DBI_0.5-1        
## [13] mapproj_1.2-4     yaml_2.1.14       rgdal_1.2-7      
## [16] proto_1.0.0       raster_2.5-8      stringr_1.1.0    
## [19] dplyr_0.5.0       knitr_1.15.1      RgoogleMaps_1.4.1
## [22] maps_3.1.1        rprojroot_1.2     grid_3.3.2       
## [25] data.table_1.10.0 R6_2.2.0          jpeg_0.1-8       
## [28] rmarkdown_1.5     sp_1.2-3          ggmap_2.7        
## [31] reshape2_1.4.2    magrittr_1.5      codetools_0.2-15 
## [34] backports_1.0.5   htmltools_0.3.5   assertthat_0.1   
## [37] colorspace_1.3-1  geosphere_1.5-5   labeling_0.3     
## [40] stringi_1.1.2     lazyeval_0.2.0    munsell_0.4.3    
## [43] rjson_0.2.15
PlotFdc  ## this function is available in the global environment.
## function (strDf, strCol = "q_cms", spline = TRUE, fdcProb = NULL) 
## {
##     plot(strDf[, paste0(strCol, ".fdc")], strDf[, strCol], log = "y", 
##         xlab = "Probability of Exceedance", ylab = c("Flow (log scale)"), 
##         main = c(paste("Flow Duration Curve: ", deparse(substitute(strDf)), 
##             ":", deparse(substitute(strCol)), ", n=", sum(!is.na(strDf[, 
##                 strCol])))))
##     if (spline | !is.null(fdcProb)) {
##         fdcSplineFun <- splinefun(strDf[, paste0(strCol, ".fdc")], 
##             strDf[, strCol], method = "natural")
##         if (spline) {
##             curve(fdcSplineFun(x), col = "red", lwd = 2, lty = 1, 
##                 add = T)
##         }
##         if (!is.null(fdcProb)) {
##             abline(v = fdcProb, h = fdcSplineFun(fdcProb), col = "grey")
##             text(fdcProb, fdcSplineFun(fdcProb), labels = paste("P =", 
##                 fdcProb * 100, "%, Q=", round(fdcSplineFun(fdcProb), 
##                   2)), adj = c(-0.05, -1), cex = 0.9)
##         }
##     }
## }
## <environment: namespace:rwrfhydro>

Now all the functions in the rwrfhydro namespace are available because it is attached.

Now we grab a specific tool (melt) from the “reshape2” package, but this dosent make the whole toolbox available, though we see it’s namespace is

mtcars$model <- rownames(mtcars)
head(reshape2::melt(mtcars[,c("mpg","cyl","disp","model")], id='model')) ## use a function in plyr without attaching it
model variable value
Mazda RX4 mpg 21.0
Mazda RX4 Wag mpg 21.0
Datsun 710 mpg 22.8
Hornet 4 Drive mpg 21.4
Hornet Sportabout mpg 18.7
Valiant mpg 18.1
sessionInfo() ## attaches plyr, reshape2, Rcpp,  & stringr (some already attached.)
## R version 3.3.2 (2016-10-31)
## Platform: x86_64-apple-darwin13.4.0 (64-bit)
## Running under: macOS Sierra 10.12.4
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] parallel  stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
## [1] printr_0.0.6       scales_0.4.1       doMC_1.3.4        
## [4] iterators_1.0.8    foreach_1.4.3      ncdf4_1.15        
## [7] ggplot2_2.2.0      rwrfhydro_1.0.9000
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_0.12.10      highr_0.6         plyr_1.8.4       
##  [4] bitops_1.0-6      tools_3.3.2       digest_0.6.12    
##  [7] evaluate_0.10     tibble_1.3.0      gtable_0.2.0     
## [10] lattice_0.20-34   png_0.1-7         DBI_0.5-1        
## [13] mapproj_1.2-4     yaml_2.1.14       rgdal_1.2-7      
## [16] proto_1.0.0       raster_2.5-8      stringr_1.1.0    
## [19] dplyr_0.5.0       knitr_1.15.1      RgoogleMaps_1.4.1
## [22] maps_3.1.1        rprojroot_1.2     grid_3.3.2       
## [25] data.table_1.10.0 R6_2.2.0          jpeg_0.1-8       
## [28] rmarkdown_1.5     sp_1.2-3          ggmap_2.7        
## [31] reshape2_1.4.2    magrittr_1.5      codetools_0.2-15 
## [34] backports_1.0.5   htmltools_0.3.5   assertthat_0.1   
## [37] colorspace_1.3-1  geosphere_1.5-5   labeling_0.3     
## [40] stringi_1.1.2     lazyeval_0.2.0    munsell_0.4.3    
## [43] rjson_0.2.15
print(try(melt))  ## since plyr is not attached, the melt function is not available.
## [1] "Error in try(melt) : object 'melt' not found\n"
## attr(,"class")
## [1] "try-error"
## attr(,"condition")
## <simpleError in doTryCatch(return(expr), name, parentenv, handler): object 'melt' not found>

The namespace of a package is the set of exported objects. Internal (non-exported objects) in a package can be accessed via ::: though this is often frowned upon.

Bonus: Computing on the language

R is an extremely flexible language. The non-standard evaluation mechanisms allow for a variety of powerful behaviours. These can be confusing to new users. Here’s one simple example showing a few useful functions.

assign('one',1)
two <- eval(parse(text='one+one'))
get('two')
## [1] 2