list_* functions are not currently checking if they support the RAS version specified. This should be added to the case statement

stop("RAS version ", ras.version, " is not currently supported", .call = FALSE)

Appears to only ever return "Clay".

Right now the read_* methods label columns in the format XS_###.## with cross section stationing. River and Reach information should also be included, either in the format of the column names (e.g. River/Reach/###.##) or as attributes of the data frame.

waaaaaay faster

test case: Compare the master branch (h5-based) to hdf5r_transition branch (hdf5r-based).

require(microbenchmark)
ras.file = system.file("sample-data/SampleQuasiUnsteady.hdf", package = "RAStestR")
microbenchmark(vol.change.cum <- read_sediment(ras.file, "Vol Bed Change Cum"))

microbenchmark results:

Unit: milliseconds
expr        min       lq     mean   median       uq      max neval
h5       100.51 104.1777 110.2355 106.9395 111.2867 197.3422   100
hdf5r  5685.172 5761.895 5860.317 5813.281 5908.393 6482.691   100

Benchmark for single table reads:

get_dataset_hdf5r = function(f, table.path) {
  x = hdf5r::H5File$new(f)
  g = x$open(table.path)
  res = g$read()
  g$close()
  x$close()
  res
}

get_dataset_h5 = function(f, table.path, type = "double") {
  x = h5::h5file(f)
  g = h5::openDataSet(x, table.path, type)
  res = h5::readDataSet(g)
  h5::h5close(g)
  h5::h5close(x)
  res
}

myfile = system.file("sample-data/SampleQuasiUnsteady.hdf", package = "RAStestR")
mytable =  "Results/Sediment/Output Blocks/Sediment/Sediment Time Series/Cross Sections/Vol Bed Change Cum"

microbenchmark(
  get_dataset_hdf5r(myfile, mytable),
  get_dataset_h5(myfile, mytable)
)

microbenchmark results:

Unit: milliseconds
                               expr      min       lq     mean   median       uq       max neval
 get_dataset_hdf5r(myfile, mytable) 3.898140 3.995330 4.196941 4.093295 4.254240  6.102233   100
    get_dataset_h5(myfile, mytable) 1.558758 1.607431 2.190121 1.677407 1.758579 50.932394   100

Tasks:

1. Migrate backend from hdf5r to hdfqlr.
2. Use long table format by default. This will resolve some of the complications with River/Reach/Station naming convention and avoid need for matrix transposing (since HDFql swaps row-column order).
3. Separate some of the advanced functionality into separate package. Maybe time to rename/start a fresh repository...

Seems to be caused by the automatic name matching that occurs in dplyr::bind_rows. Need to decide how to handle this. Probably time to replace the "XS_" prefix names with something that combines river/reach/column.

Creates column "Station" with NA values if the Station column does not exist (e.g. all wide tables). Should not try to do anything to columns that don't exist in dataframe.