## ----cleanup, echo=FALSE, include=FALSE---------------------------------------
if (file.exists("myhdf5file.h5")) {
  file.remove("myhdf5file.h5")
}
if (file.exists("newfile.h5")) {
  file.remove("newfile.h5")
}
if (file.exists("newfile2.h5")) {
  file.remove("newfile2.h5")
}
if (file.exists("newfile3.h5")) {
  file.remove("newfile3.h5")
}

## ----installation,eval=FALSE--------------------------------------------------
# install.packages("BiocManager")
# BiocManager::install("rhdf5")

## ----createHDF5file-----------------------------------------------------------
library(rhdf5)
h5createFile("myhdf5file.h5")

## ----create groups------------------------------------------------------------
h5createGroup("myhdf5file.h5", "foo")
h5createGroup("myhdf5file.h5", "baa")
h5createGroup("myhdf5file.h5", "foo/foobaa")
h5ls("myhdf5file.h5")

## ----writeMatrix--------------------------------------------------------------
A <- matrix(1:10, nrow = 5, ncol = 2)
h5write(A, "myhdf5file.h5", "foo/A")
B <- array(seq(0.1, 2.0, by = 0.1), dim = c(5, 2, 2))
attr(B, "scale") <- "liter"
h5write(B, "myhdf5file.h5", "foo/B")
C <- matrix(paste(LETTERS[1:10], LETTERS[11:20], collapse = ""),
  nr = 2, nc = 5
)
h5write(C, "myhdf5file.h5", "foo/foobaa/C")
df <- data.frame(1L:5L, seq(0, 1, length.out = 5),
  c("ab", "cde", "fghi", "a", "s"),
  stringsAsFactors = FALSE
)
h5write(df, "myhdf5file.h5", "df")
h5ls("myhdf5file.h5")
D <- h5read("myhdf5file.h5", "foo/A")
E <- h5read("myhdf5file.h5", "foo/B")
F <- h5read("myhdf5file.h5", "foo/foobaa/C")
G <- h5read("myhdf5file.h5", "df")

## ----accessorH5Fopen----------------------------------------------------------
h5f <- H5Fopen("myhdf5file.h5")
h5f

## ----accessorDF---------------------------------------------------------------
h5f$df
h5f & "df"

## ----accessorC1---------------------------------------------------------------
h5f$foo$foobaa$C
h5f$"/foo/foobaa/C"

## ----accessorB1---------------------------------------------------------------
h5d <- h5f & "/foo/B"
h5d[]
h5d[3, , ]

## ----accessorB2---------------------------------------------------------------
h5d[3, , ] <- 1:4
H5Fflush(h5f)

## ----accessorB3,eval=FALSE----------------------------------------------------
# h5f$foo$B <- 101:120
# h5f$"/foo/B" <- 101:120

## ----accessorClose1-----------------------------------------------------------
H5Dclose(h5d)
H5Fclose(h5f)

## ----accessorClose2-----------------------------------------------------------
h5closeAll()

## ----writeMatrixSubsetting----------------------------------------------------
h5createDataset("myhdf5file.h5", "foo/S", c(5, 8),
  storage.mode = "integer", chunk = c(5, 1), level = 7
)
h5write(matrix(1:5, nr = 5, nc = 1),
  file = "myhdf5file.h5",
  name = "foo/S", index = list(NULL, 1)
)
h5read("myhdf5file.h5", "foo/S")
h5write(6:10,
  file = "myhdf5file.h5",
  name = "foo/S", index = list(1, 2:6)
)
h5read("myhdf5file.h5", "foo/S")
h5write(matrix(11:40, nr = 5, nc = 6),
  file = "myhdf5file.h5",
  name = "foo/S", index = list(1:5, 3:8)
)
h5read("myhdf5file.h5", "foo/S")
h5write(matrix(141:144, nr = 2, nc = 2),
  file = "myhdf5file.h5",
  name = "foo/S", index = list(3:4, 1:2)
)
h5read("myhdf5file.h5", "foo/S")
h5write(matrix(151:154, nr = 2, nc = 2),
  file = "myhdf5file.h5",
  name = "foo/S", index = list(2:3, c(3, 6))
)
h5read("myhdf5file.h5", "foo/S")
h5read("myhdf5file.h5", "foo/S", index = list(2:3, 2:3))
h5read("myhdf5file.h5", "foo/S", index = list(2:3, c(2, 4)))
h5read("myhdf5file.h5", "foo/S", index = list(2:3, c(1, 2, 4, 5)))

## ----writeMatrixHyperslab-----------------------------------------------------
h5createDataset("myhdf5file.h5", "foo/H", c(5, 8),
  storage.mode = "integer",
  chunk = c(5, 1), level = 7
)
h5write(matrix(1:5, nr = 5, nc = 1),
  file = "myhdf5file.h5", name = "foo/H",
  start = c(1, 1)
)
h5read("myhdf5file.h5", "foo/H")
h5write(6:10,
  file = "myhdf5file.h5", name = "foo/H",
  start = c(1, 2), count = c(1, 5)
)
h5read("myhdf5file.h5", "foo/H")
h5write(matrix(11:40, nr = 5, nc = 6),
  file = "myhdf5file.h5", name = "foo/H",
  start = c(1, 3)
)
h5read("myhdf5file.h5", "foo/H")
h5write(matrix(141:144, nr = 2, nc = 2),
  file = "myhdf5file.h5", name = "foo/H",
  start = c(3, 1)
)
h5read("myhdf5file.h5", "foo/H")
h5write(matrix(151:154, nr = 2, nc = 2),
  file = "myhdf5file.h5", name = "foo/H",
  start = c(2, 3), stride = c(1, 3)
)
h5read("myhdf5file.h5", "foo/H")
h5read("myhdf5file.h5", "foo/H",
  start = c(2, 2), count = c(2, 2)
)
h5read("myhdf5file.h5", "foo/H",
  start = c(2, 2), stride = c(1, 2), count = c(2, 2)
)
h5read("myhdf5file.h5", "foo/H",
  start = c(2, 1), stride = c(1, 3), count = c(2, 2), block = c(1, 2)
)

## ----h5save-------------------------------------------------------------------
A <- 1:7
B <- 1:18
D <- seq(0, 1, by = 0.1)
h5save(A, B, D, file = "newfile2.h5")
h5dump("newfile2.h5")

## ----h5ls---------------------------------------------------------------------
h5ls("myhdf5file.h5")
h5ls("myhdf5file.h5", all = TRUE)
h5ls("myhdf5file.h5", recursive = 2)

## ----h5dump-------------------------------------------------------------------
h5dump("myhdf5file.h5", load = FALSE)
D <- h5dump("myhdf5file.h5")

## ----h5dump2, eval=FALSE------------------------------------------------------
# system2("h5dump", "myhdf5file.h5")

## ----h5delete1----------------------------------------------------------------
h5ls("myhdf5file.h5", recursive = 2)
file.size("myhdf5file.h5")

## ----h5delete2----------------------------------------------------------------
h5delete(file = "myhdf5file.h5", name = "df")
h5ls("myhdf5file.h5", recursive = 2)

## ----h5delete3----------------------------------------------------------------
h5delete(file = "myhdf5file.h5", name = "foo")
h5ls("myhdf5file.h5", recursive = 2)
file.size("myhdf5file.h5")

## ----bit64integer1------------------------------------------------------------
x <- h5createFile("newfile3.h5")

D <- array(1L:30L, dim = c(3, 5, 2))
d <- h5createDataset(file = "newfile3.h5", dataset = "D64", dims = c(3, 5, 2), H5type = "H5T_NATIVE_INT64")
h5write(D, file = "newfile3.h5", name = "D64")

## ----bit64integer2------------------------------------------------------------
D64a <- h5read(file = "newfile3.h5", name = "D64", bit64conversion = "int")
D64a
storage.mode(D64a)

## ----bit64integer3------------------------------------------------------------
D64b <- h5read(file = "newfile3.h5", name = "D64", bit64conversion = "double")
D64b
storage.mode(D64b)

## ----bit64integer4------------------------------------------------------------
D64c <- h5read(file = "newfile3.h5", name = "D64", bit64conversion = "bit64")
D64c
class(D64c)

## ----createfile,quiet=FALSE---------------------------------------------------
library(rhdf5)
h5file <- H5Fcreate("newfile.h5")
h5file

## ----create_groups, quiet=FALSE-----------------------------------------------
h5group1 <- H5Gcreate(h5file, "foo")
h5group2 <- H5Gcreate(h5file, "baa")
h5group3 <- H5Gcreate(h5group1, "foobaa")
h5group3

## ----createdataspace, quiet=FALSE---------------------------------------------
d <- c(5, 7)
h5space1 <- H5Screate_simple(d, d)
h5space2 <- H5Screate_simple(d, NULL)
h5space3 <- H5Scopy(h5space1)
h5space4 <- H5Screate("H5S_SCALAR")
h5space1
H5Sis_simple(h5space1)

## ----create_dataset-----------------------------------------------------------
h5dataset1 <- H5Dcreate(h5file, "dataset1", "H5T_IEEE_F32LE", h5space1)
h5dataset2 <- H5Dcreate(h5group2, "dataset2", "H5T_STD_I32LE", h5space1)
h5dataset1

## ----writedata----------------------------------------------------------------
A <- seq(0.1, 3.5, length.out = 5 * 7)
H5Dwrite(h5dataset1, A)
B <- 1:35
H5Dwrite(h5dataset2, B)

## ----closefile----------------------------------------------------------------
H5Dclose(h5dataset1)
H5Dclose(h5dataset2)

H5Sclose(h5space1)
H5Sclose(h5space2)
H5Sclose(h5space3)
H5Sclose(h5space4)

H5Gclose(h5group1)
H5Gclose(h5group2)
H5Gclose(h5group3)

H5Fclose(h5file)

## ----sessioninfo--------------------------------------------------------------
sessionInfo()

## ----cleanup_after, echo=FALSE, include=FALSE---------------------------------
for (file in c("myhdf5file.h5", "newfile.h5", "newfile2.h5", "newfile3.h5")) {
  if (file.exists(file)) {
    file.remove(file)
  }
}