What are Data Types (and Why Should You Care?)
A data type is a description of how information is stored digitally and in which format. In the context of BLOSC compression this is relevant as it is used to compress arrays of structured data. How this data is structured is described by the data type.
For the use of BLOSC in R, this is also relevant, because
R (by design) provides access to a limited number of data
types, most importantly: raw(), logical(),
integer(), numeric() and
complex(). Below you will find a table of typical storage
formats and how these are converted to R types.
Therefore, you probably need to convert the data type of stored data
to something that can be handled in R (or vice versa). For
your convenience the functions r_to_dtype() and
dtype_to_r() handle such conversions. Note that these
functions do not provide exhaustive features, but are meant to handle
most common conversions.
Specification Version
The package at hand uses version 2 of data type specifications, while they are superseded by version 3. Why is this?
The old version is used as it still includes the endianness in its encoding and is more compact. In combination with the endianness version 3 types can easily be annotated with version 2 data types. You have to do this conversion yourself, it is not implemented by this package.
Overview of Data Types
Data types are represented by a code where the first character
reflects the byte order of the data (see Wikipedia article about Endianness). The
second character reflects the main type of the data (such as integer, or
floating point). The following numerical characters indicate the size
(in bytes) of each element. For data types M (date time)
and m (delta time), the specification also includes the
unit of time used to store the information.
The table below shows an overview of common types, how the are
converted from and to R types, and some important notes to
consider while converting data.
| dtype code | Alternative notation | R type | Notes | |
|b1 |
8 bit boolean | logical() |
In R logical values are actually stored as a 32 bit
integer. |
|
|i1, <i2, >i2,
<i4, >i4
|
8 bit, 16 bit and 32 bit signed integers. | integer() |
||
|u1, <u2, >u2
|
8 bit and 16 bit unsigned integers | integer() |
||
<u4, >u4, <u8,
>u8
|
32 and 64 bit unsigned integers | numeric() |
Not all numbers of these types can be adequately represented by
neither R’s numeric() nor integer(). Handle
these types with caution |
|
<i8, >i8
|
64 bit signed integers | numeric() |
Not all numbers of these types can be adequately represented by
neither R’s numeric() nor integer(). Handle
these types with caution |
|
<f2, >f2, <f4,
>f4, <f8, >f8, |
16, 32 and 64 bit floating point numbers | numeric() |
||
<c8, >c8, <c16,
>c16, |
64 bit and 128 bit complex numbers | complex() |
||
<M8[*] >M8[*] where *=unit |
64 bit date time object | as.POSIXct() |
Note that the dtype stores the time unit as a 64 bit
integer, whereas POSIXct stores the object as a double. Use
with caution |
|
<m8[*] >m8[*] where *=unit |
64 bit delta time object | difftime() |
Note that the dtype stores the time unit as a 64 bit
integer, whereas difftime stores the object as a
double. Use with caution |
|
|S* |
UTF8 string | character() |
||
|U* |
UTF32 string | character() |
Note that UTF8 encoding is used in the conversion process. Hence, information may get lost. Use with caution | |
Some examples of encoding r data to dtypes
library(blosc)
r_to_dtype(c(TRUE, FALSE), "|b1")
#> [1] 01 00
r_to_dtype(1L:4L, "|u1")
#> [1] 01 02 03 04
r_to_dtype(c(1.4, 9.8e-6), "<f8")
#> [1] 66 66 66 66 66 66 f6 3f 33 76 78 be 55 8d e4 3e
r_to_dtype(1+1i, "<c16")
#> [1] 00 00 00 00 00 00 f0 3f 00 00 00 00 00 00 f0 3f
r_to_dtype(as.POSIXct("2023-06-23 15:32:19", tz = "UTC"), "<M8[ms]")
#> [1] b8 83 e2 e8 88 01 00 00
r_to_dtype(as.difftime(1, units = "weeks"), "<m8[D]")
#> [1] 07 00 00 00 00 00 00 00
r_to_dtype(c("foo", "bar", "foobar"), "|S6")
#> [1] 66 6f 6f 00 00 00 62 61 72 00 00 00 66 6f 6f 62 61 72Precision of Types
Beware that when encoding R types to a
dtype, you may lose precision. You will receive no
notification, so it is your own responsibility. Loss of precision
happens when the data type you use for encoding is less precise than
R’s native type. For instance when you encode an
R numeric (64 bit floating point) to dtype
"<f2" (16 bit floating point). This will become apparent
when you convert your dtype back to an R type.
Some examples where you will lose precision:
## Encoding numeric (64 bit) as a 16 bit float:
r_to_dtype(0.123, "<f2") |>
dtype_to_r("<f2")
#> [1] 0.1229858
## Encoding a date-time object in whole hours
## as opposed to a floating point of seconds
r_to_dtype(as.POSIXct("2024-05-31 19:58:01", tz = "UTC"), "<M8[h]") |>
dtype_to_r("<M8[h]")
#> [1] "2024-05-31 19:00:00 UTC"Note that you will always need to use an identical dtype
to back-transform encoded data. Otherwise you will get nonsensical
results.
Missing Values
When storing raw data, you may want to reserve a value to represent
missing values. This is also what R does for
NA values. Other software may use different values to
represent missing values. Also, some data types have insufficient
storage capacity to store R NA values
The examples below show how you can use custom values to represent missing values.
## As `na_value` is not specified for `dtype_to_r()`
## and the NA value is masked to 8 bit, the `NA`
## value is mistakenly interpreted as `TRUE`
r_to_dtype(c(TRUE, NA, FALSE, TRUE), "|b1") |>
dtype_to_r("|b1", na_value = NA_integer_)
#> [1] TRUE TRUE FALSE TRUE
## This can be fixed by specifying `na_value`
r_to_dtype(c(TRUE, NA, FALSE, TRUE), "|b1", na_value = -1) |>
dtype_to_r("|b1", na_value = -1)
#> [1] TRUE NA FALSE TRUE
## If the `na_value` is not specified for `dtype_to_r()`,
## it will be taken literally
r_to_dtype(c(1, NA, 4, 5), "<i4", na_value = -999) |>
dtype_to_r("<i4")
#> [1] 1 -999 4 5
## If the `na_value` is specified for `dtype_to_r()`,
## it will be interpreted as NA
r_to_dtype(c(1, NA, 4, 5), "<i4", na_value = -999) |>
dtype_to_r("<i4", na_value = -999)
#> [1] 1 NA 4 5