---
title: "Get Started with h5lite"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Get Started with h5lite}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")
```

The `h5lite` package provides a simplified, user-friendly interface for interacting with HDF5 files in R. While HDF5 is a complex hierarchical data format, `h5lite` is designed to feel familiar to R users by mapping HDF5 concepts directly to R's native data structures.

## HDF5 for R Users

If you are new to HDF5, the easiest way to understand it is through R analogues. HDF5 files function like a file system within a single file, containing "groups" (folders) and "datasets" (files).

| R Concept           | HDF5 Concept         | Description                                                       |
| :------------------ | :------------------- | :---------------------------------------------------------------- |
| **List**            | **Group**            | A container that holds other objects (datasets or other groups).  |
| **Vector / Matrix** | **Dataset**          | A multidimensional array of data (numeric, character, etc.).      |
| **Data Frame**      | **Compound Dataset** | A table where each column can have a different data type.         |
| **Attribute**       | **Attribute**        | Metadata attached to a specific object (e.g., units, timestamps). |

## Basic Usage

The package uses two primary functions: `h5_write()` to save data and `h5_read()` to load it.

### Writing Numeric Data

You can write standard R arrays and vectors directly to an HDF5 file. `h5lite` automatically handles dimensions.

```{r}
library(h5lite)
file <- tempfile(fileext = ".h5")

# 1. 1D Array (Vector)
vec <- c(1.5, 2.3, 4.2)
h5_write(vec, file, "examples/vector")

# 2. 2D Array (Matrix)
mat <- matrix(1:9, nrow = 3, ncol = 3)
h5_write(mat, file, "examples/matrix")

# 3. 3D Array
arr <- array(1:24, dim = c(4, 3, 2))
h5_write(arr, file, "examples/array_3d")

# 4. Scalar
# By default, R treats length-1 vectors as arrays. 
# Wrap in I() to write a true HDF5 scalar.
val <- I(42)
h5_write(val, file, "examples/scalar")
```

*Note: While `h5lite` supports preserving row and column names for matrices and vectors, these examples omit them for simplicity. See `vignette('attributes-in-depth')` for details on how dimension names are stored.*

### Reading Data

Data is read back into its native R format.

```{r}
x <- h5_read(file, "examples/matrix")
print(x)
```

## Data Type Mapping

`h5lite` automatically selects the appropriate HDF5 data type based on the content of your R objects.

| R Data Type    | HDF5 Equivalent  | Description                                   |
| :------------- | :--------------- | :-------------------------------------------- |
| **Numeric**    | *variable*       | Selects optimal type: `int8`, `float32`, etc. |
| **Logical**    | `H5T_STD_U8LE`   | Stored as 0 (FALSE) or 1 (TRUE) (`uint8`).    |
| **Character**  | `H5T_STRING`     | Variable or fixed-length UTF-8 strings.       |
| **Complex**    | `H5T_COMPLEX`    | Native HDF5 2.0+ complex numbers.             |
| **Raw**        | `H5T_OPAQUE`     | Raw bytes / binary data.                      |
| **Factor**     | `H5T_ENUM`       | Integer indices with label mapping.           |
| **integer64**  | `H5T_STD_I64LE`  | 64-bit signed integers via `bit64` package.   |
| **POSIXt**     | `H5T_STRING`     | ISO 8601 string (`YYYY-MM-DDTHH:MM:SSZ`).     |
| **List**       | `H5O_TYPE_GROUP` | Recursive container structure.                |
| **Data Frame** | `H5T_COMPOUND`   | Table of mixed types.                         |
| **NULL**       | `H5S_NULL`       | Creates a placeholder.                        |

You can use the `as` argument to explicitly set the HDF5 data type for numeric, logical, and character vectors. See `vignette('data-types')` for details.

## Complex Data Structures

### Lists as Groups
R lists are naturally hierarchical, making them perfect for creating HDF5 groups.

```{r}
my_list <- list(
  config = list(id = 1L, status = "active"),
  data   = runif(10)
)
# Creates a group "/experiment" containing "config" (group) and "data" (dataset)
h5_write(my_list, file, "experiment") 
```

### Data Frames as Compound Datasets
Data frames are written as native HDF5 compound datasets, allowing efficient storage of tabular data with mixed types.

```{r}
df <- data.frame(
  id = 1:5,
  val = c(1.1, 2.2, 3.3, 4.4, 5.5)
)
h5_write(df, file, "study_data")
```

For more details on these structures, including how to handle factors and nested lists, refer to `vignette('data-frames')`.

## Attributes

Attributes are small pieces of metadata attached to objects. `h5lite` writes R attributes (like `units` or `description`) as HDF5 attributes.

```{r}
# Write a dataset
h5_write(1:10, file, "measurements")

# Attach an attribute to it
h5_write("meters", file, "measurements", attr = "units")
```

See `vignette('attributes-in-depth')` for information on reading specific attributes and how special R attributes like `dimnames` are handled.

## File Inspection

You can inspect the contents of an HDF5 file without reading the data into memory using `h5_ls()` and `h5_str()`.

```{r}
# List contents
h5_ls(file)

# Print structure tree (like R's str())
h5_str(file)
```

For advanced file operations, including moving, deleting, and verifying objects, refer to `vignette('organization')`.