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Convert data from plain text to duckdb or parquet format

Source: R/convert.R
spod_convert.Rd

[Stable]

Converts data for faster analysis into either DuckDB file or into parquet files in a hive-style directory structure. Running analysis on these files is sometimes 100x times faster than working with raw CSV files, espetially when these are in gzip archives. To connect to converted data, please use 'mydata <- spod_connect(data_path = path_returned_by_spod_convert)' passing the path to where the data was saved. The connected mydata can be analysed using dplyr functions such as select, filter, mutate, group_by, summarise, etc. In the end of any sequence of commands you will need to add collect to execute the whole chain of data manipulations and load the results into memory in an R data.frame/tibble. For more in-depth usage of such data, please refer to DuckDB documentation and examples at https://duckdb.org/docs/api/r#dbplyr . Some more useful examples can be found here https://arrow-user2022.netlify.app/data-wrangling#combining-arrow-with-duckdb . You may also use arrow package to work with parquet files https://arrow.apache.org/docs/r/.

Usage

spod_convert(
  type = c("od", "origin-destination", "os", "overnight_stays", "nt", "number_of_trips"),
  zones = c("districts", "dist", "distr", "distritos", "municipalities", "muni",
    "municip", "municipios"),
  dates = NULL,
  save_format = "duckdb",
  save_path = NULL,
  overwrite = FALSE,
  data_dir = spod_get_data_dir(),
  quiet = FALSE,
  max_mem_gb = NULL,
  max_n_cpu = max(1, parallelly::availableCores() - 1),
  max_download_size_gb = 1,
  ignore_missing_dates = FALSE
)

Arguments

type

The type of data to download. Can be "origin-destination" (or ust "od"), or "number_of_trips" (or just "nt") for v1 data. For v2 data "overnight_stays" (or just "os") is also available. More data types to be supported in the future. See codebooks for v1 and v2 data in vignettes with spod_codebook(1) and spod_codebook(2) (spod_codebook).

zones

The zones for which to download the data. Can be "districts" (or "dist", "distr", or the original Spanish "distritos") or "municipalities" (or "muni", "municip", or the original Spanish "municipios") for both data versions. Additionaly, these can be "large_urban_areas" (or "lua", or the original Spanish "grandes_areas_urbanas", or "gau") for v2 data (2022 onwards).

dates

A character or Date vector of dates to process. Kindly keep in mind that v1 and v2 data follow different data collection methodologies and may not be directly comparable. Therefore, do not try to request data from both versions for the same date range. If you need to compare data from both versions, please refer to the respective codebooks and methodology documents. The v1 data covers the period from 2020-02-14 to 2021-05-09, and the v2 data covers the period from 2022-01-01 to the present until further notice. The true dates range is checked against the available data for each version on every function run.

The possible values can be any of the following:

  • For the spod_get() and spod_convert() functions, the dates can be set to "cached_v1" or "cached_v2" to request data from cached (already previously downloaded) v1 (2020-2021) or v2 (2022 onwards) data. In this case, the function will identify and use all data files that have been downloaded and cached locally, (e.g. using an explicit run of spod_download(), or any data requests made using the spod_get() or spod_convert() functions).

  • A single date in ISO (YYYY-MM-DD) or YYYYMMDD format. character or Date object.

  • A vector of dates in ISO (YYYY-MM-DD) or YYYYMMDD format. character or Date object. Can be any non-consecutive sequence of dates.

  • A date range

    • eigher a character or Date object of length 2 with clearly named elements start and end in ISO (YYYY-MM-DD) or YYYYMMDD format. E.g. c(start = "2020-02-15", end = "2020-02-17");

    • or a character object of the form YYYY-MM-DD_YYYY-MM-DD or YYYYMMDD_YYYYMMDD. For example, 2020-02-15_2020-02-17 or 20200215_20200217.

  • A regular expression to match dates in the format YYYYMMDD. character object. For example, ^202002 will match all dates in February 2020.

save_format

A character vector of length 1 with values "duckdb" or "parquet". Defaults to "duckdb". If NULL automatically inferred from the save_path argument. If only save_format is provided, save_path will be set to the default location set in SPANISH_OD_DATA_DIR environment variable using spod_set_data_dir(path = 'path/to/your/cache/dir'). So for v1 data that path would be <data_dir>/clean_data/v1/tabular/duckdb/ or <data_dir>/clean_data/v1/tabular/parquet/.

You can also set save_path. If it ends with ".duckdb", will save to DuckDB database format, if save_path does not end with ".duckdb", will save to parquet format and will treat the save_path as a path to a folder, not a file, will create necessary hive-style subdirectories in that folder. Hive style looks like year=2020/month=2/day=14 and inside each such directory there will be a data_0.parquet file that contains the data for that day.

save_path

A character vector of length 1. The full (not relative) path to a DuckDB database file or parquet folder.

  • If save_path ends with .duckdb, it will be saved as a DuckDB database file. The format argument will be automatically set to save_format='duckdb'.

  • If save_path ends with a folder name (e.g. /data_dir/clean_data/v1/tabular/parquet/od_distr for origin-destination data for district level), the data will be saved as a collection of parquet files in a hive-style directory structure. So the subfolders of od_distr will be year=2020/month=2/day=14 and inside each of these folders a single parquet file will be placed containing the data for that day.

  • If NULL, uses the default location in data_dir (set by the SPANISH_OD_DATA_DIR environment variable using spod_set_data_dir(path = 'path/to/your/cache/dir'). Therefore, the default relative path for DuckDB is <data_dir>/clean_data/v1/tabular/duckdb/<type>_<zones>.duckdb and for parquet files is <data_dir>/clean_data/v1/tabular/parquet/<type>_<zones>/, where type is the type of data (e.g. 'od', 'os', 'nt', that correspoind to 'origin-destination', 'overnight-stays', 'number-of-trips', etc.) and zones is the name of the geographic zones (e.g. 'distr', 'muni', etc.). See the details below in the function arguments description.

overwrite

A logical or a character vector of length 1. If TRUE, overwrites existing DuckDB or parquet files. Defaults to FALSE. For parquet files can also be set to 'update', so that only parquet files are only created for the dates that have not yet been converted.

data_dir

The directory where the data is stored. Defaults to the value returned by spod_get_data_dir() which returns the value of the environment variable SPANISH_OD_DATA_DIR or a temporary directory if the variable is not set. To set the data directory, use spod_set_data_dir.

quiet

A logical value indicating whether to suppress messages. Default is FALSE.

max_mem_gb

integer value of the maximum operating memory to use in GB. NULL by default, delegates the choice to the DuckDB engine which usually sets it to 80% of available memory. Caution, in HPC use, the amount of memory available to your job may be determined incorrectly by the DuckDB engine, so it is recommended to set this parameter explicitly according to your job's memory limits.

max_n_cpu

The maximum number of threads to use. Defaults to the number of available cores minus 1.

max_download_size_gb

The maximum download size in gigabytes. Defaults to 1.

ignore_missing_dates

Logical. If TRUE, the function will not raise an error if the some of the specified dates are missing. Any dates that are missing will be skipped, however the data for any valid dates will be acquired. Defaults to FALSE.

Value

Path to saved DuckDB database file or to a folder with parquet files in hive-style directory structure.

Examples

if (FALSE) { # interactive()
# \donttest{
# Set data dir for file downloads
spod_set_data_dir(tempdir())

# download and convert data
dates_1 <- c(start = "2020-02-17", end = "2020-02-18")
db_2 <- spod_convert(
  type = "number_of_trips",
  zones = "distr",
  dates = dates_1,
  overwrite = TRUE
)

# now connect to the converted data
my_od_data_2 <- spod_connect(db_2)

# disconnect from the database
spod_disconnect(my_od_data_2)
# }
}