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Working with larger-than-memory data

2024-09-18

Larger-than-memory Data

Many data sets of Brazilian censuses are too big to load in users’ RAM memory. To avoid this problem, {censobr} works with files saved in .parquet format and, by default, the functions in {censobr} returns an Arrow table rather than a data.frame. There are a few really simple alternative ways to work with Arrow tables in R without loading the full data to memory. We cover four alternative approaches in this vignette.

First, let’s read the 2010 mortality data, which we’ll use throughout vignette for illustration purposes.

library(censobr)

# read 2010 mortality data
df <- censobr::read_mortality(
  year = 2010,
  add_labels = 'pt',
  showProgress = FALSE
  )

1. `{dplyr}`

Because of the seamless integration between {arrow} and {dplyr}, Arrow tables can be analyzed pretty much like a regular data.frame using the {dplyr}syntax. There is a small but important difference, though. When using {dplyr} with an Arrow table, the operations are not executed immediately. Instead, {dplyr} builds a lazy query plan that is only evaluated when you explicitly ask for the results. To retrieve the actual results, you need to call either:

collect(): This brings the results into memory as a regular data.frame.
compute(): This materializes the result in the Arrow format (e.g., as a new Arrow table).

Without calling one of these, the query is just prepared but not executed, which is useful for delaying heavy computations until needed.

In the example below, we create a new Arrow table that only includes the deaths records of men in the state of Rio de Janeiro without loading the data to memory. Note that we only piece of data we collect() (i.e. load to memory) here are the first observations of the data.

library(dplyr)

# Filter deaths of men in the state of Rio de Janeiro
rio <- df |>
      filter(V0704 == 'Masculino' & abbrev_state == 'RJ')

head(rio) |> 
  collect()
#>    code_muni code_state abbrev_state     name_state code_region name_region
#>        <int>      <int>       <char>         <char>       <int>      <char>
#> 1:   3300100         33           RJ Rio de Janeiro           3     Sudeste
#> 2:   3300100         33           RJ Rio de Janeiro           3     Sudeste
#> 3:   3300100         33           RJ Rio de Janeiro           3     Sudeste
#> 4:   3300100         33           RJ Rio de Janeiro           3     Sudeste
#> 5:   3300100         33           RJ Rio de Janeiro           3     Sudeste
#> 6:   3300100         33           RJ Rio de Janeiro           3     Sudeste
#>    code_weighting  V0001  V0002         V0011   V0300    V0010  V1001  V1002
#>            <char> <char> <char>        <char>   <num>    <num> <char> <char>
#> 1:  3300100003001     33  00100 3300100003001 1285657 13.51819      3     05
#> 2:  3300100003001     33  00100 3300100003001 6084726 12.76395      3     05
#> 3:  3300100003002     33  00100 3300100003002  898500 10.68108      3     05
#> 4:  3300100003002     33  00100 3300100003002 2581116 11.61204      3     05
#> 5:  3300100003002     33  00100 3300100003002 3768175 12.93833      3     05
#> 6:  3300100003002     33  00100 3300100003002 4125020 10.66262      3     05
#>     V1003  V1004  V1006             V0703     V0704 V7051 V7052  M0703  M0704
#>    <char> <char> <char>            <char>    <char> <num> <num> <char> <char>
#> 1:    013     00 Urbana     Março de 2010 Masculino    69    NA      2      2
#> 2:    013     00 Urbana Fevereiro de 2010 Masculino    84    NA      2      2
#> 3:    013     00 Urbana     Abril de 2010 Masculino    38    NA      2      2
#> 4:    013     00 Urbana      Maio de 2010 Masculino    54    NA      2      2
#> 5:    013     00  Rural    Agosto de 2009 Masculino    31    NA      2      2
#> 6:    013     00 Urbana  Setembro de 2009 Masculino    28    NA      2      2
#>     M7051  M7052                                 V1005
#>    <char> <char>                                <char>
#> 1:      2      2                       Área urbanizada
#> 2:      2      2                   Área não urbanizada
#> 3:      2      2                       Área urbanizada
#> 4:      2      2                       Área urbanizada
#> 5:      2      2 Área rural exclusive aglomerado rural
#> 6:      2      2                       Área urbanizada

2. `{duckdb}`

{duckdb} is another powerful library to work with larger-than-memory data in R through database interface. There are different ways to use {duckdb}, but here cover three alternatives

2.1 Combining `{duckdb}` & `{dplyr}`

One easy option is to combine {duckdb} & {dplyr}. Note here that first you need to convert the Arrow table into a DuckDB table with arrow::to_duckdb(). Also note that the you need to use a bit of SQL syntax inside the dplyr call. Using the same example as above:

library(duckdb)
library(dplyr)
library(arrow)

# Filter deaths of men in the state of Rio de Janeiro
rio1 <- df |>
        arrow::to_duckdb() |>
        filter(sql("V0704 LIKE '%Masculino%' AND abbrev_state = 'RJ'"))

head(rio1) |> 
  collect()
#> # A tibble: 6 × 26
#>   code_muni code_state abbrev_state name_state     code_region name_region
#>       <int>      <int> <chr>        <chr>                <int> <chr>      
#> 1   3300100         33 RJ           Rio de Janeiro           3 Sudeste    
#> 2   3300100         33 RJ           Rio de Janeiro           3 Sudeste    
#> 3   3300100         33 RJ           Rio de Janeiro           3 Sudeste    
#> 4   3300100         33 RJ           Rio de Janeiro           3 Sudeste    
#> 5   3300100         33 RJ           Rio de Janeiro           3 Sudeste    
#> 6   3300100         33 RJ           Rio de Janeiro           3 Sudeste    
#> # ℹ 20 more variables: code_weighting <chr>, V0001 <chr>, V0002 <chr>,
#> #   V0011 <chr>, V0300 <dbl>, V0010 <dbl>, V1001 <chr>, V1002 <chr>,
#> #   V1003 <chr>, V1004 <chr>, V1006 <chr>, V0703 <chr>, V0704 <chr>,
#> #   V7051 <dbl>, V7052 <dbl>, M0703 <chr>, M0704 <chr>, M7051 <chr>,
#> #   M7052 <chr>, V1005 <chr>

2.2 Combining `{duckdb}` & `SQL`

Another alternative is to combine {duckdb} with {DBI} using database interface and SQL syntax.

library(duckdb)
library(DBI)

# create databse connection
con <- duckdb::dbConnect(duckdb::duckdb())

# register the data in the data base
duckdb::duckdb_register_arrow(con, 'mortality_2010_tbl', df)

# Filter deaths of men in the state of Rio de Janeiro
rio2 <- DBI::dbGetQuery(con, "SELECT * FROM 'mortality_2010_tbl' WHERE V0704 LIKE '%Masculino%' AND abbrev_state = 'RJ'")

head(rio2)
#>   code_muni code_state abbrev_state     name_state code_region name_region
#> 1   3300100         33           RJ Rio de Janeiro           3     Sudeste
#> 2   3300100         33           RJ Rio de Janeiro           3     Sudeste
#> 3   3300100         33           RJ Rio de Janeiro           3     Sudeste
#> 4   3300100         33           RJ Rio de Janeiro           3     Sudeste
#> 5   3300100         33           RJ Rio de Janeiro           3     Sudeste
#> 6   3300100         33           RJ Rio de Janeiro           3     Sudeste
#>   code_weighting V0001 V0002         V0011   V0300    V0010 V1001 V1002 V1003
#> 1  3300100003001    33 00100 3300100003001 1285657 13.51819     3    05   013
#> 2  3300100003001    33 00100 3300100003001 6084726 12.76395     3    05   013
#> 3  3300100003002    33 00100 3300100003002  898500 10.68108     3    05   013
#> 4  3300100003002    33 00100 3300100003002 2581116 11.61204     3    05   013
#> 5  3300100003002    33 00100 3300100003002 3768175 12.93833     3    05   013
#> 6  3300100003002    33 00100 3300100003002 4125020 10.66262     3    05   013
#>   V1004  V1006             V0703     V0704 V7051 V7052 M0703 M0704 M7051 M7052
#> 1    00 Urbana     Março de 2010 Masculino    69    NA     2     2     2     2
#> 2    00 Urbana Fevereiro de 2010 Masculino    84    NA     2     2     2     2
#> 3    00 Urbana     Abril de 2010 Masculino    38    NA     2     2     2     2
#> 4    00 Urbana      Maio de 2010 Masculino    54    NA     2     2     2     2
#> 5    00  Rural    Agosto de 2009 Masculino    31    NA     2     2     2     2
#> 6    00 Urbana  Setembro de 2009 Masculino    28    NA     2     2     2     2
#>                                   V1005
#> 1                       Área urbanizada
#> 2                   Área não urbanizada
#> 3                       Área urbanizada
#> 4                       Área urbanizada
#> 5 Área rural exclusive aglomerado rural
#> 6                       Área urbanizada

2.3 `{duckplyr}`

A third alternative is the new {duckplyr} package. This this library is under development so it still does not cover many of the {dplyr}verbs. (See here). Nonetheless, it looks like a really promising and seamless approach that allow users to leverage the powerful capabilities of {duckdb}.

library(duckplyr)

rio3 <- df |>
        duckplyr::filter(V0704 == 'Masculino' & abbrev_state == 'RJ')

head(rio3) |> 
  collect()
#>    code_muni code_state abbrev_state     name_state code_region name_region
#>        <int>      <int>       <char>         <char>       <int>      <char>
#> 1:   3300100         33           RJ Rio de Janeiro           3     Sudeste
#> 2:   3300100         33           RJ Rio de Janeiro           3     Sudeste
#> 3:   3300100         33           RJ Rio de Janeiro           3     Sudeste
#> 4:   3300100         33           RJ Rio de Janeiro           3     Sudeste
#> 5:   3300100         33           RJ Rio de Janeiro           3     Sudeste
#> 6:   3300100         33           RJ Rio de Janeiro           3     Sudeste
#>    code_weighting  V0001  V0002         V0011   V0300    V0010  V1001  V1002
#>            <char> <char> <char>        <char>   <num>    <num> <char> <char>
#> 1:  3300100003001     33  00100 3300100003001 1285657 13.51819      3     05
#> 2:  3300100003001     33  00100 3300100003001 6084726 12.76395      3     05
#> 3:  3300100003002     33  00100 3300100003002  898500 10.68108      3     05
#> 4:  3300100003002     33  00100 3300100003002 2581116 11.61204      3     05
#> 5:  3300100003002     33  00100 3300100003002 3768175 12.93833      3     05
#> 6:  3300100003002     33  00100 3300100003002 4125020 10.66262      3     05
#>     V1003  V1004  V1006             V0703     V0704 V7051 V7052  M0703  M0704
#>    <char> <char> <char>            <char>    <char> <num> <num> <char> <char>
#> 1:    013     00 Urbana     Março de 2010 Masculino    69    NA      2      2
#> 2:    013     00 Urbana Fevereiro de 2010 Masculino    84    NA      2      2
#> 3:    013     00 Urbana     Abril de 2010 Masculino    38    NA      2      2
#> 4:    013     00 Urbana      Maio de 2010 Masculino    54    NA      2      2
#> 5:    013     00  Rural    Agosto de 2009 Masculino    31    NA      2      2
#> 6:    013     00 Urbana  Setembro de 2009 Masculino    28    NA      2      2
#>     M7051  M7052                                 V1005
#>    <char> <char>                                <char>
#> 1:      2      2                       Área urbanizada
#> 2:      2      2                   Área não urbanizada
#> 3:      2      2                       Área urbanizada
#> 4:      2      2                       Área urbanizada
#> 5:      2      2 Área rural exclusive aglomerado rural
#> 6:      2      2                       Área urbanizada

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.

Working with larger-than-memory data

2024-09-18

Larger-than-memory Data

1. {dplyr}

2. {duckdb}

2.1 Combining {duckdb} & {dplyr}

2.2 Combining {duckdb} & SQL

2.3 {duckplyr}

1. `{dplyr}`

2. `{duckdb}`

2.1 Combining `{duckdb}` & `{dplyr}`

2.2 Combining `{duckdb}` & `SQL`

2.3 `{duckplyr}`