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Convert a datras_raw object to a tibble

Source: R/formatting.R
as_tibble.datras_raw.Rd

Method for tibble::as_tibble(): the same table as as_table(), returned as a tibble, so that as_tibble(x) and x |> as_tibble() work in tidyverse workflows. All arguments of as_table() are available, including table for the length (HL) and individual (CA) data.

Usage

# S3 method for class 'datras_raw'
as_tibble(
  x,
  ...,
  vars = .default_hh_vars,
  add_vars = NULL,
  remove_vars = NULL,
  type = "long",
  table = c("HH", "HL", "CA"),
  hl_by = c("Valid_Aphia", "LngtCm"),
  zeros = TRUE,
  ca_vars = .default_ca_vars
)

Arguments

x

A datras_raw object.

...

Passed to tibble::as_tibble() for the converted table, e.g. .name_repair.

vars

Character vector of HH variable names to include. Defaults to 15 common haul-level columns: Survey, Gear, Country, Ship, Year, Quarter, Month, Day, lon, lat, timeOfYear, abstime, DayNight, TimeShotHour, HaulDur.

add_vars

Character vector of additional HH variable names to append to vars. Applied after remove_vars.

remove_vars

Character vector of variable names to drop from vars. Applied before add_vars.

type

Character string specifying the output format: "long" (default) or "wide". See Details for what each means per table.

table

Character string naming the table to export: "HH" (default) for one row per haul, "HL" for numbers at length by haul and species, or "CA" for one row per individual record.

hl_by

Character vector of HL columns that define a row for table = "HL", in addition to the haul. Default c("Valid_Aphia", "LngtCm"): species x length class, summed over sex and catch category. Add "Sex" to keep sexes apart. Must contain "Valid_Aphia".

zeros

Logical. For table = "HL": if TRUE (default), add a row with Count = 0 for every haul in HH and species in HL without a record, so that averages over hauls include the hauls where a species was not caught.

ca_vars

Character vector of CA columns to include for table = "CA". Columns not found are omitted with a warning.

Value

A tibble. See as_table() for the rows and columns of each table and type.

Details

The method is registered when the tibble package is installed; tibble is not required otherwise.

See also

as_table(), as_long_format(), as_wide_format()

Examples

if (requireNamespace("tibble", quietly = TRUE)) {
  dab <- add_numbers_at_length(dab)
  dab <- add_total_numbers_by_haul(dab, length_cuts = c(0, 20, Inf))

  tibble::as_tibble(dab)
  tibble::as_tibble(dab, type = "wide", add_vars = "Depth")
  tibble::as_tibble(dab, table = "HL", vars = c("Year", "lon", "lat"))
}
#> Warning: Mixed accuracies found in var[[3]]$LngtCode - worst chosen: 1 cm
#> Warning: NAs found in var[[3]]$LngtCode - assumed to be 1 cm
#> # A tibble: 25,596 × 8
#>    haul.id                    Year    lon   lat Valid_Aphia LngtCm Species Count
#>    <fct>                      <fct> <dbl> <dbl>       <dbl>  <dbl> <fct>   <dbl>
#>  1 NS-IBTS:2020:1:DK:26D4:GO… 2020   7.14  56.6      127139     12 Limand…  6.34
#>  2 NS-IBTS:2020:1:DK:26D4:GO… 2020   7.14  56.6      127139     13 Limand…  4.22
#>  3 NS-IBTS:2020:1:DK:26D4:GO… 2020   7.14  56.6      127139     14 Limand…  4.22
#>  4 NS-IBTS:2020:1:DK:26D4:GO… 2020   7.14  56.6      127139     15 Limand…  4.22
#>  5 NS-IBTS:2020:1:DK:26D4:GO… 2020   7.14  56.6      127139     16 Limand…  2.11
#>  6 NS-IBTS:2020:1:DK:26D4:GO… 2020   7.14  56.6      127139     17 Limand…  6.34
#>  7 NS-IBTS:2020:1:DK:26D4:GO… 2020   7.14  56.6      127139     18 Limand… 21.1 
#>  8 NS-IBTS:2020:1:DK:26D4:GO… 2020   7.14  56.6      127139     19 Limand… 21.1 
#>  9 NS-IBTS:2020:1:DK:26D4:GO… 2020   7.14  56.6      127139     20 Limand… 27.5 
#> 10 NS-IBTS:2020:1:DK:26D4:GO… 2020   7.14  56.6      127139     21 Limand… 21.1 
#> # ℹ 25,586 more rows