Formats a tidydiversity result as a table for a manuscript or report:
rounds numbers, combines estimates and confidence limits into one cell
in APA style, for example 12.34 [10.10, 14.50], renames columns to
readable titles, and can spread the orders q into columns so each site
takes one row. The result can be returned as a tibble, or rendered with
knitr, gt or flextable for HTML, PDF or Word output.
Arguments
- x
A tibble from
div_estimate(),div_standardise(),div_hill(),div_coverage(),beta_pair()orbeta_multi().- digits
Number of decimal places.
- ci
Combine the estimate with its confidence limits in one cell.
- ci_style
Style of the interval:
"apa"([lower, upper]),"parentheses"((lower-upper)) or"pm"(+/- SE).- wide
Spread the orders
qinto columns, one row per site.- output
"tibble","kable"(knitr::kable()),"gt"(gt::gt()) or"flextable"(flextable::flextable()).- caption
Optional table caption for the rendered formats.
Examples
set.seed(1)
est <- div_estimate(png_ants, .by = season, nboot = 20)
div_table(est)
#> # A tibble: 30 x 5
#> season site `Order q` Observed `Estimate [95% CI]`
#> <chr> <chr> <chr> <chr> <chr>
#> 1 dry MW0200 0 16.00 18.45 [16.15, 56.45]
#> 2 dry MW0200 1 12.28 15.18 [12.55, 17.81]
#> 3 dry MW0200 2 9.91 12.28 [9.91, 15.51]
#> 4 wet MW0200 0 21.00 32.94 [23.58, 76.23]
#> 5 wet MW0200 1 10.88 13.79 [10.88, 19.09]
#> 6 wet MW0200 2 6.99 7.60 [6.99, 10.19]
#> 7 dry MW0700 0 15.00 83.87 [49.95, 150.69]
#> 8 dry MW0700 1 11.76 38.45 [15.67, 61.23]
#> 9 dry MW0700 2 8.67 13.32 [8.67, 28.21]
#> 10 wet MW0700 0 28.00 75.34 [42.19, 185.93]
#> # i 20 more rows
div_table(est, wide = TRUE, digits = 1)
#> # A tibble: 10 x 8
#> season site `observed (q = 0)` `estimate (q = 0)` `observed (q = 1)`
#> <chr> <chr> <chr> <chr> <chr>
#> 1 dry MW0200 16.0 18.4 [16.1, 56.5] 12.3
#> 2 wet MW0200 21.0 32.9 [23.6, 76.2] 10.9
#> 3 dry MW0700 15.0 83.9 [50.0, 150.7] 11.8
#> 4 wet MW0700 28.0 75.3 [42.2, 185.9] 21.6
#> 5 dry MW1200 13.0 20.9 [13.9, 85.7] 9.4
#> 6 wet MW1200 20.0 33.3 [22.2, 98.6] 13.9
#> 7 dry MW1700 5.0 5.2 [5.0, 17.4] 3.9
#> 8 wet MW1700 10.0 18.7 [10.9, 98.4] 5.3
#> 9 dry MW2200 6.0 10.2 [6.6, 34.1] 5.0
#> 10 wet MW2200 5.0 6.9 [5.2, 26.9] 3.6
#> # i 3 more variables: `estimate (q = 1)` <chr>, `observed (q = 2)` <chr>,
#> # `estimate (q = 2)` <chr>
div_table(est, output = "kable", caption = "Asymptotic diversity")
#>
#>
#> Table: Asymptotic diversity
#>
#> |season | site| Order q| Observed| Estimate [95% CI]|
#> |:------|------:|-------:|--------:|---------------------:|
#> |dry | MW0200| 0| 16.00| 18.45 [16.15, 56.45]|
#> |dry | MW0200| 1| 12.28| 15.18 [12.55, 17.81]|
#> |dry | MW0200| 2| 9.91| 12.28 [9.91, 15.51]|
#> |wet | MW0200| 0| 21.00| 32.94 [23.58, 76.23]|
#> |wet | MW0200| 1| 10.88| 13.79 [10.88, 19.09]|
#> |wet | MW0200| 2| 6.99| 7.60 [6.99, 10.19]|
#> |dry | MW0700| 0| 15.00| 83.87 [49.95, 150.69]|
#> |dry | MW0700| 1| 11.76| 38.45 [15.67, 61.23]|
#> |dry | MW0700| 2| 8.67| 13.32 [8.67, 28.21]|
#> |wet | MW0700| 0| 28.00| 75.34 [42.19, 185.93]|
#> |wet | MW0700| 1| 21.58| 38.81 [21.58, 56.41]|
#> |wet | MW0700| 2| 17.16| 23.96 [17.16, 31.89]|
#> |dry | MW1200| 0| 13.00| 20.89 [13.86, 85.67]|
#> |dry | MW1200| 1| 9.37| 13.81 [9.37, 22.38]|
#> |dry | MW1200| 2| 6.73| 8.46 [6.73, 14.86]|
#> |wet | MW1200| 0| 20.00| 33.26 [22.24, 98.57]|
#> |wet | MW1200| 1| 13.88| 18.83 [13.88, 26.45]|
#> |wet | MW1200| 2| 10.06| 12.00 [10.06, 18.80]|
#> |dry | MW1700| 0| 5.00| 5.24 [5.00, 17.42]|
#> |dry | MW1700| 1| 3.92| 4.51 [3.92, 6.26]|
#> |dry | MW1700| 2| 3.25| 3.78 [3.25, 5.68]|
#> |wet | MW1700| 0| 10.00| 18.74 [10.86, 98.37]|
#> |wet | MW1700| 1| 5.30| 7.05 [5.30, 11.16]|
#> |wet | MW1700| 2| 3.61| 3.92 [3.61, 4.99]|
#> |dry | MW2200| 0| 6.00| 10.15 [6.61, 34.08]|
#> |dry | MW2200| 1| 4.98| 7.34 [4.98, 12.57]|
#> |dry | MW2200| 2| 4.33| 6.00 [4.33, 8.78]|
#> |wet | MW2200| 0| 5.00| 6.87 [5.16, 26.93]|
#> |wet | MW2200| 1| 3.62| 4.54 [3.62, 7.67]|
#> |wet | MW2200| 2| 2.85| 3.28 [2.85, 6.10]|