Turns a crosstable object into a formatted flextable — as

These objects are imported from other packages. Follow the links below to see their documentation.

flextable: as_flextable

Usage

# S3 method for crosstable
as_flextable(
  x,
  keep_id = FALSE,
  by_header = NULL,
  autofit = TRUE,
  compact = FALSE,
  show_test_name = TRUE,
  fontsizes = list(body = 11, subheaders = 11, header = 11),
  padding_v = NULL,
  remove_header_keys = FALSE,
  header_show_n = FALSE,
  header_show_n_pattern = "{.col} (N={.n})",
  generic_labels = list(id = ".id", variable = "variable", value = "value", total =
    "Total", label = "label", test = "test", effect = "effect"),
  ...
)

Arguments

x: the result of crosstable().
keep_id: whether to keep the .id column.
by_header: a string to override the header if x has only one by stratum.
autofit: whether to use flextable::autofit() on the table.
compact: whether to compact the table. If TRUE, see ct_compact.crosstable() to see how to use keep_id.
show_test_name: in the test column, show the test name.
fontsizes: font sizes as a list of keys. Default to list(body=11, subheaders=11, header=11). If set through arguments instead of options, all 3 names should be specified.
padding_v: vertical padding (body).
remove_header_keys: if TRUE and x has several by strata, header will only display values.
header_show_n: numeric vector telling on which depth the group size should be indicated in the header. You can control the pattern using option crosstable_options. See crosstable_options() for details about it. See example for use case.
header_show_n_pattern: glue pattern used when header_show_n==TRUE. .col is the name of the column and .n the size of the group. Default to {.col} (N={.n}); you can also use {.col_key} and {.col_val} when by has multiple stratum. To control the "Total" column, enter this as a list with names "cell" and "total".
generic_labels: names of the crosstable default columns. Useful for translation for instance.
...: unused.

Value

a flextable.

Methods (by class)

as_flextable(crosstable): Turns a crosstable object into a formatted flextable.

Author

Dan Chaltiel

Examples

#Crosstables
library(crosstable)
library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union
crosstable_options(crosstable_fontsize_header=14,
                   crosstable_fontsize_subheaders=10,
                   crosstable_fontsize_body=8)
crosstable(iris) %>% as_flextable()
label variable value
Sepal.Length Min / Max 4.3 / 7.9
Med [IQR] 5.8 [5.1;6.4]
Mean (std) 5.8 (0.8)
N (NA) 150 (0)
Sepal.Width Min / Max 2.0 / 4.4
Med [IQR] 3.0 [2.8;3.3]
Mean (std) 3.1 (0.4)
N (NA) 150 (0)
Petal.Length Min / Max 1.0 / 6.9
Med [IQR] 4.3 [1.6;5.1]
Mean (std) 3.8 (1.8)
N (NA) 150 (0)
Petal.Width Min / Max 0.1 / 2.5
Med [IQR] 1.3 [0.3;1.8]
Mean (std) 1.2 (0.8)
N (NA) 150 (0)
Species setosa 50 (33.33%)
versicolor 50 (33.33%)
virginica 50 (33.33%)
crosstable(mtcars2, -model, by=c(am, vs)) %>% as_flextable(header_show_n=1:2)
label variable vs=straight (N=14) vs=vshaped (N=18)
am=auto (N=7) am=manual (N=7) am=auto (N=12) am=manual (N=6)
Miles/(US) gallon Min / Max 17.8 / 24.4 21.4 / 33.9 10.4 / 19.2 15.0 / 26.0
Med [IQR] 21.4 [18.6;22.1] 30.4 [25.1;31.4] 15.2 [14.1;16.6] 20.4 [16.8;21.0]
Mean (std) 20.7 (2.5) 28.4 (4.8) 15.1 (2.8) 19.8 (4.0)
N (NA) 7 (0) 7 (0) 12 (0) 6 (0)
Number of cylinders 4 3 (27.27%) 7 (63.64%) 0 (0%) 1 (9.09%)
6 4 (57.14%) 0 (0%) 0 (0%) 3 (42.86%)
8 0 (0%) 0 (0%) 12 (85.71%) 2 (14.29%)
Displacement (cu.in.) Min / Max 120.1 / 258.0 71.1 / 121.0 275.8 / 472.0 120.3 / 351.0
Med [IQR] 167.6 [143.8;196.3] 79.0 [77.2;101.5] 355.0 [296.9;410.0] 160.0 [148.8;265.8]
Mean (std) 175.1 (49.1) 89.8 (18.8) 357.6 (71.8) 206.2 (95.2)
N (NA) 7 (0) 7 (0) 12 (0) 6 (0)
Gross horsepower Min / Max 62.0 / 123.0 52.0 / 113.0 150.0 / 245.0 91.0 / 335.0
Med [IQR] 105.0 [96.0;116.5] 66.0 [65.5;101.0] 180.0 [175.0;218.8] 142.5 [110.0;241.8]
Mean (std) 102.1 (20.9) 80.6 (24.1) 194.2 (33.4) 180.8 (98.8)
N (NA) 7 (0) 7 (0) 12 (0) 6 (0)
Rear axle ratio Min / Max 2.8 / 3.9 3.8 / 4.9 2.8 / 3.7 3.5 / 4.4
Med [IQR] 3.7 [3.4;3.9] 4.1 [4.0;4.2] 3.1 [3.1;3.2] 3.9 [3.7;4.1]
Mean (std) 3.6 (0.5) 4.1 (0.4) 3.1 (0.2) 3.9 (0.3)
N (NA) 7 (0) 7 (0) 12 (0) 6 (0)
Weight (1000 lbs) Min / Max 2.5 / 3.5 1.5 / 2.8 3.4 / 5.4 2.1 / 3.6
Med [IQR] 3.2 [3.2;3.4] 1.9 [1.7;2.3] 3.8 [3.6;4.4] 2.8 [2.7;3.1]
Mean (std) 3.2 (0.3) 2.0 (0.4) 4.1 (0.8) 2.9 (0.5)
N (NA) 7 (0) 7 (0) 12 (0) 6 (0)
1/4 mile time Min / Max 18.3 / 22.9 16.9 / 19.9 15.4 / 18.0 14.5 / 17.0
Med [IQR] 20.0 [19.2;20.1] 18.6 [18.6;19.2] 17.4 [17.0;17.7] 16.0 [14.8;16.6]
Mean (std) 20.0 (1.5) 18.7 (0.9) 17.1 (0.8) 15.8 (1.1)
N (NA) 7 (0) 7 (0) 12 (0) 6 (0)
Number of forward gears 3 3 (20.00%) 0 (0%) 12 (80.00%) 0 (0%)
4 4 (33.33%) 6 (50.00%) 0 (0%) 2 (16.67%)
5 0 (0%) 1 (20.00%) 0 (0%) 4 (80.00%)
Number of carburetors Min / Max 1.0 / 4.0 1.0 / 2.0 2.0 / 4.0 2.0 / 8.0
Med [IQR] 2.0 [1.0;3.0] 1.0 [1.0;2.0] 3.0 [2.0;4.0] 4.0 [4.0;5.5]
Mean (std) 2.1 (1.3) 1.4 (0.5) 3.1 (0.9) 4.7 (2.1)
N (NA) 7 (0) 7 (0) 12 (0) 6 (0)
Some nonsense date Min / Max 2010-03-04 - 2010-05-04 2010-02-22 - 2010-04-24 2010-05-31 - 2010-09-03 2010-04-02 - 2010-12-02
Med [IQR] 2010-04-16 [2010-04-06;2010-05-04] 2010-03-08 [2010-03-07;2010-04-20] 2010-06-30 [2010-06-25;2010-08-04] 2010-05-23 [2010-04-21;2010-09-22]
Mean (std) 2010-04-13 (20.9 days) 2010-03-22 (24.1 days) 2010-07-14 (1.1 months) 2010-06-30 (3.2 months)
N (NA) 7 (0) 7 (0) 12 (0) 6 (0)
Date+time Min / Max 2010-01-19 07:12:00 - 2010-01-23 21:36:00 2010-01-17 21:36:00 - 2010-01-20 21:36:00 2010-01-16 09:50:24 - 2010-01-19 2010-01-15 12:00:00 - 2010-01-18 00:28:48
Med [IQR] 2010-01-21 [2010-01-19 21:36:00;2010-01-21 05:16:48] 2010-01-19 14:38:24 [2010-01-19 12:28:48;2010-01-20 11:16:48] 2010-01-18 08:24:00 [2010-01-17 20:52:48;2010-01-18 14:24:00] 2010-01-16 23:31:12 [2010-01-15 14:24:00;2010-01-17 16:48:00]
Mean (std) 2010-01-20 23:12:41 (1.5 days) 2010-01-19 16:48:00 (22.7 hours) 2010-01-18 03:25:12 (19.2 hours) 2010-01-16 19:07:12 (1.1 days)
N (NA) 7 (0) 7 (0) 12 (0) 6 (0)
crosstable(mtcars2, cols=c(mpg, cyl), by=am, effect=TRUE) %>%
   as_flextable(keep_id=TRUE, autofit=FALSE)
.id label variable Transmission effect
auto manual
mpg Miles/(US) gallon Min / Max 10.4 / 24.4 15.0 / 33.9 Difference in means (t-test CI), ref='auto'
manual minus auto: 7.24 [3.64 to 10.85]
Med [IQR] 17.3 [14.9;19.2] 22.8 [21.0;30.4]
Mean (std) 17.1 (3.8) 24.4 (6.2)
N (NA) 19 (0) 13 (0)
cyl Number of cylinders 4 3 (27.27%) 8 (72.73%) Odds ratio [95% Wald CI], ref='manual vs auto'
6 vs 4: 0.28 [0.03 to 1.99]
8 vs 4: 0.06 [0.01 to 0.39]
6 4 (57.14%) 3 (42.86%)
8 12 (85.71%) 2 (14.29%)
crosstable(mtcars2, cols=c(mpg, cyl), by=am, effect=TRUE, total=TRUE) %>%
   as_flextable(compact=TRUE, header_show_n=TRUE,
                header_show_n_pattern=list(cell="{.col} (N={.n})", total="Total\n(N={.n})"))
Transmission Total
(N=32) effect
auto (N=19) manual (N=13)
Miles/(US) gallon Difference in means (t-test CI), ref='auto'
manual minus auto: 7.24 [3.64 to 10.85]
Min / Max 10.4 / 24.4 15.0 / 33.9 10.4 / 33.9 
Med [IQR] 17.3 [14.9;19.2] 22.8 [21.0;30.4] 19.2 [15.4;22.8] 
Mean (std) 17.1 (3.8) 24.4 (6.2) 20.1 (6.0) 
N (NA) 19 (0) 13 (0) 32 (0) 
Number of cylinders Odds ratio [95% Wald CI], ref='manual vs auto'
6 vs 4: 0.28 [0.03 to 1.99]
8 vs 4: 0.06 [0.01 to 0.39]
4 3 (27.27%) 8 (72.73%) 11 (34.38%) 
6 4 (57.14%) 3 (42.86%) 7 (21.88%) 
8 12 (85.71%) 2 (14.29%) 14 (43.75%) 
Total 19 (59.38%) 13 (40.62%) 32 (100.00%) 

#Renaming (because why not?)
crosstable(mtcars2, am, by=vs, total="both", test=TRUE, effect=TRUE) %>%
   rename(ID=.id, math=variable, Tot=Total, lab=label, pval=test, fx=effect) %>%
   as_flextable(by_header = "Engine shape",
                generic_labels=list(id = "ID", variable = "math", total="Tot",
                                    label = "lab", test = "pval", effect="fx"))
#> Warning: Be aware that automatic global testing should only be done in an exploratory
#> context, as it would cause extensive alpha inflation otherwise.
#> This warning is displayed once every 8 hours.
lab math Engine shape Tot fx pval
straight vshaped
Transmission auto 7 (36.84%) 12 (63.16%) 19 (59.38%) Odds ratio [95% Wald CI], ref='vshaped vs straight'
manual vs auto: 0.50 [0.11 to 2.08] p value: 0.3409 
(Pearson's Chi-squared test)
manual 7 (53.85%) 6 (46.15%) 13 (40.62%)
Total 14 (43.75%) 18 (56.25%) 32 (100.00%)

Turns a `crosstable` object into a formatted `flextable`

Usage

Arguments

Value

Methods (by class)

See also

Author

Examples

label	variable	value
Sepal.Length	Min / Max	4.3 / 7.9
	Med [IQR]	5.8 [5.1;6.4]
	Mean (std)	5.8 (0.8)
	N (NA)	150 (0)
Sepal.Width	Min / Max	2.0 / 4.4
	Med [IQR]	3.0 [2.8;3.3]
	Mean (std)	3.1 (0.4)
	N (NA)	150 (0)
Petal.Length	Min / Max	1.0 / 6.9
	Med [IQR]	4.3 [1.6;5.1]
	Mean (std)	3.8 (1.8)
	N (NA)	150 (0)
Petal.Width	Min / Max	0.1 / 2.5
	Med [IQR]	1.3 [0.3;1.8]
	Mean (std)	1.2 (0.8)
	N (NA)	150 (0)
Species	setosa	50 (33.33%)
	versicolor	50 (33.33%)
	virginica	50 (33.33%)

label	variable	vs=straight (N=14)		vs=vshaped (N=18)
label	variable	am=auto (N=7)	am=manual (N=7)	am=auto (N=12)	am=manual (N=6)
Miles/(US) gallon	Min / Max	17.8 / 24.4	21.4 / 33.9	10.4 / 19.2	15.0 / 26.0
	Med [IQR]	21.4 [18.6;22.1]	30.4 [25.1;31.4]	15.2 [14.1;16.6]	20.4 [16.8;21.0]
	Mean (std)	20.7 (2.5)	28.4 (4.8)	15.1 (2.8)	19.8 (4.0)
	N (NA)	7 (0)	7 (0)	12 (0)	6 (0)
Number of cylinders	4	3 (27.27%)	7 (63.64%)	0 (0%)	1 (9.09%)
	6	4 (57.14%)	0 (0%)	0 (0%)	3 (42.86%)
	8	0 (0%)	0 (0%)	12 (85.71%)	2 (14.29%)
Displacement (cu.in.)	Min / Max	120.1 / 258.0	71.1 / 121.0	275.8 / 472.0	120.3 / 351.0
	Med [IQR]	167.6 [143.8;196.3]	79.0 [77.2;101.5]	355.0 [296.9;410.0]	160.0 [148.8;265.8]
	Mean (std)	175.1 (49.1)	89.8 (18.8)	357.6 (71.8)	206.2 (95.2)
	N (NA)	7 (0)	7 (0)	12 (0)	6 (0)
Gross horsepower	Min / Max	62.0 / 123.0	52.0 / 113.0	150.0 / 245.0	91.0 / 335.0
	Med [IQR]	105.0 [96.0;116.5]	66.0 [65.5;101.0]	180.0 [175.0;218.8]	142.5 [110.0;241.8]
	Mean (std)	102.1 (20.9)	80.6 (24.1)	194.2 (33.4)	180.8 (98.8)
	N (NA)	7 (0)	7 (0)	12 (0)	6 (0)
Rear axle ratio	Min / Max	2.8 / 3.9	3.8 / 4.9	2.8 / 3.7	3.5 / 4.4
	Med [IQR]	3.7 [3.4;3.9]	4.1 [4.0;4.2]	3.1 [3.1;3.2]	3.9 [3.7;4.1]
	Mean (std)	3.6 (0.5)	4.1 (0.4)	3.1 (0.2)	3.9 (0.3)
	N (NA)	7 (0)	7 (0)	12 (0)	6 (0)
Weight (1000 lbs)	Min / Max	2.5 / 3.5	1.5 / 2.8	3.4 / 5.4	2.1 / 3.6
	Med [IQR]	3.2 [3.2;3.4]	1.9 [1.7;2.3]	3.8 [3.6;4.4]	2.8 [2.7;3.1]
	Mean (std)	3.2 (0.3)	2.0 (0.4)	4.1 (0.8)	2.9 (0.5)
	N (NA)	7 (0)	7 (0)	12 (0)	6 (0)
1/4 mile time	Min / Max	18.3 / 22.9	16.9 / 19.9	15.4 / 18.0	14.5 / 17.0
	Med [IQR]	20.0 [19.2;20.1]	18.6 [18.6;19.2]	17.4 [17.0;17.7]	16.0 [14.8;16.6]
	Mean (std)	20.0 (1.5)	18.7 (0.9)	17.1 (0.8)	15.8 (1.1)
	N (NA)	7 (0)	7 (0)	12 (0)	6 (0)
Number of forward gears	3	3 (20.00%)	0 (0%)	12 (80.00%)	0 (0%)
	4	4 (33.33%)	6 (50.00%)	0 (0%)	2 (16.67%)
	5	0 (0%)	1 (20.00%)	0 (0%)	4 (80.00%)
Number of carburetors	Min / Max	1.0 / 4.0	1.0 / 2.0	2.0 / 4.0	2.0 / 8.0
	Med [IQR]	2.0 [1.0;3.0]	1.0 [1.0;2.0]	3.0 [2.0;4.0]	4.0 [4.0;5.5]
	Mean (std)	2.1 (1.3)	1.4 (0.5)	3.1 (0.9)	4.7 (2.1)
	N (NA)	7 (0)	7 (0)	12 (0)	6 (0)
Some nonsense date	Min / Max	2010-03-04 - 2010-05-04	2010-02-22 - 2010-04-24	2010-05-31 - 2010-09-03	2010-04-02 - 2010-12-02
	Med [IQR]	2010-04-16 [2010-04-06;2010-05-04]	2010-03-08 [2010-03-07;2010-04-20]	2010-06-30 [2010-06-25;2010-08-04]	2010-05-23 [2010-04-21;2010-09-22]
	Mean (std)	2010-04-13 (20.9 days)	2010-03-22 (24.1 days)	2010-07-14 (1.1 months)	2010-06-30 (3.2 months)
	N (NA)	7 (0)	7 (0)	12 (0)	6 (0)
Date+time	Min / Max	2010-01-19 07:12:00 - 2010-01-23 21:36:00	2010-01-17 21:36:00 - 2010-01-20 21:36:00	2010-01-16 09:50:24 - 2010-01-19	2010-01-15 12:00:00 - 2010-01-18 00:28:48
	Med [IQR]	2010-01-21 [2010-01-19 21:36:00;2010-01-21 05:16:48]	2010-01-19 14:38:24 [2010-01-19 12:28:48;2010-01-20 11:16:48]	2010-01-18 08:24:00 [2010-01-17 20:52:48;2010-01-18 14:24:00]	2010-01-16 23:31:12 [2010-01-15 14:24:00;2010-01-17 16:48:00]
	Mean (std)	2010-01-20 23:12:41 (1.5 days)	2010-01-19 16:48:00 (22.7 hours)	2010-01-18 03:25:12 (19.2 hours)	2010-01-16 19:07:12 (1.1 days)
	N (NA)	7 (0)	7 (0)	12 (0)	6 (0)

.id	label	variable	Transmission		effect
.id	label	variable	auto	manual	effect
mpg	Miles/(US) gallon	Min / Max	10.4 / 24.4	15.0 / 33.9	Difference in means (t-test CI), ref='auto' manual minus auto: 7.24 [3.64 to 10.85]
		Med [IQR]	17.3 [14.9;19.2]	22.8 [21.0;30.4]
		Mean (std)	17.1 (3.8)	24.4 (6.2)
		N (NA)	19 (0)	13 (0)
cyl	Number of cylinders	4	3 (27.27%)	8 (72.73%)	Odds ratio [95% Wald CI], ref='manual vs auto' 6 vs 4: 0.28 [0.03 to 1.99] 8 vs 4: 0.06 [0.01 to 0.39]
		6	4 (57.14%)	3 (42.86%)
		8	12 (85.71%)	2 (14.29%)

	Transmission		Total (N=32)	effect
	auto (N=19)	manual (N=13)	Total (N=32)	effect
Miles/(US) gallon				Difference in means (t-test CI), ref='auto' manual minus auto: 7.24 [3.64 to 10.85]
Min / Max	10.4 / 24.4	15.0 / 33.9	10.4 / 33.9
Med [IQR]	17.3 [14.9;19.2]	22.8 [21.0;30.4]	19.2 [15.4;22.8]
Mean (std)	17.1 (3.8)	24.4 (6.2)	20.1 (6.0)
N (NA)	19 (0)	13 (0)	32 (0)
Number of cylinders				Odds ratio [95% Wald CI], ref='manual vs auto' 6 vs 4: 0.28 [0.03 to 1.99] 8 vs 4: 0.06 [0.01 to 0.39]
4	3 (27.27%)	8 (72.73%)	11 (34.38%)
6	4 (57.14%)	3 (42.86%)	7 (21.88%)
8	12 (85.71%)	2 (14.29%)	14 (43.75%)
Total	19 (59.38%)	13 (40.62%)	32 (100.00%)

lab	math	Engine shape		Tot	fx	pval
lab	math	straight	vshaped	Tot	fx	pval
Transmission	auto	7 (36.84%)	12 (63.16%)	19 (59.38%)	Odds ratio [95% Wald CI], ref='vshaped vs straight' manual vs auto: 0.50 [0.11 to 2.08]	p value: 0.3409 (Pearson's Chi-squared test)
	manual	7 (53.85%)	6 (46.15%)	13 (40.62%)
	Total	14 (43.75%)	18 (56.25%)	32 (100.00%)