Author: Tina Gunderson and Ethan Heinzen

# The freqlist function

#### Tina Gunderson and Ethan Heinzen

# Overview

`freqlist()` is a function meant to produce output similar to SAS’s `PROC FREQ` procedure when using the `/list` option of the `TABLE` statement. `freqlist()` provides options for handling missing or sparse data and can provide cumulative counts and percentages based on subgroups. It depends on the `knitr` package for printing.

    require(arsenal)

## Sample dataset

For our examples, we’ll load the `mockstudy` data included with this package and use it to create a basic table. Because they have fewer levels, for brevity, we’ll use the variables arm, sex, and mdquality.s to create the example table. We’ll retain NAs in the table creation. See the appendix for notes regarding default NA handling and other useful information regarding tables in R.

    # load the data
    data(mockstudy)

    # retain NAs when creating the table using the useNA argument
    tab.ex <- table(mockstudy[, c("arm", "sex", "mdquality.s")], useNA="ifany")

# The `freqlist` object

The `freqlist()` function is an S3 generic (with methods for tables and formulas) which returns an object of class `"freqlist"`.

    example1 <- freqlist(tab.ex)

    str(example1)

    List of 3
     $ Call   : language freqlist.table(object = tab.ex)
     $ control:List of 5
      ..$ sparse      : logi FALSE
      ..$ single      : logi FALSE
      ..$ dupLabels   : logi FALSE
      ..$ digits.count: int 0
      ..$ digits.pct  : int 2
     $ tables :List of 1
      ..$ :List of 6
      .. ..$ y         :List of 2
      .. .. ..$ term : chr ""
      .. .. ..$ label: chr ""
      .. ..$ strata    :List of 4
      .. .. ..$ term     : chr ""
      .. .. ..$ values   : chr ""
      .. .. ..$ label    : chr ""
      .. .. ..$ hasStrata: logi FALSE
      .. ..$ x         :List of 7
      .. .. ..$ arm        :List of 3
      .. .. .. ..$ variable: chr "arm"
      .. .. .. ..$ label   : chr "arm"
      .. .. .. ..$ term    : chr "arm"
      .. .. ..$ sex        :List of 3
      .. .. .. ..$ variable: chr "sex"
      .. .. .. ..$ label   : chr "sex"
      .. .. .. ..$ term    : chr "sex"
      .. .. ..$ mdquality.s:List of 3
      .. .. .. ..$ variable: chr "mdquality.s"
      .. .. .. ..$ label   : chr "mdquality.s"
      .. .. .. ..$ term    : chr "mdquality.s"
      .. .. ..$ Freq       :List of 3
      .. .. .. ..$ variable: chr "Freq"
      .. .. .. ..$ label   : chr "Freq"
      .. .. .. ..$ term    : chr "Freq"
      .. .. ..$ cumFreq    :List of 3
      .. .. .. ..$ variable: chr "cumFreq"
      .. .. .. ..$ label   : chr "Cumulative Freq"
      .. .. .. ..$ term    : chr "cumFreq"
      .. .. ..$ freqPercent:List of 3
      .. .. .. ..$ variable: chr "freqPercent"
      .. .. .. ..$ label   : chr "Percent"
      .. .. .. ..$ term    : chr "freqPercent"
      .. .. ..$ cumPercent :List of 3
      .. .. .. ..$ variable: chr "cumPercent"
      .. .. .. ..$ label   : chr "Cumulative Percent"
      .. .. .. ..$ term    : chr "cumPercent"
      .. ..$ tables    :List of 1
      .. .. ..$ :'data.frame':  18 obs. of  7 variables:
      .. .. .. ..$ arm        : Factor w/ 3 levels "A: IFL","F: FOLFOX",..: 1 1 1 1 1 1 2 2 2 2 ...
      .. .. .. ..$ sex        : Factor w/ 2 levels "Male","Female": 1 1 1 2 2 2 1 1 1 2 ...
      .. .. .. ..$ mdquality.s: Factor w/ 2 levels "0","1": 1 2 NA 1 2 NA 1 2 NA 1 ...
      .. .. .. ..$ Freq       : int [1:18] 29 214 34 12 118 21 31 285 95 21 ...
      .. .. .. ..$ cumFreq    : int [1:18] 29 243 277 289 407 428 459 744 839 860 ...
      .. .. .. ..$ freqPercent: num [1:18] 1.935 14.276 2.268 0.801 7.872 ...
      .. .. .. ..$ cumPercent : num [1:18] 1.93 16.21 18.48 19.28 27.15 ...
      .. ..$ hasWeights: logi FALSE
      .. ..$ na.options: chr "include"
     - attr(*, "class")= chr [1:2] "freqlist" "arsenal_table"

    # view the data frame portion of freqlist output
    head(as.data.frame(example1)) ## or use as.data.frame(example1)

         arm    sex mdquality.s Freq cumFreq freqPercent cumPercent
    1 A: IFL   Male           0   29      29   1.9346231   1.934623
    2 A: IFL   Male           1  214     243  14.2761841  16.210807
    3 A: IFL   Male        <NA>   34     277   2.2681788  18.478986
    4 A: IFL Female           0   12     289   0.8005337  19.279520
    5 A: IFL Female           1  118     407   7.8719146  27.151434
    6 A: IFL Female        <NA>   21     428   1.4009340  28.552368

# Basic output using `summary()`

The `summary` method for `freqlist()` relies on the `kable()` function (in the `knitr` package) for printing. `knitr::kable()` converts the output to markdown which can be printed in the console or easily rendered in Word, PDF, or HTML documents.

Note that you must supply `results="asis"` to properly format the markdown output.

    summary(example1)

arm | sex | mdquality.s | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
A: IFL | Male | 0 | 29 | 29 | 1.93 | 1.93
|  | 1 | 214 | 243 | 14.28 | 16.21
|  | NA | 34 | 277 | 2.27 | 18.48
| Female | 0 | 12 | 289 | 0.80 | 19.28
|  | 1 | 118 | 407 | 7.87 | 27.15
|  | NA | 21 | 428 | 1.40 | 28.55
F: FOLFOX | Male | 0 | 31 | 459 | 2.07 | 30.62
|  | 1 | 285 | 744 | 19.01 | 49.63
|  | NA | 95 | 839 | 6.34 | 55.97
| Female | 0 | 21 | 860 | 1.40 | 57.37
|  | 1 | 198 | 1058 | 13.21 | 70.58
|  | NA | 61 | 1119 | 4.07 | 74.65
G: IROX | Male | 0 | 17 | 1136 | 1.13 | 75.78
|  | 1 | 187 | 1323 | 12.47 | 88.26
|  | NA | 24 | 1347 | 1.60 | 89.86
| Female | 0 | 14 | 1361 | 0.93 | 90.79
|  | 1 | 121 | 1482 | 8.07 | 98.87
|  | NA | 17 | 1499 | 1.13 | 100.00

You can print a title for the table using the `title=` argument.

    summary(example1, title="Basic freqlist output")

Basic freqlist output
arm | sex | mdquality.s | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
A: IFL | Male | 0 | 29 | 29 | 1.93 | 1.93
|  | 1 | 214 | 243 | 14.28 | 16.21
|  | NA | 34 | 277 | 2.27 | 18.48
| Female | 0 | 12 | 289 | 0.80 | 19.28
|  | 1 | 118 | 407 | 7.87 | 27.15
|  | NA | 21 | 428 | 1.40 | 28.55
F: FOLFOX | Male | 0 | 31 | 459 | 2.07 | 30.62
|  | 1 | 285 | 744 | 19.01 | 49.63
|  | NA | 95 | 839 | 6.34 | 55.97
| Female | 0 | 21 | 860 | 1.40 | 57.37
|  | 1 | 198 | 1058 | 13.21 | 70.58
|  | NA | 61 | 1119 | 4.07 | 74.65
G: IROX | Male | 0 | 17 | 1136 | 1.13 | 75.78
|  | 1 | 187 | 1323 | 12.47 | 88.26
|  | NA | 24 | 1347 | 1.60 | 89.86
| Female | 0 | 14 | 1361 | 0.93 | 90.79
|  | 1 | 121 | 1482 | 8.07 | 98.87
|  | NA | 17 | 1499 | 1.13 | 100.00

You can also easily pull out the `freqlist` data frame for more complicated formatting or manipulation (e.g. with another function such as `xtable()` or `pander()`) using `as.data.frame(summary())`:

    head(as.data.frame(summary(example1)))

         arm    sex mdquality.s Freq Cumulative Freq Percent Cumulative Percent
    1 A: IFL   Male           0   29              29    1.93               1.93
    2                         1  214             243   14.28              16.21
    3                      <NA>   34             277    2.27              18.48
    4        Female           0   12             289    0.80              19.28
    5                         1  118             407    7.87              27.15
    6                      <NA>   21             428    1.40              28.55

# Using a formula with `freqlist`

Instead of passing a pre-computed table to `freqlist()`, you can instead pass a formula, which will be in turn passed to the `xtabs()` function. Additional `freqlist()` arguments are passed through the `...` to the `freqlist()` table method.

Note that `freqlist()` sets the `addNA=TRUE` argument by default:

    summary(freqlist(~ arm + sex + mdquality.s, data = mockstudy))

Treatment Arm | sex | mdquality.s | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
A: IFL | Male | 0 | 29 | 29 | 1.93 | 1.93
|  | 1 | 214 | 243 | 14.28 | 16.21
|  | NA | 34 | 277 | 2.27 | 18.48
| Female | 0 | 12 | 289 | 0.80 | 19.28
|  | 1 | 118 | 407 | 7.87 | 27.15
|  | NA | 21 | 428 | 1.40 | 28.55
F: FOLFOX | Male | 0 | 31 | 459 | 2.07 | 30.62
|  | 1 | 285 | 744 | 19.01 | 49.63
|  | NA | 95 | 839 | 6.34 | 55.97
| Female | 0 | 21 | 860 | 1.40 | 57.37
|  | 1 | 198 | 1058 | 13.21 | 70.58
|  | NA | 61 | 1119 | 4.07 | 74.65
G: IROX | Male | 0 | 17 | 1136 | 1.13 | 75.78
|  | 1 | 187 | 1323 | 12.47 | 88.26
|  | NA | 24 | 1347 | 1.60 | 89.86
| Female | 0 | 14 | 1361 | 0.93 | 90.79
|  | 1 | 121 | 1482 | 8.07 | 98.87
|  | NA | 17 | 1499 | 1.13 | 100.00

One can also set NAs to an explicit value using `includeNA()`.

    summary(freqlist(~ arm + sex + includeNA(mdquality.s, "Missing"), data = mockstudy))

Treatment Arm | sex | includeNA(mdquality.s, “Missing”) | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
A: IFL | Male | 0 | 29 | 29 | 1.93 | 1.93
|  | 1 | 214 | 243 | 14.28 | 16.21
|  | Missing | 34 | 277 | 2.27 | 18.48
| Female | 0 | 12 | 289 | 0.80 | 19.28
|  | 1 | 118 | 407 | 7.87 | 27.15
|  | Missing | 21 | 428 | 1.40 | 28.55
F: FOLFOX | Male | 0 | 31 | 459 | 2.07 | 30.62
|  | 1 | 285 | 744 | 19.01 | 49.63
|  | Missing | 95 | 839 | 6.34 | 55.97
| Female | 0 | 21 | 860 | 1.40 | 57.37
|  | 1 | 198 | 1058 | 13.21 | 70.58
|  | Missing | 61 | 1119 | 4.07 | 74.65
G: IROX | Male | 0 | 17 | 1136 | 1.13 | 75.78
|  | 1 | 187 | 1323 | 12.47 | 88.26
|  | Missing | 24 | 1347 | 1.60 | 89.86
| Female | 0 | 14 | 1361 | 0.93 | 90.79
|  | 1 | 121 | 1482 | 8.07 | 98.87
|  | Missing | 17 | 1499 | 1.13 | 100.00

In fact, since `xtabs()` allows for left-hand-side weights, so does `freqlist()`!

    mockstudy$weights <- c(10000, rep(1, nrow(mockstudy) - 1))
    summary(freqlist(weights ~ arm + sex + addNA(mdquality.s), data = mockstudy))

Treatment Arm | sex | addNA(mdquality.s) | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
A: IFL | Male | 0 | 29 | 29 | 0.25 | 0.25
|  | 1 | 214 | 243 | 1.86 | 2.11
|  | NA | 34 | 277 | 0.30 | 2.41
| Female | 0 | 12 | 289 | 0.10 | 2.51
|  | 1 | 118 | 407 | 1.03 | 3.54
|  | NA | 21 | 428 | 0.18 | 3.72
F: FOLFOX | Male | 0 | 31 | 459 | 0.27 | 3.99
|  | 1 | 285 | 744 | 2.48 | 6.47
|  | NA | 10094 | 10838 | 87.79 | 94.26
| Female | 0 | 21 | 10859 | 0.18 | 94.44
|  | 1 | 198 | 11057 | 1.72 | 96.16
|  | NA | 61 | 11118 | 0.53 | 96.70
G: IROX | Male | 0 | 17 | 11135 | 0.15 | 96.84
|  | 1 | 187 | 11322 | 1.63 | 98.47
|  | NA | 24 | 11346 | 0.21 | 98.68
| Female | 0 | 14 | 11360 | 0.12 | 98.80
|  | 1 | 121 | 11481 | 1.05 | 99.85
|  | NA | 17 | 11498 | 0.15 | 100.00

You can also specify multiple weights:

    mockstudy$weights2 <- c(rep(1, nrow(mockstudy) - 1), 10000)
    summary(freqlist(list(weights, weights2) ~ arm + sex + addNA(mdquality.s), data = mockstudy))

Treatment Arm | sex | addNA(mdquality.s) | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
A: IFL | Male | 0 | 29 | 29 | 0.25 | 0.25
|  | 1 | 214 | 243 | 1.86 | 2.11
|  | NA | 34 | 277 | 0.30 | 2.41
| Female | 0 | 12 | 289 | 0.10 | 2.51
|  | 1 | 118 | 407 | 1.03 | 3.54
|  | NA | 21 | 428 | 0.18 | 3.72
F: FOLFOX | Male | 0 | 31 | 459 | 0.27 | 3.99
|  | 1 | 285 | 744 | 2.48 | 6.47
|  | NA | 10094 | 10838 | 87.79 | 94.26
| Female | 0 | 21 | 10859 | 0.18 | 94.44
|  | 1 | 198 | 11057 | 1.72 | 96.16
|  | NA | 61 | 11118 | 0.53 | 96.70
G: IROX | Male | 0 | 17 | 11135 | 0.15 | 96.84
|  | 1 | 187 | 11322 | 1.63 | 98.47
|  | NA | 24 | 11346 | 0.21 | 98.68
| Female | 0 | 14 | 11360 | 0.12 | 98.80
|  | 1 | 121 | 11481 | 1.05 | 99.85
|  | NA | 17 | 11498 | 0.15 | 100.00

Treatment Arm | sex | addNA(mdquality.s) | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
A: IFL | Male | 0 | 29 | 29 | 0.25 | 0.25
|  | 1 | 214 | 243 | 1.86 | 2.11
|  | NA | 34 | 277 | 0.30 | 2.41
| Female | 0 | 12 | 289 | 0.10 | 2.51
|  | 1 | 118 | 407 | 1.03 | 3.54
|  | NA | 21 | 428 | 0.18 | 3.72
F: FOLFOX | Male | 0 | 31 | 459 | 0.27 | 3.99
|  | 1 | 285 | 744 | 2.48 | 6.47
|  | NA | 95 | 839 | 0.83 | 7.30
| Female | 0 | 21 | 860 | 0.18 | 7.48
|  | 1 | 198 | 1058 | 1.72 | 9.20
|  | NA | 10060 | 11118 | 87.49 | 96.70
G: IROX | Male | 0 | 17 | 11135 | 0.15 | 96.84
|  | 1 | 187 | 11322 | 1.63 | 98.47
|  | NA | 24 | 11346 | 0.21 | 98.68
| Female | 0 | 14 | 11360 | 0.12 | 98.80
|  | 1 | 121 | 11481 | 1.05 | 99.85
|  | NA | 17 | 11498 | 0.15 | 100.00

# Rounding percentage digits or changing variable names for printing

The `digits.pct=` argument takes a single numeric value and controls the number of digits of percentages in the output. The `digits.count=` argument takes a similar argument and controls the number of digits of the count columns. The `labelTranslations=` argument is a named character vector or list. Both options are applied in the following example.

    example2 <- freqlist(tab.ex, labelTranslations = c(arm = "Treatment Arm", sex = "Gender", mdquality.s = "LASA QOL"),
                          digits.pct = 1, digits.count = 1)
    summary(example2)

Treatment Arm | Gender | LASA QOL | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
A: IFL | Male | 0 | 29.0 | 29.0 | 1.9 | 1.9
|  | 1 | 214.0 | 243.0 | 14.3 | 16.2
|  | NA | 34.0 | 277.0 | 2.3 | 18.5
| Female | 0 | 12.0 | 289.0 | 0.8 | 19.3
|  | 1 | 118.0 | 407.0 | 7.9 | 27.2
|  | NA | 21.0 | 428.0 | 1.4 | 28.6
F: FOLFOX | Male | 0 | 31.0 | 459.0 | 2.1 | 30.6
|  | 1 | 285.0 | 744.0 | 19.0 | 49.6
|  | NA | 95.0 | 839.0 | 6.3 | 56.0
| Female | 0 | 21.0 | 860.0 | 1.4 | 57.4
|  | 1 | 198.0 | 1058.0 | 13.2 | 70.6
|  | NA | 61.0 | 1119.0 | 4.1 | 74.6
G: IROX | Male | 0 | 17.0 | 1136.0 | 1.1 | 75.8
|  | 1 | 187.0 | 1323.0 | 12.5 | 88.3
|  | NA | 24.0 | 1347.0 | 1.6 | 89.9
| Female | 0 | 14.0 | 1361.0 | 0.9 | 90.8
|  | 1 | 121.0 | 1482.0 | 8.1 | 98.9
|  | NA | 17.0 | 1499.0 | 1.1 | 100.0

# Additional examples

## Including combinations with frequencies of zero

The `sparse=` argument takes a single logical value as input. The default option is `FALSE`. If set to `TRUE`, the sparse option will include combinations with frequencies of zero in the list of results. As our initial table did not have any such levels, we create a second table to use in our example.

    summary(freqlist(~ race + sex + arm, data = mockstudy, sparse = TRUE, digits.pct=1))

Race | sex | Treatment Arm | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
African-Am | Male | A: IFL | 25 | 25 | 1.7 | 1.7
|  | F: FOLFOX | 24 | 49 | 1.6 | 3.3
|  | G: IROX | 16 | 65 | 1.1 | 4.3
| Female | A: IFL | 14 | 79 | 0.9 | 5.3
|  | F: FOLFOX | 25 | 104 | 1.7 | 6.9
|  | G: IROX | 11 | 115 | 0.7 | 7.7
Asian | Male | A: IFL | 0 | 115 | 0.0 | 7.7
|  | F: FOLFOX | 10 | 125 | 0.7 | 8.3
|  | G: IROX | 1 | 126 | 0.1 | 8.4
| Female | A: IFL | 1 | 127 | 0.1 | 8.5
|  | F: FOLFOX | 4 | 131 | 0.3 | 8.7
|  | G: IROX | 2 | 133 | 0.1 | 8.9
Caucasian | Male | A: IFL | 240 | 373 | 16.0 | 24.9
|  | F: FOLFOX | 352 | 725 | 23.5 | 48.4
|  | G: IROX | 195 | 920 | 13.0 | 61.4
| Female | A: IFL | 131 | 1051 | 8.7 | 70.1
|  | F: FOLFOX | 234 | 1285 | 15.6 | 85.7
|  | G: IROX | 136 | 1421 | 9.1 | 94.8
Hawaii/Pacific | Male | A: IFL | 1 | 1422 | 0.1 | 94.9
|  | F: FOLFOX | 1 | 1423 | 0.1 | 94.9
|  | G: IROX | 0 | 1423 | 0.0 | 94.9
| Female | A: IFL | 0 | 1423 | 0.0 | 94.9
|  | F: FOLFOX | 2 | 1425 | 0.1 | 95.1
|  | G: IROX | 1 | 1426 | 0.1 | 95.1
Hispanic | Male | A: IFL | 8 | 1434 | 0.5 | 95.7
|  | F: FOLFOX | 17 | 1451 | 1.1 | 96.8
|  | G: IROX | 12 | 1463 | 0.8 | 97.6
| Female | A: IFL | 4 | 1467 | 0.3 | 97.9
|  | F: FOLFOX | 11 | 1478 | 0.7 | 98.6
|  | G: IROX | 2 | 1480 | 0.1 | 98.7
Native-Am/Alaska | Male | A: IFL | 1 | 1481 | 0.1 | 98.8
|  | F: FOLFOX | 0 | 1481 | 0.0 | 98.8
|  | G: IROX | 2 | 1483 | 0.1 | 98.9
| Female | A: IFL | 1 | 1484 | 0.1 | 99.0
|  | F: FOLFOX | 1 | 1485 | 0.1 | 99.1
|  | G: IROX | 0 | 1485 | 0.0 | 99.1
Other | Male | A: IFL | 2 | 1487 | 0.1 | 99.2
|  | F: FOLFOX | 2 | 1489 | 0.1 | 99.3
|  | G: IROX | 1 | 1490 | 0.1 | 99.4
| Female | A: IFL | 0 | 1490 | 0.0 | 99.4
|  | F: FOLFOX | 2 | 1492 | 0.1 | 99.5
|  | G: IROX | 0 | 1492 | 0.0 | 99.5
NA | Male | A: IFL | 0 | 1492 | 0.0 | 99.5
|  | F: FOLFOX | 5 | 1497 | 0.3 | 99.9
|  | G: IROX | 1 | 1498 | 0.1 | 99.9
| Female | A: IFL | 0 | 1498 | 0.0 | 99.9
|  | F: FOLFOX | 1 | 1499 | 0.1 | 100.0
|  | G: IROX | 0 | 1499 | 0.0 | 100.0

## Options for NA handling

The various `na.options=` allow you to include or exclude data with missing values for one or more factor levels in the counts and percentages, as well as show the missing data but exclude it from the cumulative counts and percentages. The default option is to include all combinations with missing values.

    summary(freqlist(tab.ex, na.options="include"))

arm | sex | mdquality.s | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
A: IFL | Male | 0 | 29 | 29 | 1.93 | 1.93
|  | 1 | 214 | 243 | 14.28 | 16.21
|  | NA | 34 | 277 | 2.27 | 18.48
| Female | 0 | 12 | 289 | 0.80 | 19.28
|  | 1 | 118 | 407 | 7.87 | 27.15
|  | NA | 21 | 428 | 1.40 | 28.55
F: FOLFOX | Male | 0 | 31 | 459 | 2.07 | 30.62
|  | 1 | 285 | 744 | 19.01 | 49.63
|  | NA | 95 | 839 | 6.34 | 55.97
| Female | 0 | 21 | 860 | 1.40 | 57.37
|  | 1 | 198 | 1058 | 13.21 | 70.58
|  | NA | 61 | 1119 | 4.07 | 74.65
G: IROX | Male | 0 | 17 | 1136 | 1.13 | 75.78
|  | 1 | 187 | 1323 | 12.47 | 88.26
|  | NA | 24 | 1347 | 1.60 | 89.86
| Female | 0 | 14 | 1361 | 0.93 | 90.79
|  | 1 | 121 | 1482 | 8.07 | 98.87
|  | NA | 17 | 1499 | 1.13 | 100.00

    summary(freqlist(tab.ex, na.options="showexclude"))

arm | sex | mdquality.s | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
A: IFL | Male | 0 | 29 | 29 | 2.33 | 2.33
|  | 1 | 214 | 243 | 17.16 | 19.49
|  | NA | 34 | NA | NA | NA
| Female | 0 | 12 | 255 | 0.96 | 20.45
|  | 1 | 118 | 373 | 9.46 | 29.91
|  | NA | 21 | NA | NA | NA
F: FOLFOX | Male | 0 | 31 | 404 | 2.49 | 32.40
|  | 1 | 285 | 689 | 22.85 | 55.25
|  | NA | 95 | NA | NA | NA
| Female | 0 | 21 | 710 | 1.68 | 56.94
|  | 1 | 198 | 908 | 15.88 | 72.81
|  | NA | 61 | NA | NA | NA
G: IROX | Male | 0 | 17 | 925 | 1.36 | 74.18
|  | 1 | 187 | 1112 | 15.00 | 89.17
|  | NA | 24 | NA | NA | NA
| Female | 0 | 14 | 1126 | 1.12 | 90.30
|  | 1 | 121 | 1247 | 9.70 | 100.00
|  | NA | 17 | NA | NA | NA

    summary(freqlist(tab.ex, na.options="remove"))

arm | sex | mdquality.s | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
A: IFL | Male | 0 | 29 | 29 | 2.33 | 2.33
|  | 1 | 214 | 243 | 17.16 | 19.49
| Female | 0 | 12 | 255 | 0.96 | 20.45
|  | 1 | 118 | 373 | 9.46 | 29.91
F: FOLFOX | Male | 0 | 31 | 404 | 2.49 | 32.40
|  | 1 | 285 | 689 | 22.85 | 55.25
| Female | 0 | 21 | 710 | 1.68 | 56.94
|  | 1 | 198 | 908 | 15.88 | 72.81
G: IROX | Male | 0 | 17 | 925 | 1.36 | 74.18
|  | 1 | 187 | 1112 | 15.00 | 89.17
| Female | 0 | 14 | 1126 | 1.12 | 90.30
|  | 1 | 121 | 1247 | 9.70 | 100.00

## Frequency counts and percentages subset by factor levels

The `strata=` argument internally subsets the data by the specified factor prior to calculating cumulative counts and percentages. By default, when used each subset will print in a separate table. Using the `single = TRUE` option when printing will collapse the subsetted result into a single table.

    example3 <- freqlist(tab.ex, strata = c("arm","sex"))
    summary(example3)

arm | sex | mdquality.s | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
A: IFL | Male | 0 | 29 | 29 | 10.47 | 10.47
|  | 1 | 214 | 243 | 77.26 | 87.73
|  | NA | 34 | 277 | 12.27 | 100.00

arm | sex | mdquality.s | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
A: IFL | Female | 0 | 12 | 12 | 7.95 | 7.95
|  | 1 | 118 | 130 | 78.15 | 86.09
|  | NA | 21 | 151 | 13.91 | 100.00

arm | sex | mdquality.s | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
F: FOLFOX | Male | 0 | 31 | 31 | 7.54 | 7.54
|  | 1 | 285 | 316 | 69.34 | 76.89
|  | NA | 95 | 411 | 23.11 | 100.00

arm | sex | mdquality.s | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
F: FOLFOX | Female | 0 | 21 | 21 | 7.50 | 7.50
|  | 1 | 198 | 219 | 70.71 | 78.21
|  | NA | 61 | 280 | 21.79 | 100.00

arm | sex | mdquality.s | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
G: IROX | Male | 0 | 17 | 17 | 7.46 | 7.46
|  | 1 | 187 | 204 | 82.02 | 89.47
|  | NA | 24 | 228 | 10.53 | 100.00

arm | sex | mdquality.s | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
G: IROX | Female | 0 | 14 | 14 | 9.21 | 9.21
|  | 1 | 121 | 135 | 79.61 | 88.82
|  | NA | 17 | 152 | 11.18 | 100.00

    #using the single = TRUE argument will collapse results into a single table for printing
    summary(example3, single = TRUE)

arm | sex | mdquality.s | Freq | Cumulative Freq | Percent | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
A: IFL | Male | 0 | 29 | 29 | 10.47 | 10.47
|  | 1 | 214 | 243 | 77.26 | 87.73
|  | NA | 34 | 277 | 12.27 | 100.00
| Female | 0 | 12 | 12 | 7.95 | 7.95
|  | 1 | 118 | 130 | 78.15 | 86.09
|  | NA | 21 | 151 | 13.91 | 100.00
F: FOLFOX | Male | 0 | 31 | 31 | 7.54 | 7.54
|  | 1 | 285 | 316 | 69.34 | 76.89
|  | NA | 95 | 411 | 23.11 | 100.00
| Female | 0 | 21 | 21 | 7.50 | 7.50
|  | 1 | 198 | 219 | 70.71 | 78.21
|  | NA | 61 | 280 | 21.79 | 100.00
G: IROX | Male | 0 | 17 | 17 | 7.46 | 7.46
|  | 1 | 187 | 204 | 82.02 | 89.47
|  | NA | 24 | 228 | 10.53 | 100.00
| Female | 0 | 14 | 14 | 9.21 | 9.21
|  | 1 | 121 | 135 | 79.61 | 88.82
|  | NA | 17 | 152 | 11.18 | 100.00

## Show only the “n” most common combinations in each table (`head()` and `sort()`)

You can now sort `freqlist()` objects, and, by taking the `head()` of the summary, output the most common frequencies. This looks the prettiest with `dupLabels=TRUE`.

    head(summary(sort(example1, decreasing = TRUE), dupLabels = TRUE))

    |arm       |sex    |mdquality.s | Freq| Cumulative Freq| Percent| Cumulative Percent|
    |:---------|:------|:-----------|----:|---------------:|-------:|------------------:|
    |F: FOLFOX |Male   |1           |  285|             285|   19.01|              19.01|
    |A: IFL    |Male   |1           |  214|             499|   14.28|              33.29|
    |F: FOLFOX |Female |1           |  198|             697|   13.21|              46.50|
    |G: IROX   |Male   |1           |  187|             884|   12.47|              58.97|
    |G: IROX   |Female |1           |  121|            1005|    8.07|              67.04|
    |A: IFL    |Female |1           |  118|            1123|    7.87|              74.92|

## Change labels on the fly

    labs <- c(arm = "Arm", sex = "Sex", mdquality.s = "QOL", freqPercent = "%")
    labels(example1) <- labs
    summary(example1)

Arm | Sex | QOL | Freq | Cumulative Freq | % | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
A: IFL | Male | 0 | 29 | 29 | 1.93 | 1.93
|  | 1 | 214 | 243 | 14.28 | 16.21
|  | NA | 34 | 277 | 2.27 | 18.48
| Female | 0 | 12 | 289 | 0.80 | 19.28
|  | 1 | 118 | 407 | 7.87 | 27.15
|  | NA | 21 | 428 | 1.40 | 28.55
F: FOLFOX | Male | 0 | 31 | 459 | 2.07 | 30.62
|  | 1 | 285 | 744 | 19.01 | 49.63
|  | NA | 95 | 839 | 6.34 | 55.97
| Female | 0 | 21 | 860 | 1.40 | 57.37
|  | 1 | 198 | 1058 | 13.21 | 70.58
|  | NA | 61 | 1119 | 4.07 | 74.65
G: IROX | Male | 0 | 17 | 1136 | 1.13 | 75.78
|  | 1 | 187 | 1323 | 12.47 | 88.26
|  | NA | 24 | 1347 | 1.60 | 89.86
| Female | 0 | 14 | 1361 | 0.93 | 90.79
|  | 1 | 121 | 1482 | 8.07 | 98.87
|  | NA | 17 | 1499 | 1.13 | 100.00

You can also supply `labelTranslations=` to `summary()`.

    summary(example1, labelTranslations = labs)

Arm | Sex | QOL | Freq | Cumulative Freq | % | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
A: IFL | Male | 0 | 29 | 29 | 1.93 | 1.93
|  | 1 | 214 | 243 | 14.28 | 16.21
|  | NA | 34 | 277 | 2.27 | 18.48
| Female | 0 | 12 | 289 | 0.80 | 19.28
|  | 1 | 118 | 407 | 7.87 | 27.15
|  | NA | 21 | 428 | 1.40 | 28.55
F: FOLFOX | Male | 0 | 31 | 459 | 2.07 | 30.62
|  | 1 | 285 | 744 | 19.01 | 49.63
|  | NA | 95 | 839 | 6.34 | 55.97
| Female | 0 | 21 | 860 | 1.40 | 57.37
|  | 1 | 198 | 1058 | 13.21 | 70.58
|  | NA | 61 | 1119 | 4.07 | 74.65
G: IROX | Male | 0 | 17 | 1136 | 1.13 | 75.78
|  | 1 | 187 | 1323 | 12.47 | 88.26
|  | NA | 24 | 1347 | 1.60 | 89.86
| Female | 0 | 14 | 1361 | 0.93 | 90.79
|  | 1 | 121 | 1482 | 8.07 | 98.87
|  | NA | 17 | 1499 | 1.13 | 100.00

## Using `xtable()` to format and print `freqlist()` results

Fair warning: `xtable()` has kind of a steep learning curve. These examples are given without explanation, for more advanced users.

    require(xtable)

    Loading required package: xtable

    # set up custom function for xtable text
    italic <- function(x) paste0('<i>', x, '</i>')

    xftbl <- xtable(as.data.frame(summary(example1)),
      caption = "xtable formatted output of freqlist data frame", align="|r|r|r|r|c|c|c|r|")

    # change the column names
    names(xftbl)[1:3] <- c("Arm", "Gender", "LASA QOL")

    print(xftbl, sanitize.colnames.function = italic, include.rownames = FALSE, type = "html", comment = FALSE)

xtable formatted output of freqlist data frame
Arm | Gender | LASA QOL | Freq | Cumulative Freq | % | Cumulative Percent
--- | --- | --- | --- | --- | --- | ---
A: IFL | Male | 0 | 29 | 29 | 1.93 | 1.93
|  | 1 | 214 | 243 | 14.28 | 16.21
|  |  | 34 | 277 | 2.27 | 18.48
| Female | 0 | 12 | 289 | 0.80 | 19.28
|  | 1 | 118 | 407 | 7.87 | 27.15
|  |  | 21 | 428 | 1.40 | 28.55
F: FOLFOX | Male | 0 | 31 | 459 | 2.07 | 30.62
|  | 1 | 285 | 744 | 19.01 | 49.63
|  |  | 95 | 839 | 6.34 | 55.97
| Female | 0 | 21 | 860 | 1.40 | 57.37
|  | 1 | 198 | 1058 | 13.21 | 70.58
|  |  | 61 | 1119 | 4.07 | 74.65
G: IROX | Male | 0 | 17 | 1136 | 1.13 | 75.78
|  | 1 | 187 | 1323 | 12.47 | 88.26
|  |  | 24 | 1347 | 1.60 | 89.86
| Female | 0 | 14 | 1361 | 0.93 | 90.79
|  | 1 | 121 | 1482 | 8.07 | 98.87
|  |  | 17 | 1499 | 1.13 | 100.00

## Use `freqlist` in bookdown

Since the backbone of `freqlist()` is `knitr::kable()`, tables still render well in bookdown. However, `print.summary.freqlist()` doesn’t use the `caption=` argument of `kable()`, so some tables may not have a properly numbered caption. To fix this, use the method described on the bookdown site to give the table a tag/ID.

    summary(freqlist(~ sex + age, data = mockstudy), title="(\\#tab:mytableby) Caption here")

# Appendix: Notes regarding table options in R

## NAs

There are several widely used options for basic tables in R. The `table()` function in base R is probably the most common; by default it excludes NA values. You can change NA handling in `base::table()` using the `useNA=` or `exclude=` arguments.

    # base table default removes NAs
    tab.d1 <- base::table(mockstudy[, c("arm", "sex", "mdquality.s")], useNA="ifany")
    tab.d1

    , , mdquality.s = 0

               sex
    arm         Male Female
      A: IFL      29     12
      F: FOLFOX   31     21
      G: IROX     17     14

    , , mdquality.s = 1

               sex
    arm         Male Female
      A: IFL     214    118
      F: FOLFOX  285    198
      G: IROX    187    121

    , , mdquality.s = NA

               sex
    arm         Male Female
      A: IFL      34     21
      F: FOLFOX   95     61
      G: IROX     24     17

`xtabs()` is similar to `table()`, but uses a formula-based syntax. However, NAs must be explicitly added to each factor using the `addNA()` function or using the argument `addNA = TRUE`.

    # without specifying addNA
    tab.d2 <- xtabs(formula = ~ arm + sex + mdquality.s, data = mockstudy)
    tab.d2

    , , mdquality.s = 0

               sex
    arm         Male Female
      A: IFL      29     12
      F: FOLFOX   31     21
      G: IROX     17     14

    , , mdquality.s = 1

               sex
    arm         Male Female
      A: IFL     214    118
      F: FOLFOX  285    198
      G: IROX    187    121

    # now with addNA
    tab.d3 <- xtabs(~ arm + sex + addNA(mdquality.s), data = mockstudy)
    tab.d3

    , , addNA(mdquality.s) = 0

               sex
    arm         Male Female
      A: IFL      29     12
      F: FOLFOX   31     21
      G: IROX     17     14

    , , addNA(mdquality.s) = 1

               sex
    arm         Male Female
      A: IFL     214    118
      F: FOLFOX  285    198
      G: IROX    187    121

    , , addNA(mdquality.s) = NA

               sex
    arm         Male Female
      A: IFL      34     21
      F: FOLFOX   95     61
      G: IROX     24     17

Since the formula method of `freqlist()` uses `xtabs()`, NAs should be treated in the same way. `includeNA()` can also be helpful here for setting explicit NA values.

## Table dimname names (dnn)

Supplying a data.frame to the `table()` function without giving columns individually will create a contingency table using all variables in the data.frame.

However, if the columns of a data.frame or matrix are supplied separately (i.e., as vectors), column names will not be preserved.

    # providing variables separately (as vectors) drops column names
    table(mockstudy$arm, mockstudy$sex, mockstudy$mdquality.s)

    , ,  = 0

                Male Female
      A: IFL      29     12
      F: FOLFOX   31     21
      G: IROX     17     14

    , ,  = 1

                Male Female
      A: IFL     214    118
      F: FOLFOX  285    198
      G: IROX    187    121

If desired, you can use the `dnn=` argument to pass variable names.

    # add the column name labels back using dnn option in base::table
    table(mockstudy$arm, mockstudy$sex, mockstudy$mdquality.s, dnn=c("Arm", "Sex", "QOL"))

    , , QOL = 0

               Sex
    Arm         Male Female
      A: IFL      29     12
      F: FOLFOX   31     21
      G: IROX     17     14

    , , QOL = 1

               Sex
    Arm         Male Female
      A: IFL     214    118
      F: FOLFOX  285    198
      G: IROX    187    121

You can also name the arguments to `table()`:

    table(Arm = mockstudy$arm, Sex = mockstudy$sex, QOL = mockstudy$mdquality.s)

    , , QOL = 0

               Sex
    Arm         Male Female
      A: IFL      29     12
      F: FOLFOX   31     21
      G: IROX     17     14

    , , QOL = 1

               Sex
    Arm         Male Female
      A: IFL     214    118
      F: FOLFOX  285    198
      G: IROX    187    121

If using `freqlist()`, you can provide the labels directly to `freqlist()` or to `summary()` using `labelTranslations=`.