freq {tidytlg}

Frequency counts and percentages

Description

Frequency counts and percentages for a variable by treatment and/or group.

Usage

freq(
  df,
  denom_df = df,
  colvar = NULL,
  tablebyvar = NULL,
  rowvar = NULL,
  rowbyvar = NULL,
  statlist = getOption("tidytlg.freq.statlist.default"),
  decimal = 1,
  nested = FALSE,
  cutoff = NULL,
  cutoff_stat = "pct",
  subset = TRUE,
  descending_by = NULL,
  display_missing = FALSE,
  rowtext = NULL,
  row_header = NULL,
  .keep = TRUE,
  .ord = FALSE,
  pad = TRUE,
  ...
)

Arguments

df

(required) dataframe containing records to summarize by treatment

denom_df

(optional) dataframe used for population based denominators (default = df)

colvar

(required) treatment variable within df to use to summarize

tablebyvar

(optional) repeat entire table by variable within df

rowvar

(required) character vector of variables to summarize within the dataframe

rowbyvar

(optional) repeat rowvar by variable within df

statlist

(optional) statlist object of stats to keep of length 1 or 2 specifying list of statistics and format desired (e.g statlist(c("N", "n (x.x\ (x.x)")))

decimal

(optional) decimal precision root level default (default = 1)

nested

(optional) INTERNAL USE ONLY. The default should not be changed. Switch on when this function is called by nested_freq() so we will not include the by variables as part of the group denominators (default = FALSE)

cutoff

(optional) percentage cutoff threshold. This can be passed as a numeric cutoff, in that case any rows with greater than or equal to that cutoff will be preserved, others will be dropped. To specify a single column to define the cutoff logic, pass a character value of the form "colName >= value" and only that column will be used.

cutoff_stat

(optional) The value to cutoff by, n or pct. (default = 'pct'). Can be done with multiple columns by adding & or | ex. col1 >= val1 & col2 >= val2

subset

(optional) An R expression that will be passed to a dplyr::filter() function to subset the data.frame. This is performed on the numerator before any other derivations. Denominators must be preprocessed and passed through using denom_df.

descending_by

(optional) The column or columns to sort descending counts. Can also provide a named list to do ascending order ex. c("VarName1" = "asc", "VarName2" = "desc") would sort by VarName1 in ascending order and VarName2 in descending order. In case of a tie in count or descending_by not provided, the columns will be sorted alphabetically.

display_missing

(optional) Should the "missing" values be displayed? If missing values are displayed, denominators will include missing values. (default = FALSE)

rowtext

(optional) A character vector used to rename the label column. If named, names will give the new level and values will be the replaced value. If unnamed, and the table has only one row, the rowtext will rename the label of the row. If the rowtext is unnamed, the table has no rows, and there is a subset, the table will be populated with zeros and the label will be the only row.

row_header

(optional) A character vector to be added to the table.

.keep

(optional) Should the rowbyvar and tablebyvar be output in the table. If FALSE, rowbyvar will still be output in the label column. (default = TRUE)

.ord

Should the ordering columns be output with the table? This is useful if a table needs to be merged or reordered in any way after build.

pad

(optional) A boolean that controls if levels with zero records should be included in the final table. (default = TRUE)

...

(optional) Named arguments to be included as columns on the table.

Value

A dataframe of results

Sorting a 'freq' table

By default, a frequency table is sorted based on the factor level of the rowvar variable. If the rowvar variable isn't a factor, it will be sorted alphabetically. This behavior can be modified in two ways, the first is the char2factor() function that offers a interface for releveling a variable based on a numeric variable, like VISITN. The second is based on the descending_by argument which will sort based on counts on a variable.

Examples

adsl <- data.frame(
      USUBJID = c("DEMO-101", "DEMO-102", "DEMO-103"),
      RACE = c("WHITE", "BLACK", "ASIAN"),
      SEX = c("F", "M", "F"),
      colnbr = factor(c("Placebo", "Low", "High"))
  )

# Unique subject count of a single variable
freq(adsl
     ,colvar = "colnbr"
     ,rowvar = "RACE"
     ,statlist = statlist("n"))

# Unique subject count and percent of a single variable
freq(adsl
     ,colvar = "colnbr"
     ,rowvar = "RACE"
     ,statlist = statlist(c("N", "n (x.x%)")))

# Unique subject count of a variable by another variable
freq(adsl
     ,colvar = "colnbr"
     ,rowvar = "RACE"
     ,rowbyvar = "SEX"
     ,statlist = statlist("n"))

# Unique subject count of a variable by another variable using colvar and
# group to define the denominator
freq(adsl
     ,colvar = "colnbr"
     ,rowvar = "RACE"
     ,rowbyvar = "SEX"
     ,statlist = statlist("n (x.x%)", denoms_by = c("colnbr", "SEX")))

# Cut records where count meets threshold for any column
freq(cdisc_adsl
     ,rowvar = "ETHNIC"
     ,colvar = "TRT01P"
     ,statlist = statlist("n (x.x%)")
     ,cutoff = "5"
     ,cutoff_stat = "n")

# Cut records where count meets threshold for a specific column
freq(cdisc_adsl
     ,rowvar = "ETHNIC"
     ,colvar = "TRT01P"
     ,statlist = statlist("n (x.x%)")
     ,cutoff = "Placebo >= 3"
     ,cutoff_stat = "n")

# Below illustrates how to make the same calls to freq() as above, using
# table and column metadata.

# Unique subject count of a single variable
table_metadata <- tibble::tribble(
  ~anbr,  ~func,          ~df,   ~rowvar,      ~statlist,  ~colvar,
  1,     "freq", "cdisc_adsl",  "ETHNIC",  statlist("n"), "TRT01PN"
)

generate_results(table_metadata,
                 column_metadata = column_metadata,
                 tbltype = "type1")

# Unique subject count and percent of a single variable
table_metadata <- tibble::tribble(
  ~anbr,  ~func,    ~df,     ~rowvar,     ~statlist,            ~colvar,
  "1", "freq", "cdisc_adsl", "ETHNIC", statlist(c("N", "n (x.x%)")),"TRT01PN"
)

generate_results(table_metadata,
                 column_metadata = column_metadata,
                 tbltype = "type1")

# Cut records where count meets threshold for any column
table_metadata <- tibble::tibble(
  anbr= "1", func = "freq", df = "cdisc_adsl", rowvar = "ETHNIC",
  statlist = statlist("n (x.x%)"), colvar = "TRT01PN", cutoff = 5,
  cutoff_stat = "n")

generate_results(table_metadata,
                 column_metadata = column_metadata,
                 tbltype = "type1")

# Cut records where count meets threshold for a specific column
table_metadata <- tibble::tibble(
  anbr= 1, func = "freq", df = "cdisc_adsl", rowvar = "ETHNIC",
  statlist = statlist("n (x.x%)"), colvar = "TRT01PN",
  cutoff = 'col1 >= 3', cutoff_stat = "n")

generate_results(table_metadata,
                 column_metadata = column_metadata,
                 tbltype = "type1")