describe.data.frame: Compute descriptive statistic

In dlookr: Tools for Data Diagnosis, Exploration, Transformation

Compute descriptive statistic

Description

The describe() compute descriptive statistic of numeric variable for exploratory data analysis.

Usage

describe(.data, ...)

## S3 method for class 'data.frame'
describe(.data, ..., statistics = NULL, quantiles = NULL)

## S3 method for class 'grouped_df'
describe(
  .data,
  ...,
  statistics = NULL,
  quantiles = NULL,
  all.combinations = FALSE
)

Arguments

.data	a data.frame or a tbl_df or a grouped_df.
...	one or more unquoted expressions separated by commas. You can treat variable names like they are positions. Positive values select variables; negative values to drop variables. If the first expression is negative, describe() will automatically start with all variables. These arguments are automatically quoted and evaluated in a context where column names represent column positions. They support unquoting and splicing. See vignette("EDA") for an introduction to these concepts.
statistics	character. the name of the descriptive statistic to calculate. The defaults is c("mean", "sd", "se_mean", "IQR", "skewness", "kurtosis", "quantiles")
quantiles	numeric. list of quantiles to calculate. The values of elements must be between 0 and 1. and to calculate quantiles, you must include "quantiles" in the statistics argument value. The default is c(0, .01, .05, 0.1, 0.2, 0.25, 0.3, 0.4, 0.5, 0.6, 0.7, 0.75, 0.8, 0.9, 0.95, 0.99, 1).
all.combinations	logical. When used with group_by(), this argument expresses all combinations of group combinations. If the argument value is TRUE, cases that do not exist as actual data are also included in the output.

Details

This function is useful when used with the group_by function of the dplyr package. If you want to calculate the statistic by level of the categorical data you are interested in, rather than the whole statistic, you can use grouped_df as the group_by() function.

From version 0.5.5, the 'variable' column in the "descriptive statistic information" tibble object has been changed to 'described_variables'. This is because there are cases where 'variable' is included in the variable name of the data. There is probably no case where 'described_variables' is included in the variable name of the data.

Value

An object of the same class as .data.

Descriptive statistic information

The information derived from the numerical data describe is as follows.

• n : number of observations excluding missing values

• na : number of missing values

• mean : arithmetic average

• sd : standard deviation

• se_mean : standard error mean. sd/sqrt(n)

• IQR : interquartile range (Q3-Q1)

• skewness : skewness

• kurtosis : kurtosis

• p25 : Q1. 25% percentile

• p50 : median. 50% percentile

• p75 : Q3. 75% percentile

• p01, p05, p10, p20, p30 : 1%, 5%, 20%, 30% percentiles

• p40, p60, p70, p80 : 40%, 60%, 70%, 80% percentiles

• p90, p95, p99, p100 : 90%, 95%, 99%, 100% percentiles

See Also

describe.tbl_dbi, diagnose_numeric.data.frame.

Examples

# Generate data for the example
heartfailure2 <- heartfailure
heartfailure2[sample(seq(NROW(heartfailure2)), 20), "sodium"] <- NA
heartfailure2[sample(seq(NROW(heartfailure2)), 5), "smoking"] <- NA

# Describe descriptive statistics of numerical variables
describe(heartfailure2)

# Select the variable to describe
describe(heartfailure2, sodium, platelets, statistics = c("mean", "sd", "quantiles"))
describe(heartfailure2, -sodium, -platelets)
describe(heartfailure2, 5, statistics = c("mean", "sd", "quantiles"), quantiles = c(0.01, 0.1))

# Using dplyr::grouped_dt
library(dplyr)

gdata <- group_by(heartfailure2, hblood_pressure, death_event)
describe(gdata, "creatinine")

# Using pipes ---------------------------------
# Positive values select variables
heartfailure2 %>%
  describe(platelets, sodium, creatinine)

# Negative values to drop variables
heartfailure2 %>%
  describe(-platelets, -sodium, -creatinine)

# Using pipes & dplyr -------------------------
# Find the statistic of all numerical variables by 'hblood_pressure' and 'death_event',
# and extract only those with 'hblood_pressure' variable level is "Yes".
heartfailure2 %>%
  group_by(hblood_pressure, death_event) %>%
  describe() %>%
  filter(hblood_pressure == "Yes")
  
# Using all.combinations = TRUE
heartfailure2 %>%
  filter(!hblood_pressure %in% "Yes" | !death_event %in% "Yes") %>% 
  group_by(hblood_pressure, death_event) %>%
  describe(all.combinations = TRUE) 
  
# extract only those with 'smoking' variable level is "Yes",
# and find 'creatinine' statistics by 'hblood_pressure' and 'death_event'
heartfailure2 %>%
  filter(smoking == "Yes") %>%
  group_by(hblood_pressure, death_event) %>%
  describe(creatinine)

dlookr documentation built on July 9, 2023, 6:31 p.m.