nsample_by_var: nsample_by_var

In OxfordCMS/OCMSutility: Utility functions for OCMS

nsample_by_var

Description

Tallies the number of samples per identifier for metadata variables by counting the number of non-NA values for each metadata variable for a given identifier. This can be helpful in time course data where you want to check the number of samples per individual. This can also be used to check how complete your metadata is.

Usage

nsample_by_var(ddata, id, var)

Arguments

ddata	dataframe. samples in rows. with metadata variables in columns
id	character. sample identifier
var	character vector. metadata variables to be tallied

Value

dataframe. tally of number of id per variable

Examples

set.seed(1)
# time course data: checking number of samples per patient for each metadata
# variable
df <- data.frame(sample_id = paste0("sample", 1:100),
                 patient_id = rep(LETTERS[1:25], 4),
                 var1 = sample(c(rnorm(30, 10, 0.5), rnorm(40, 25, 2),
                                 rep(NA, 30)), 100),
                 var2 = sample(c(rnorm(65, 0.5, 0.01),
                                 rep(0, 20),
rep(NA, 15)), 100),
                 var3 = sample(c(letters[1:5], NA), 100, replace=TRUE))

nsample_by_var(df, 'patient_id', c('var1','var2','var3'))

OxfordCMS/OCMSutility documentation built on Feb. 27, 2025, 8:19 p.m.