Tag: Excel

Create a publication-ready correlation matrix, with significance levels, in R

Create a publication-ready correlation matrix, with significance levels, in R

In most (observational) research papers you read, you will probably run into a correlation matrix. Often it looks something like this:

FACTOR ANALYSIS

In Social Sciences, like Psychology, researchers like to denote the statistical significance levels of the correlation coefficients, often using asterisks (i.e., *). Then the table will look more like this:

Table 4 from Family moderators of relation between community ...

Regardless of my personal preferences and opinions, I had to make many of these tables for the scientific (non-)publications of my Ph.D..

I remember that, when I first started using R, I found it quite difficult to generate these correlation matrices automatically.

Yes, there is the cor function, but it does not include significance levels.

Then there the (in)famous Hmisc package, with its rcorr function. But this tool provides a whole new range of issues.

What’s this storage.mode, and what are we trying to coerce again?

Soon you figure out that Hmisc::rcorr only takes in matrices (thus with only numeric values). Hurray, now you can run a correlation analysis on your dataframe, you think…

Yet, the output is all but publication-ready!

You wanted one correlation matrix, but now you have two… Double the trouble?

To spare future scholars the struggle of the early day R programming, I would like to share my custom function correlation_matrix.

My correlation_matrix takes in a dataframe, selects only the numeric (and boolean/logical) columns, calculates the correlation coefficients and p-values, and outputs a fully formatted publication-ready correlation matrix!

You can specify many formatting options in correlation_matrix.

For instance, you can use only 2 decimals. You can focus on the lower triangle (as the lower and upper triangle values are identical). And you can drop the diagonal values:

Or maybe you are interested in a different type of correlation coefficients, and not so much in significance levels:

For other formatting options, do have a look at the source code below.

Now, to make matters even more easy, I wrote a second function (save_correlation_matrix) to directly save any created correlation matrices:

Once you open your new correlation matrix file in Excel, it is immediately ready to be copy-pasted into Word!

If you are looking for ways to visualize your correlations do have a look at the packages corrr and corrplot.

I hope my functions are of help to you!

Do reach out if you get to use them in any of your research papers!

I would be super interested and feel honored.

correlation_matrix

#' correlation_matrix
#' Creates a publication-ready / formatted correlation matrix, using `Hmisc::rcorr` in the backend.
#'
#' @param df dataframe; containing numeric and/or logical columns to calculate correlations for
#' @param type character; specifies the type of correlations to compute; gets passed to `Hmisc::rcorr`; options are `"pearson"` or `"spearman"`; defaults to `"pearson"`
#' @param digits integer/double; number of decimals to show in the correlation matrix; gets passed to `formatC`; defaults to `3`
#' @param decimal.mark character; which decimal.mark to use; gets passed to `formatC`; defaults to `.`
#' @param use character; which part of the correlation matrix to display; options are `"all"`, `"upper"`, `"lower"`; defaults to `"all"`
#' @param show_significance boolean; whether to add `*` to represent the significance levels for the correlations; defaults to `TRUE`
#' @param replace_diagonal boolean; whether to replace the correlations on the diagonal; defaults to `FALSE`
#' @param replacement character; what to replace the diagonal and/or upper/lower triangles with; defaults to `""` (empty string)
#'
#' @return a correlation matrix
#' @export
#'
#' @examples
#' `correlation_matrix(iris)`
#' `correlation_matrix(mtcars)`
correlation_matrix <- function(df, 
                               type = "pearson",
                               digits = 3, 
                               decimal.mark = ".",
                               use = "all", 
                               show_significance = TRUE, 
                               replace_diagonal = FALSE, 
                               replacement = ""){
  
  # check arguments
  stopifnot({
    is.numeric(digits)
    digits >= 0
    use %in% c("all", "upper", "lower")
    is.logical(replace_diagonal)
    is.logical(show_significance)
    is.character(replacement)
  })
  # we need the Hmisc package for this
  require(Hmisc)
  
  # retain only numeric and boolean columns
  isNumericOrBoolean = vapply(df, function(x) is.numeric(x) | is.logical(x), logical(1))
  if (sum(!isNumericOrBoolean) > 0) {
    cat('Dropping non-numeric/-boolean column(s):', paste(names(isNumericOrBoolean)[!isNumericOrBoolean], collapse = ', '), '\n\n')
  }
  df = df[isNumericOrBoolean]
  
  # transform input data frame to matrix
  x <- as.matrix(df)
  
  # run correlation analysis using Hmisc package
  correlation_matrix <- Hmisc::rcorr(x, type = type)
  R <- correlation_matrix$r # Matrix of correlation coeficients
  p <- correlation_matrix$P # Matrix of p-value 
  
  # transform correlations to specific character format
  Rformatted = formatC(R, format = 'f', digits = digits, decimal.mark = decimal.mark)
  
  # if there are any negative numbers, we want to put a space before the positives to align all
  if (sum(!is.na(R) & R < 0) > 0) {
    Rformatted = ifelse(!is.na(R) & R > 0, paste0(" ", Rformatted), Rformatted)
  }

  # add significance levels if desired
  if (show_significance) {
    # define notions for significance levels; spacing is important.
    stars <- ifelse(is.na(p), "", ifelse(p < .001, "***", ifelse(p < .01, "**", ifelse(p < .05, "*", ""))))
    Rformatted = paste0(Rformatted, stars)
  }
  
  # make all character strings equally long
  max_length = max(nchar(Rformatted))
  Rformatted = vapply(Rformatted, function(x) {
    current_length = nchar(x)
    difference = max_length - current_length
    return(paste0(x, paste(rep(" ", difference), collapse = ''), sep = ''))
  }, FUN.VALUE = character(1))
  
  # build a new matrix that includes the formatted correlations and their significance stars
  Rnew <- matrix(Rformatted, ncol = ncol(x))
  rownames(Rnew) <- colnames(Rnew) <- colnames(x)
  
  # replace undesired values
  if (use == 'upper') {
    Rnew[lower.tri(Rnew, diag = replace_diagonal)] <- replacement
  } else if (use == 'lower') {
    Rnew[upper.tri(Rnew, diag = replace_diagonal)] <- replacement
  } else if (replace_diagonal) {
    diag(Rnew) <- replacement
  }
  
  return(Rnew)
}

save_correlation_matrix

#' save_correlation_matrix
#' Creates and save to file a fully formatted correlation matrix, using `correlation_matrix` and `Hmisc::rcorr` in the backend
#' @param df dataframe; passed to `correlation_matrix`
#' @param filename either a character string naming a file or a connection open for writing. "" indicates output to the console; passed to `write.csv`
#' @param ... any other arguments passed to `correlation_matrix`
#'
#' @return NULL
#'
#' @examples
#' `save_correlation_matrix(df = iris, filename = 'iris-correlation-matrix.csv')`
#' `save_correlation_matrix(df = mtcars, filename = 'mtcars-correlation-matrix.csv', digits = 3, use = 'lower')`
save_correlation_matrix = function(df, filename, ...) {
  return(write.csv2(correlation_matrix(df, ...), file = filename))
}

Sign up to keep up to date on the latest R, Data Science & Tech content:

Data Visualization Tools & Resources

There’s this amazing overview of helpful dataviz resources atwww.visualisingdata.com/resources!

Browse through hundreds of helpful data visualization tools, programs, and services. All neatly organized by Andy Kirk in categories: data handling, applications, programming, web-based, qualitative, mapping, specialist, and colour. What a great repository!

A snapshot of www.visualisingdata.com/resource

Looking for expert books on data visualization?
Have a look at these recommendations!

Transitioning from Excel to R: Dictionary of common functions

Transitioning from Excel to R: Dictionary of common functions

Alyssa Columbus published maintains this GitHub repository with a great tutorial on how to move from Excel to R. Very useful for beginning useRs, the repository’s tutorial includes a translation table between Excel and R functions:

Excel Formula R Function Type
ABS abs Arithmetic
ADDRESS assign Essentials
AND &,&&,all Boolean
AVERAGE, AVG, AVERAGEIF mean Arithmetic
BETADIST pbeta Statistics
BETAINV qbeta Statistics
BINOMDIST pbinom when cumulative,dbinom when not Statistics
CEILING ceiling Arithmetic
CELL str has the same idea Essentials
CHIDIST, CHISQDIST pchisq Statistics
CHIINV, CHISQINV qchisq Statistics
CHITEST chisq.test Statistics
CHOOSE switch Essentials
CLEAN gsub Text
COLS, COLUMNS ncol Essentials
COLUMN col,:,seq Essentials
COMBIN choose Essentals
CONCATENATE paste Text
CONFIDENCE -qnorm(alpha/2)*std/sqrt(n) Statistics
CORREL cor Statistics
COUNT, COUNTIF length Arithmetic
COVAR cov Statistics
CRITBINOM qbinom Statistics
DELTA identical Boolean
EXACT == Boolean
EXP exp Arithmetic
EXPONDIST pexp when cumulative,dexp when not Statistics
FACT factorial Arithmetic
FACTDOUBLE dfactorial in the phangorn package Arithmetic
FDIST pf Statistics
FIND regexpr,grepl,grep Text
FINV qf Statistics
FISHER atanh Arithmetic
FISHERINV tanh Arithmetic
FIXED format,sprintf,formatC Essentials
FLOOR floor Arithmetic
FORECAST predict on an lm object Statistics
FREQUENCY cut,table Arithmetic
FTEST var.test Statistics
GAMMADIST pgamma if last argument T,dgamma if last arg. F Statistics
GAMMAINV qgamma Statistics
GAMMALN lgamma Statistics
GAUSS pnorm(x) - 0.5 Statistics
GCD gcd Arithmetic
GEOMEAN exp(mean(log(x))) Arithmetic
GESTEP >= Boolean
HARMEAN harmonic.mean in the psych package Arithmetic
HLOOKUP match,merge Essentials
HYPGEOMDIST dhyper Statistics
IF if,ifelse Essentials
IFERROR try,tryCatch Essentials
INDEX x[y,z] Essentials
INDIRECT get Essentials
INT as.integer(not for negative numbers),floor Arithmetic
INTERCEPT first element of coef of an lm object Statistics
ISLOGICAL is.logical Boolean
ISNA is.na Boolean
ISNUMBER is.numeric Boolean
ISTEXT is.character Boolean
KURT kurtosis in the moments package Statistics
LARGE sort Statistics
LCM scm in the schoolmath package Arithmetic
LEFT substr Text
LEN, LENGTH nchar Text
LINEST lm Statistics
LN, LOG log Arithmetic
LOG10 log10 Arithmetic
LOGINV qlnorm Statistics
LOGNORMDIST plnorm Statistics
LOWER tolower Text
MATCH match,which Essentials
MAX max (sometimes pmax) Arithmetic
MDETERM det Arithmetic
MEDIAN median Arithmetic
MID substr Text
MIN min (sometimes pmin) Arithmetic
MINVERSE solve Arithmetic
MMULT %*% Arithmetic
MOD %% Arithmetic
MODE as.numeric(names(which.max(table(x)))) Arithmetic
MUNIT diag Arithmetic
N as.numeric Arithmetic
NEGBINOMDIST dnbinom Statistics
NORMDIST, NORMSDIST pnorm when cumulative,dnorm when not Statistics
NORMINV, NORMSINV qnorm Statistics
NOT ! Boolean
NOW date,Sys.time Essentials
OR ` ,
PEARSON cor Statistics
PERCENTILE quantile Statistics
PERCENTRANK ecdf Statistics
PERMUT function(n,k) {choose(n,k)*factorial(k)} Arithmetic
PERMUTATIONA n^k Arithmetic
PHI dnorm Statistics
POISSON ppois when cumulatic,dpois when not Statistics
POWER ^ Arithmetic
PROB ecdf Statistics
PRODUCT prod Arithmetic
PROPER toupper Text
QUARTILE quantile Arithmetic
QUOTIENT %/% Arithmetic
RAND runif Arithmetic
RANDBETWEEN sample Arithmetic
RANK rank Essentials
REPLACE sub,gsub Text
REPT rep and paste or paste0 Text
RIGHT substring Text
ROUND round Arithmetic
ROUNDDOWN floor Arithmetic
ROUNDUP ceiling Arithmetic
ROW row,:,seq Essentials
ROWS nrow Essentials
RSQ summary of lm object Statistics
SEARCH regexpr,grep Text
SIGN sign Arithmetic
SKEW skewness in the moments package Statistics
SLOPE in coef of lm object Statistics
SMALL sort Arithmetic
SQRT sqrt Arithmetic
STANDARDIZE scale Statitics
STD, STDEV sd Arithmetic
STEYX predict on an lm object Statistics
STRING format,sprintf,formatC Text
SUBSTITUTE sub,gsub,paste Essentials
SUM, SUMIF sum Arithmetic
SUMPRODUCT crossprod Arithmetic
TDIST pt Statistics
TEXT format,sprintf,formatC Text
TINV abs(qt(x/2,data)) Statistics
TODAY Sys.Date Essentials
TRANSPOSE t Arithmetic
TREND fitted of an lm object Statistics
TRIM sub Essentials
TRIMMEAN mean(x,trim=tr/2) Arithmetic
TRUNC trunc Essentials
TTEST t.test Statistics
TYPE typeof,mode,class Essentials
UPPER toupper Text
VALUE as.numeric Arithmetic
VAR var Essentials
VLOOKUP match,merge Essentials
WEEKDAY weekdays Essentials
WEIBULL pweibull when cumulative,dweibull when not Statistics
ZTEST pnorm Statistics