pingouin.partial_corr

pingouin.
partial_corr
(data=None, x=None, y=None, covar=None, x_covar=None, y_covar=None, tail='twosided', method='pearson')[source] Partial and semipartial correlation.
 Parameters
 datapd.DataFrame
Dataframe. Note that this function can also directly be used as a
pandas.DataFrame
method, in which case this argument is no longer needed. x, ystring
x and y. Must be names of columns in
data
. covarstring or list
Covariate(s). Must be a names of columns in
data
. Use a list if there are two or more covariates. x_covarstring or list
Covariate(s) for the
x
variable. This is used to compute semipartial correlation (i.e. the effect ofx_covar
is removed fromx
but not fromy
). Note that you cannot specify bothcovar
andx_covar
. y_covarstring or list
Covariate(s) for the
y
variable. This is used to compute semipartial correlation (i.e. the effect ofy_covar
is removed fromy
but not fromx
). Note that you cannot specify bothcovar
andy_covar
. tailstring
Specify whether to return the ‘onesided’ or ‘twosided’ pvalue.
 methodstring
Specify which method to use for the computation of the correlation coefficient. Available methods are
'pearson' : Pearson productmoment correlation 'spearman' : Spearman rankorder correlation 'kendall' : Kendall’s tau (ordinal data) 'percbend' : percentage bend correlation (robust) 'shepherd' : Shepherd's pi correlation (robust Spearman) 'skipped' : skipped correlation (robust Spearman, requires sklearn)
 Returns
 statspandas DataFrame
Test summary
'n' : Sample size (after NaN removal) 'outliers' : number of outliers (only for 'shepherd' or 'skipped') 'r' : Correlation coefficient 'CI95' : 95% parametric confidence intervals 'r2' : Rsquared 'adj_r2' : Adjusted Rsquared 'pval' : one or two tailed pvalue 'BF10' : Bayes Factor of the alternative hypothesis (Pearson only) 'power' : achieved power of the test (= 1  type II error).
Notes
From [4]:
“With partial correlation, we find the correlation between \(x\) and \(y\) holding \(C\) constant for both \(x\) and \(y\). Sometimes, however, we want to hold \(C\) constant for just \(x\) or just \(y\). In that case, we compute a semipartial correlation. A partial correlation is computed between two residuals. A semipartial correlation is computed between one residual and another raw (or unresidualized) variable.”
Note that if you are not interested in calculating the statistics and pvalues but only the partial correlation matrix, a (faster) alternative is to use the
pingouin.pcorr()
method (see example 4).Rows with missing values are automatically removed from data. Results have been tested against the ppcor R package.
References
Examples
Partial correlation with one covariate
>>> import pingouin as pg >>> df = pg.read_dataset('partial_corr') >>> pg.partial_corr(data=df, x='x', y='y', covar='cv1') n r CI95% r2 adj_r2 pval BF10 power pearson 30 0.568 [0.26, 0.77] 0.323 0.273 0.001055 37.773 0.925
Spearman partial correlation with several covariates
>>> # Partial correlation of x and y controlling for cv1, cv2 and cv3 >>> pg.partial_corr(data=df, x='x', y='y', covar=['cv1', 'cv2', 'cv3'], ... method='spearman') n r CI95% r2 adj_r2 pval power spearman 30 0.491 [0.16, 0.72] 0.242 0.185 0.005817 0.809
As a pandas method
>>> df.partial_corr(x='x', y='y', covar=['cv1'], method='spearman') n r CI95% r2 adj_r2 pval power spearman 30 0.568 [0.26, 0.77] 0.323 0.273 0.001049 0.925
Partial correlation matrix (returns only the correlation coefficients)
>>> df.pcorr().round(3) x y cv1 cv2 cv3 x 1.000 0.493 0.095 0.130 0.385 y 0.493 1.000 0.007 0.104 0.002 cv1 0.095 0.007 1.000 0.241 0.470 cv2 0.130 0.104 0.241 1.000 0.118 cv3 0.385 0.002 0.470 0.118 1.000
Semipartial correlation on
x
>>> pg.partial_corr(data=df, x='x', y='y', x_covar=['cv1', 'cv2', 'cv3']) n r CI95% r2 adj_r2 pval BF10 power pearson 30 0.463 [0.12, 0.71] 0.215 0.156 0.009946 5.404 0.752
Semipartial on both``x`` and
y
controlling for different variables
>>> pg.partial_corr(data=df, x='x', y='y', x_covar='cv1', ... y_covar=['cv2', 'cv3'], method='spearman') n r CI95% r2 adj_r2 pval power spearman 30 0.429 [0.08, 0.68] 0.184 0.123 0.018092 0.676