As can probably(hopefully) be guessed from the name, this provides a convenient way to get variable correlations. It enables one to get correlation between one variable and all other variables in the data set.

Previously, one would set get_all to TRUE if they wanted to get correlations between all variables. This argument has been dropped in favor of simply supplying an optional other_vars vector if one does not want to get all correlations.

library(manymodelr)
#> Loading required package: caret
#> Loading required package: ggplot2
#> Loading required package: lattice
#> Loading required package: Metrics
#> 
#> Attaching package: 'Metrics'
#> The following objects are masked from 'package:caret':
#> 
#>     precision, recall
#> Loading required package: e1071
#> Welcome to manymodelr. This is manymodelr version 0.3.9.
#>  Please file issues and feedback at https://www.github.com/Nelson-Gon/manymodelr/issues
#> Turn this message off using 'suppressPackageStartupMessages(library(manymodelr))'
#>  Happy Modelling! :)
# getall correlations

# default pearson

head( corrs <- get_var_corr(mtcars,comparison_var="mpg") )
#>   comparison_var other_var      p.value correlation    lower_ci   upper_ci
#> 1            mpg       cyl 6.112687e-10  -0.8521620 -0.92576936 -0.7163171
#> 2            mpg      disp 9.380327e-10  -0.8475514 -0.92335937 -0.7081376
#> 3            mpg        hp 1.787835e-07  -0.7761684 -0.88526861 -0.5860994
#> 4            mpg      drat 1.776240e-05   0.6811719  0.43604838  0.8322010
#> 5            mpg        wt 1.293959e-10  -0.8676594 -0.93382641 -0.7440872
#> 6            mpg      qsec 1.708199e-02   0.4186840  0.08195487  0.6696186

Previously, one would also set drop_columns to TRUE if they wanted to drop factor columns. Now, a user simply provides a character vector specifying which column types(classes) should be dropped. It defaults to c("character","factor").

data("yields", package="manymodelr")
# purely demonstrative
get_var_corr(yields,"height",other_vars="weight",
             drop_columns=c("factor","character"),method="spearman",
             exact=FALSE)
#> Warning in get_var_corr.data.frame(yields, "height", other_vars = "weight", :
#> Columns with classes in drop_columns have been discarded. You can disable this
#> yourself by setting drop_columns to NULL.
#>   comparison_var other_var      p.value correlation
#> 1         height    weight 4.204642e-07  -0.1591719

Similarly, get_var_corr_ (note the underscore at the end) provides a convenient way to get combination-wise correlations.


head(get_var_corr_(yields),6)
#> Warning in get_var_corr_.data.frame(yields): Columns with classes in
#> drop_columns were dropped.
#>   comparison_var other_var      p.value correlation    lower_ci    upper_ci
#> 1         height    weight 1.470866e-08 -0.17793196 -0.23730741 -0.11723201
#> 2         height     yield 4.473683e-01  0.02405390 -0.03799584  0.08591886
#> 3         weight     yield 2.986171e-01  0.03290108 -0.02915146  0.09470100

To use only a subset of the data, we can use provide a list of columns to subset_cols. By default, the first value(vector) in the list is mapped to comparison_var and the other to other_Var. The list is therefore of length 2.


head(get_var_corr_(mtcars,subset_cols=list(c("mpg","vs"),c("disp","wt")),
                   method="spearman",exact=FALSE))
#>   comparison_var other_var      p.value correlation
#> 2            mpg      disp 6.370336e-13  -0.9088824
#> 5            mpg        wt 1.487595e-11  -0.8864220

Obtaining correlations would mostly likely benefit from some form of visualization. plot_corr aims to achieve just that. There are currently two plot styles, squares and circles. circles has a shape argument that can allow for more flexibility. It should be noted that the correlation matrix supplied to this function is an object produced by get_var_corr_.

To modify the plot a bit, we can choose to switch the x and y values as shown below.



plot_corr(mtcars,show_which = "corr",
          round_which = "correlation",decimals = 2,x="other_var",  y="comparison_var",plot_style = "squares"
          ,width = 1.1,custom_cols = c("green","blue","red"),colour_by = "correlation")
#> Warning in plot_corr(mtcars, show_which = "corr", round_which = "correlation",
#> : Using colour_by for the legend title.

To show significance of the results instead of the correlations themselves, we can set show_which to “signif” as shown below. By default, significance is set to 0.05. You can override this by supplying a different signif_cutoff.

# color by p value
# change custom colors by supplying custom_cols
# significance is default 
set.seed(233)
plot_corr(mtcars, x="other_var", y="comparison_var",plot_style = "circles",show_which = "signif", colour_by = "p.value", sample(colours(),3))
#> Warning in plot_corr(mtcars, x = "other_var", y = "comparison_var", plot_style
#> = "circles", : Using colour_by for the legend title.

To explore more options, please take a look at the documentation.