Exploring correlations in R with corrr  

@drsimonj here to share a (sort of) readable version of my presentation at the amst-R-dam meetup on 14 August, 2018: “Exploring correlations in R with corrr”.

Those who attended will know that I changed the topic of the talk, originally advertised as “R from academia to commerical business”. For anyone who’s interested, I gave that talk at useR! 2018 and, thanks to the R consortium, you can watch it here. I also gave a “Wrangling data in the Tidyverse” tutorial that you can follow at Part 1 and Part 2.

 The story of corrr

Moving to corrr — the first package I ever created. It started when I was a postgrad student studying individual differences in decision making. My research data was responses to test batteries. My statistical bread and butter was regression-based techniques like multiple regression, path analysis, factor analysis (EFA and CFA), and structural equation modelling.

I spent a lot of time exploring correlation matrices to make model decisions, and diagnose poor fits or unexpected results! If you need proof, check out some of the correlations tables published in my academic papers like “Individual Differences in Decision Making Depend on Cognitive Abilities, Monitoring and Control”

 How to explore correlations?

To illustrate some of the challenges I was facing, let’s try explore some correlations with some very fancy data:

d <- mtcars
d$hp[3] <- NA
head(d)
#>                    mpg cyl disp  hp drat    wt  qsec vs am gear carb
#> Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
#> Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
#> Datsun 710        22.8   4  108  NA 3.85 2.320 18.61  1  1    4    1
#> Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
#> Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2
#> Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1

We could be motivated by multicollinearity:

fit_1 <- lm(mpg ~ hp,        data = d)
fit_2 <- lm(mpg ~ hp + disp, data = d)
summary(fit_1)
#> 
#> Call:
#> lm(formula = mpg ~ hp, data = d)
#> 
#> Residuals:
#>     Min      1Q  Median      3Q     Max 
#> -5.7219 -2.2887 -0.8677  1.5815  8.1743 
#> 
#> Coefficients:
#>             Estimate Std. Error t value Pr(>|t|)    
#> (Intercept) 30.18457    1.69527  17.805  < 2e-16 ***
#> hp          -0.06860    0.01039  -6.604 3.08e-07 ***
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#> 
#> Residual standard error: 3.925 on 29 degrees of freedom
#>   (1 observation deleted due to missingness)
#> Multiple R-squared:  0.6006, Adjusted R-squared:  0.5868 
#> F-statistic: 43.61 on 1 and 29 DF,  p-value: 3.085e-07
summary(fit_2)
#> 
#> Call:
#> lm(formula = mpg ~ hp + disp, data = d)
#> 
#> Residuals:
#>     Min      1Q  Median      3Q     Max 
#> -4.9136 -2.3472 -0.7302  1.9798  6.7549 
#> 
#> Coefficients:
#>              Estimate Std. Error t value Pr(>|t|)    
#> (Intercept) 30.963202   1.373067  22.550  < 2e-16 ***
#> hp          -0.024840   0.013480  -1.843 0.075991 .  
#> disp        -0.030992   0.007504  -4.130 0.000296 ***
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#> 
#> Residual standard error: 3.149 on 28 degrees of freedom
#>   (1 observation deleted due to missingness)
#> Multiple R-squared:  0.7518, Adjusted R-squared:  0.7341 
#> F-statistic: 42.41 on 2 and 28 DF,  p-value: 3.368e-09

Strange result. Let’s check the correlations between mpg, hp, and disp to try and diagnose this problem. It should be simple using the base R function, cor(). Right?

Err, what is with all the NA‘s ?

rs <- cor(d)
rs
#>             mpg        cyl       disp hp        drat         wt
#> mpg   1.0000000 -0.8521620 -0.8475514 NA  0.68117191 -0.8676594
#> cyl  -0.8521620  1.0000000  0.9020329 NA -0.69993811  0.7824958
#> disp -0.8475514  0.9020329  1.0000000 NA -0.71021393  0.8879799
#> hp           NA         NA         NA  1          NA         NA
#> drat  0.6811719 -0.6999381 -0.7102139 NA  1.00000000 -0.7124406
#> wt   -0.8676594  0.7824958  0.8879799 NA -0.71244065  1.0000000
#> qsec  0.4186840 -0.5912421 -0.4336979 NA  0.09120476 -0.1747159
#> vs    0.6640389 -0.8108118 -0.7104159 NA  0.44027846 -0.5549157
#> am    0.5998324 -0.5226070 -0.5912270 NA  0.71271113 -0.6924953
#> gear  0.4802848 -0.4926866 -0.5555692 NA  0.69961013 -0.5832870
#> carb -0.5509251  0.5269883  0.3949769 NA -0.09078980  0.4276059
#>             qsec         vs          am       gear        carb
#> mpg   0.41868403  0.6640389  0.59983243  0.4802848 -0.55092507
#> cyl  -0.59124207 -0.8108118 -0.52260705 -0.4926866  0.52698829
#> disp -0.43369788 -0.7104159 -0.59122704 -0.5555692  0.39497686
#> hp            NA         NA          NA         NA          NA
#> drat  0.09120476  0.4402785  0.71271113  0.6996101 -0.09078980
#> wt   -0.17471588 -0.5549157 -0.69249526 -0.5832870  0.42760594
#> qsec  1.00000000  0.7445354 -0.22986086 -0.2126822 -0.65624923
#> vs    0.74453544  1.0000000  0.16834512  0.2060233 -0.56960714
#> am   -0.22986086  0.1683451  1.00000000  0.7940588  0.05753435
#> gear -0.21268223  0.2060233  0.79405876  1.0000000  0.27407284
#> carb -0.65624923 -0.5696071  0.05753435  0.2740728  1.00000000

Check the help page ?cor. Not so obvious. Default is use = "everything", and buried down in the details:

If use is “everything”, NAs will propagate conceptually, i.e., a resulting value will be NA whenever one of its contributing observations is NA.

Have to handle missing values with use:

rs <- cor(d, use = "pairwise.complete.obs")
rs
#>             mpg        cyl       disp         hp        drat         wt
#> mpg   1.0000000 -0.8521620 -0.8475514 -0.7749843  0.68117191 -0.8676594
#> cyl  -0.8521620  1.0000000  0.9020329  0.8298025 -0.69993811  0.7824958
#> disp -0.8475514  0.9020329  1.0000000  0.7860001 -0.71021393  0.8879799
#> hp   -0.7749843  0.8298025  0.7860001  1.0000000 -0.44258306  0.6505927
#> drat  0.6811719 -0.6999381 -0.7102139 -0.4425831  1.00000000 -0.7124406
#> wt   -0.8676594  0.7824958  0.8879799  0.6505927 -0.71244065  1.0000000
#> qsec  0.4186840 -0.5912421 -0.4336979 -0.7064809  0.09120476 -0.1747159
#> vs    0.6640389 -0.8108118 -0.7104159 -0.7162015  0.44027846 -0.5549157
#> am    0.5998324 -0.5226070 -0.5912270 -0.2196179  0.71271113 -0.6924953
#> gear  0.4802848 -0.4926866 -0.5555692 -0.1161968  0.69961013 -0.5832870
#> carb -0.5509251  0.5269883  0.3949769  0.7437843 -0.09078980  0.4276059
#>             qsec         vs          am       gear        carb
#> mpg   0.41868403  0.6640389  0.59983243  0.4802848 -0.55092507
#> cyl  -0.59124207 -0.8108118 -0.52260705 -0.4926866  0.52698829
#> disp -0.43369788 -0.7104159 -0.59122704 -0.5555692  0.39497686
#> hp   -0.70648093 -0.7162015 -0.21961793 -0.1161968  0.74378428
#> drat  0.09120476  0.4402785  0.71271113  0.6996101 -0.09078980
#> wt   -0.17471588 -0.5549157 -0.69249526 -0.5832870  0.42760594
#> qsec  1.00000000  0.7445354 -0.22986086 -0.2126822 -0.65624923
#> vs    0.74453544  1.0000000  0.16834512  0.2060233 -0.56960714
#> am   -0.22986086  0.1683451  1.00000000  0.7940588  0.05753435
#> gear -0.21268223  0.2060233  0.79405876  1.0000000  0.27407284
#> carb -0.65624923 -0.5696071  0.05753435  0.2740728  1.00000000

Can we focus on subset with dplyr? Nope.

dplyr::select(rs, mpg, hp, disp)
#> Error in UseMethod("select_"): no applicable method for 'select_' applied to an object of class "c('matrix', 'double', 'numeric')"

Riiiiiight! It’s a matrix and dplyr is for data frames.

class(rs)
#> [1] "matrix"

So we can use square brackets with matrices? Or not…

vars <- c("mpg", "hp", "disp")
rs[rownames(rs) %in% vars]
#>  [1]  1.0000000 -0.8475514 -0.7749843 -0.8521620  0.9020329  0.8298025
#>  [7] -0.8475514  1.0000000  0.7860001 -0.7749843  0.7860001  1.0000000
#> [13]  0.6811719 -0.7102139 -0.4425831 -0.8676594  0.8879799  0.6505927
#> [19]  0.4186840 -0.4336979 -0.7064809  0.6640389 -0.7104159 -0.7162015
#> [25]  0.5998324 -0.5912270 -0.2196179  0.4802848 -0.5555692 -0.1161968
#> [31] -0.5509251  0.3949769  0.7437843

Mm, square brackets can take on different functions with matrices. Without a comma, it’s treated like a vector. With a comma, we can separately specify the dimensions.

vars <- c("mpg", "hp", "disp")
rs[rownames(rs) %in% vars, colnames(rs) %in% vars]
#>             mpg       disp         hp
#> mpg   1.0000000 -0.8475514 -0.7749843
#> disp -0.8475514  1.0000000  0.7860001
#> hp   -0.7749843  0.7860001  1.0000000

Aha! High correlation between input variables (multicollinearity).

But seriously, this syntax is pretty ugly.

vars <- c("mpg", "hp", "disp")
rs[rownames(rs) %in% vars, colnames(rs) %in% vars]

We diagnosed our multicollinearity problem. What if we want to something a bit more complex like exploring clustering of variables in high dimensional space? Could use exploratory factor analysis.

factanal(na.omit(d), factors = 2)
#> 
#> Call:
#> factanal(x = na.omit(d), factors = 2)
#> 
#> Uniquenesses:
#>   mpg   cyl  disp    hp  drat    wt  qsec    vs    am  gear  carb 
#> 0.155 0.072 0.101 0.145 0.295 0.174 0.154 0.264 0.160 0.245 0.387 
#> 
#> Loadings:
#>      Factor1 Factor2
#> mpg   0.694  -0.603 
#> cyl  -0.629   0.729 
#> disp -0.730   0.605 
#> hp   -0.335   0.862 
#> drat  0.810  -0.221 
#> wt   -0.809   0.414 
#> qsec -0.162  -0.905 
#> vs    0.280  -0.811 
#> am    0.910   0.110 
#> gear  0.859   0.133 
#> carb          0.781 
#> 
#>                Factor1 Factor2
#> SS loadings      4.506   4.342
#> Proportion Var   0.410   0.395
#> Cumulative Var   0.410   0.804
#> 
#> Test of the hypothesis that 2 factors are sufficient.
#> The chi square statistic is 68.49 on 34 degrees of freedom.
#> The p-value is 0.000414
factanal(na.omit(d), factors = 5)
#> 
#> Call:
#> factanal(x = na.omit(d), factors = 5)
#> 
#> Uniquenesses:
#>   mpg   cyl  disp    hp  drat    wt  qsec    vs    am  gear  carb 
#> 0.112 0.044 0.012 0.066 0.275 0.005 0.091 0.128 0.136 0.143 0.045 
#> 
#> Loadings:
#>      Factor1 Factor2 Factor3 Factor4 Factor5
#> mpg   0.647  -0.441  -0.483  -0.203         
#> cyl  -0.604   0.694   0.293   0.128         
#> disp -0.645   0.543   0.202   0.451   0.182 
#> hp   -0.264   0.659   0.544   0.205   0.305 
#> drat  0.806  -0.250                         
#> wt   -0.725   0.226   0.420   0.488         
#> qsec -0.184  -0.890  -0.269                 
#> vs    0.242  -0.848  -0.209  -0.155   0.163 
#> am    0.916   0.118                         
#> gear  0.892           0.237                 
#> carb  0.119   0.458   0.853                 
#> 
#>                Factor1 Factor2 Factor3 Factor4 Factor5
#> SS loadings      4.186   3.255   1.739   0.582   0.180
#> Proportion Var   0.381   0.296   0.158   0.053   0.016
#> Cumulative Var   0.381   0.676   0.835   0.887   0.904
#> 
#> Test of the hypothesis that 5 factors are sufficient.
#> The chi square statistic is 2.17 on 10 degrees of freedom.
#> The p-value is 0.995

So many questions! I’d much rather explore the correlations.

Let’s try to find all variables with a correlation greater than 0.90. Why doesn’t this work?!

col_has_over_90 <- apply(rs, 2, function(x) any(x > .9))
rs[, col_has_over_90]
#>             mpg        cyl       disp         hp        drat         wt
#> mpg   1.0000000 -0.8521620 -0.8475514 -0.7749843  0.68117191 -0.8676594
#> cyl  -0.8521620  1.0000000  0.9020329  0.8298025 -0.69993811  0.7824958
#> disp -0.8475514  0.9020329  1.0000000  0.7860001 -0.71021393  0.8879799
#> hp   -0.7749843  0.8298025  0.7860001  1.0000000 -0.44258306  0.6505927
#> drat  0.6811719 -0.6999381 -0.7102139 -0.4425831  1.00000000 -0.7124406
#> wt   -0.8676594  0.7824958  0.8879799  0.6505927 -0.71244065  1.0000000
#> qsec  0.4186840 -0.5912421 -0.4336979 -0.7064809  0.09120476 -0.1747159
#> vs    0.6640389 -0.8108118 -0.7104159 -0.7162015  0.44027846 -0.5549157
#> am    0.5998324 -0.5226070 -0.5912270 -0.2196179  0.71271113 -0.6924953
#> gear  0.4802848 -0.4926866 -0.5555692 -0.1161968  0.69961013 -0.5832870
#> carb -0.5509251  0.5269883  0.3949769  0.7437843 -0.09078980  0.4276059
#>             qsec         vs          am       gear        carb
#> mpg   0.41868403  0.6640389  0.59983243  0.4802848 -0.55092507
#> cyl  -0.59124207 -0.8108118 -0.52260705 -0.4926866  0.52698829
#> disp -0.43369788 -0.7104159 -0.59122704 -0.5555692  0.39497686
#> hp   -0.70648093 -0.7162015 -0.21961793 -0.1161968  0.74378428
#> drat  0.09120476  0.4402785  0.71271113  0.6996101 -0.09078980
#> wt   -0.17471588 -0.5549157 -0.69249526 -0.5832870  0.42760594
#> qsec  1.00000000  0.7445354 -0.22986086 -0.2126822 -0.65624923
#> vs    0.74453544  1.0000000  0.16834512  0.2060233 -0.56960714
#> am   -0.22986086  0.1683451  1.00000000  0.7940588  0.05753435
#> gear -0.21268223  0.2060233  0.79405876  1.0000000  0.27407284
#> carb -0.65624923 -0.5696071  0.05753435  0.2740728  1.00000000

The diagonal is 1. All cols have a value greater than .90!

Exclude diagonal:

diag(rs) <- NA
col_has_over_90 <- apply(rs, 2, function(x) any(x > .9, na.rm = TRUE))
rs[, col_has_over_90]
#>             cyl       disp
#> mpg  -0.8521620 -0.8475514
#> cyl          NA  0.9020329
#> disp  0.9020329         NA
#> hp    0.8298025  0.7860001
#> drat -0.6999381 -0.7102139
#> wt    0.7824958  0.8879799
#> qsec -0.5912421 -0.4336979
#> vs   -0.8108118 -0.7104159
#> am   -0.5226070 -0.5912270
#> gear -0.4926866 -0.5555692
#> carb  0.5269883  0.3949769

Again, this syntax is pretty gross. Imagine showing this to a beginner and asking them to write down as much as they remember. Probably not much would be my guess.

What about vizualising correlations? I’d suggest giving up at this point.

depressed.gif

 Exploring data with the tidyverse

Remember me as postgrad? I’d discovered the tidyverse and really liked it, because exploring data with the tidyverse is easy.

library(tidyverse)
d %>% 
  select(mpg:drat) %>% 
  gather() %>% 
  ggplot(aes(value)) +
    geom_histogram() +
    facet_wrap(~key, scales = "free")

unnamed-chunk-17-1.png

Can’t we have this for correlations? I don’t want to do any crazy mathematical operations or statistical tests. I just want to quickly explore the value. It’s not a big ask.

Good news! This is why I developed corrr as a tidyverse-style package for exploring correlations in R.

 corrr

corrr_logo.png

Here’s a quick example to get a feel for the syntax:

library(corrr)
d %>% 
  correlate() %>% 
  focus(mpg:drat, mirror = TRUE) %>% 
  network_plot()
#> 
#> Correlation method: 'pearson'
#> Missing treated using: 'pairwise.complete.obs'

unnamed-chunk-18-1.png

The first objective of corrr was to write a new function that uses cor() but:

Now, meet correlate()

rs <- correlate(d)
#> 
#> Correlation method: 'pearson'
#> Missing treated using: 'pairwise.complete.obs'
rs
#> # A tibble: 11 x 12
#>    rowname     mpg     cyl    disp      hp     drat      wt     qsec
#>    <chr>     <dbl>   <dbl>   <dbl>   <dbl>    <dbl>   <dbl>    <dbl>
#>  1 mpg      NA      -0.852  -0.848  -0.775   0.681   -0.868   0.419 
#>  2 cyl      -0.852  NA       0.902   0.830  -0.700    0.782  -0.591 
#>  3 disp     -0.848   0.902  NA       0.786  -0.710    0.888  -0.434 
#>  4 hp       -0.775   0.830   0.786  NA      -0.443    0.651  -0.706 
#>  5 drat      0.681  -0.700  -0.710  -0.443  NA       -0.712   0.0912
#>  6 wt       -0.868   0.782   0.888   0.651  -0.712   NA      -0.175 
#>  7 qsec      0.419  -0.591  -0.434  -0.706   0.0912  -0.175  NA     
#>  8 vs        0.664  -0.811  -0.710  -0.716   0.440   -0.555   0.745 
#>  9 am        0.600  -0.523  -0.591  -0.220   0.713   -0.692  -0.230 
#> 10 gear      0.480  -0.493  -0.556  -0.116   0.700   -0.583  -0.213 
#> 11 carb     -0.551   0.527   0.395   0.744  -0.0908   0.428  -0.656 
#> # ... with 4 more variables: vs <dbl>, am <dbl>, gear <dbl>, carb <dbl>

Same args as cor() with some extras

correlate(d, method = "spearman", diagonal = 1)
#> 
#> Correlation method: 'spearman'
#> Missing treated using: 'pairwise.complete.obs'
#> # A tibble: 11 x 12
#>    rowname    mpg    cyl   disp     hp    drat     wt    qsec     vs
#>    <chr>    <dbl>  <dbl>  <dbl>  <dbl>   <dbl>  <dbl>   <dbl>  <dbl>
#>  1 mpg      1.00  -0.911 -0.909 -0.889  0.651  -0.886  0.467   0.707
#>  2 cyl     -0.911  1.00   0.928  0.899 -0.679   0.858 -0.572  -0.814
#>  3 disp    -0.909  0.928  1.00   0.845 -0.684   0.898 -0.460  -0.724
#>  4 hp      -0.889  0.899  0.845  1.00  -0.504   0.763 -0.660  -0.747
#>  5 drat     0.651 -0.679 -0.684 -0.504  1.00   -0.750  0.0919  0.447
#>  6 wt      -0.886  0.858  0.898  0.763 -0.750   1.00  -0.225  -0.587
#>  7 qsec     0.467 -0.572 -0.460 -0.660  0.0919 -0.225  1.00    0.792
#>  8 vs       0.707 -0.814 -0.724 -0.747  0.447  -0.587  0.792   1.00 
#>  9 am       0.562 -0.522 -0.624 -0.326  0.687  -0.738 -0.203   0.168
#> 10 gear     0.543 -0.564 -0.594 -0.316  0.745  -0.676 -0.148   0.283
#> 11 carb    -0.657  0.580  0.540  0.723 -0.125   0.500 -0.659  -0.634
#> # ... with 3 more variables: am <dbl>, gear <dbl>, carb <dbl>

The output of correlate()

It’s now super easy to pipe straight into tidyverse functions that work with data frames. For example:

rs %>% 
  select(mpg:drat) %>% 
  gather() %>% 
  ggplot(aes(value)) +
    geom_histogram() +
    facet_wrap(~key)

unnamed-chunk-21-1.png

How about that challenge to find cols with a correlation greater than .9?

any_over_90 <- function(x) any(x > .9, na.rm = TRUE)
rs %>% select_if(any_over_90)
#> # A tibble: 11 x 3
#>    rowname     cyl    disp
#>    <chr>     <dbl>   <dbl>
#>  1 mpg      -0.852  -0.848
#>  2 cyl      NA       0.902
#>  3 disp      0.902  NA    
#>  4 hp        0.830   0.786
#>  5 drat     -0.700  -0.710
#>  6 wt        0.782   0.888
#>  7 qsec     -0.591  -0.434
#>  8 vs       -0.811  -0.710
#>  9 am       -0.523  -0.591
#> 10 gear     -0.493  -0.556
#> 11 carb      0.527   0.395

self_five.gif

Here’s a diagram to get you started after library(corrr):

corrr_flow.png

 Correlation data frames are not tidy

Tidy data functions target columns OR rows, but I found myself frequently wanting to make changes to both. So next came the ability to focus() on columns and rows. This function acts just like dplyr’s select(), but also excludes the selected colums from the rows (or everything else with the mirror argument).

rs %>% 
  focus(mpg, disp, hp)
#> # A tibble: 8 x 4
#>   rowname    mpg   disp     hp
#>   <chr>    <dbl>  <dbl>  <dbl>
#> 1 cyl     -0.852  0.902  0.830
#> 2 drat     0.681 -0.710 -0.443
#> 3 wt      -0.868  0.888  0.651
#> 4 qsec     0.419 -0.434 -0.706
#> 5 vs       0.664 -0.710 -0.716
#> 6 am       0.600 -0.591 -0.220
#> 7 gear     0.480 -0.556 -0.116
#> 8 carb    -0.551  0.395  0.744
rs %>% 
  focus(-mpg, -disp, -hp)
#> # A tibble: 3 x 9
#>   rowname    cyl   drat     wt   qsec     vs     am   gear   carb
#>   <chr>    <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>  <dbl>
#> 1 mpg     -0.852  0.681 -0.868  0.419  0.664  0.600  0.480 -0.551
#> 2 disp     0.902 -0.710  0.888 -0.434 -0.710 -0.591 -0.556  0.395
#> 3 hp       0.830 -0.443  0.651 -0.706 -0.716 -0.220 -0.116  0.744
rs %>% 
  focus(mpg, disp, hp, mirror = TRUE)
#> # A tibble: 3 x 4
#>   rowname     mpg    disp      hp
#>   <chr>     <dbl>   <dbl>   <dbl>
#> 1 mpg      NA      -0.848  -0.775
#> 2 disp     -0.848  NA       0.786
#> 3 hp       -0.775   0.786  NA
rs %>% 
  focus(matches("^d"))
#> # A tibble: 9 x 3
#>   rowname   disp    drat
#>   <chr>    <dbl>   <dbl>
#> 1 mpg     -0.848  0.681 
#> 2 cyl      0.902 -0.700 
#> 3 hp       0.786 -0.443 
#> 4 wt       0.888 -0.712 
#> 5 qsec    -0.434  0.0912
#> 6 vs      -0.710  0.440 
#> 7 am      -0.591  0.713 
#> 8 gear    -0.556  0.700 
#> 9 carb     0.395 -0.0908
rs %>% 
  focus_if(any_over_90, mirror = TRUE)
#> # A tibble: 2 x 3
#>   rowname    cyl   disp
#>   <chr>    <dbl>  <dbl>
#> 1 cyl     NA      0.902
#> 2 disp     0.902 NA

One of my favourite uses is to focus() on correlations of one variable with all others and plot the results.

rs %>% 
  focus(mpg)
#> # A tibble: 10 x 2
#>    rowname    mpg
#>    <chr>    <dbl>
#>  1 cyl     -0.852
#>  2 disp    -0.848
#>  3 hp      -0.775
#>  4 drat     0.681
#>  5 wt      -0.868
#>  6 qsec     0.419
#>  7 vs       0.664
#>  8 am       0.600
#>  9 gear     0.480
#> 10 carb    -0.551
rs %>%
  focus(mpg) %>%
  mutate(rowname = reorder(rowname, mpg)) %>%
  ggplot(aes(rowname, mpg)) +
    geom_col() + coord_flip()

unnamed-chunk-29-1.png

You can also rearrange() the entire data frame based on clustering algorithms:

rs %>% rearrange()
#> # A tibble: 11 x 12
#>    rowname       am    gear     drat      wt    disp     mpg     cyl
#>    <chr>      <dbl>   <dbl>    <dbl>   <dbl>   <dbl>   <dbl>   <dbl>
#>  1 am       NA        0.794   0.713   -0.692  -0.591   0.600  -0.523
#>  2 gear      0.794   NA       0.700   -0.583  -0.556   0.480  -0.493
#>  3 drat      0.713    0.700  NA       -0.712  -0.710   0.681  -0.700
#>  4 wt       -0.692   -0.583  -0.712   NA       0.888  -0.868   0.782
#>  5 disp     -0.591   -0.556  -0.710    0.888  NA      -0.848   0.902
#>  6 mpg       0.600    0.480   0.681   -0.868  -0.848  NA      -0.852
#>  7 cyl      -0.523   -0.493  -0.700    0.782   0.902  -0.852  NA    
#>  8 vs        0.168    0.206   0.440   -0.555  -0.710   0.664  -0.811
#>  9 hp       -0.220   -0.116  -0.443    0.651   0.786  -0.775   0.830
#> 10 carb      0.0575   0.274  -0.0908   0.428   0.395  -0.551   0.527
#> 11 qsec     -0.230   -0.213   0.0912  -0.175  -0.434   0.419  -0.591
#> # ... with 4 more variables: vs <dbl>, hp <dbl>, carb <dbl>, qsec <dbl>

Or shave() the upper/lower triangle to missing values

rs %>% shave()
#> # A tibble: 11 x 12
#>    rowname     mpg     cyl    disp      hp     drat      wt    qsec
#>    <chr>     <dbl>   <dbl>   <dbl>   <dbl>    <dbl>   <dbl>   <dbl>
#>  1 mpg      NA      NA      NA      NA      NA       NA      NA    
#>  2 cyl      -0.852  NA      NA      NA      NA       NA      NA    
#>  3 disp     -0.848   0.902  NA      NA      NA       NA      NA    
#>  4 hp       -0.775   0.830   0.786  NA      NA       NA      NA    
#>  5 drat      0.681  -0.700  -0.710  -0.443  NA       NA      NA    
#>  6 wt       -0.868   0.782   0.888   0.651  -0.712   NA      NA    
#>  7 qsec      0.419  -0.591  -0.434  -0.706   0.0912  -0.175  NA    
#>  8 vs        0.664  -0.811  -0.710  -0.716   0.440   -0.555   0.745
#>  9 am        0.600  -0.523  -0.591  -0.220   0.713   -0.692  -0.230
#> 10 gear      0.480  -0.493  -0.556  -0.116   0.700   -0.583  -0.213
#> 11 carb     -0.551   0.527   0.395   0.744  -0.0908   0.428  -0.656
#> # ... with 4 more variables: vs <dbl>, am <dbl>, gear <dbl>, carb <dbl>

Or stretch() into a more tidy format

rs %>% stretch()
#> # A tibble: 121 x 3
#>    x     y           r
#>    <chr> <chr>   <dbl>
#>  1 mpg   mpg    NA    
#>  2 mpg   cyl    -0.852
#>  3 mpg   disp   -0.848
#>  4 mpg   hp     -0.775
#>  5 mpg   drat    0.681
#>  6 mpg   wt     -0.868
#>  7 mpg   qsec    0.419
#>  8 mpg   vs      0.664
#>  9 mpg   am      0.600
#> 10 mpg   gear    0.480
#> # ... with 111 more rows

And combine with tidyverse to do things like get a histogram of all correlations:

rs %>%
  shave() %>% 
  stretch(na.rm = FALSE) %>% 
  ggplot(aes(r)) +
    geom_histogram()
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
#> Warning: Removed 66 rows containing non-finite values (stat_bin).

unnamed-chunk-33-1.png

As a tidyverse-style package, it’s important that the functions take a data.frame in, data.frame out principle. This let’s you flow through pipelines and intermix functions from many packages with ease.

rs %>%
  focus(mpg:drat, mirror = TRUE) %>% 
  rearrange() %>% 
  shave(upper = FALSE) %>% 
  select(-hp) %>% 
  filter(rowname != "drat")
#> # A tibble: 4 x 5
#>   rowname    cyl     mpg    disp   drat
#>   <chr>    <dbl>   <dbl>   <dbl>  <dbl>
#> 1 hp       0.830  -0.775   0.786 -0.443
#> 2 cyl     NA      -0.852   0.902 -0.700
#> 3 mpg     NA      NA      -0.848  0.681
#> 4 disp    NA      NA      NA     -0.710

 Seems cool, but it’s still hard to get quick insights

corrr also provides some helpful methods to interpret/visualize the correlations. You can get fashionable:

rs %>% fashion()
#>    rowname  mpg  cyl disp   hp drat   wt qsec   vs   am gear carb
#> 1      mpg      -.85 -.85 -.77  .68 -.87  .42  .66  .60  .48 -.55
#> 2      cyl -.85       .90  .83 -.70  .78 -.59 -.81 -.52 -.49  .53
#> 3     disp -.85  .90       .79 -.71  .89 -.43 -.71 -.59 -.56  .39
#> 4       hp -.77  .83  .79      -.44  .65 -.71 -.72 -.22 -.12  .74
#> 5     drat  .68 -.70 -.71 -.44      -.71  .09  .44  .71  .70 -.09
#> 6       wt -.87  .78  .89  .65 -.71      -.17 -.55 -.69 -.58  .43
#> 7     qsec  .42 -.59 -.43 -.71  .09 -.17       .74 -.23 -.21 -.66
#> 8       vs  .66 -.81 -.71 -.72  .44 -.55  .74       .17  .21 -.57
#> 9       am  .60 -.52 -.59 -.22  .71 -.69 -.23  .17       .79  .06
#> 10    gear  .48 -.49 -.56 -.12  .70 -.58 -.21  .21  .79       .27
#> 11    carb -.55  .53  .39  .74 -.09  .43 -.66 -.57  .06  .27
rs %>%
  focus(mpg:drat, mirror = TRUE) %>% 
  rearrange() %>% 
  shave(upper = FALSE) %>% 
  select(-hp) %>% 
  filter(rowname != "drat") %>% 
  fashion()
#>   rowname  cyl  mpg disp drat
#> 1      hp  .83 -.77  .79 -.44
#> 2     cyl      -.85  .90 -.70
#> 3     mpg           -.85  .68
#> 4    disp                -.71

Make an rplot()

rs %>% rplot()

unnamed-chunk-37-1.png

rs %>%
  rearrange(method = "MDS", absolute = FALSE) %>%
  shave() %>% 
  rplot(shape = 15, colors = c("red", "green"))

unnamed-chunk-38-1.png

Or make a network_plot()

rs %>% network_plot(min_cor = .6)

unnamed-chunk-39-1.png

But if you want to get custom, check out my blog post combining corrr with ggraph.

 Latest addition by Edgar Ruiz

So corrr was starting to look pretty good, but these days it’s not all me. There are three official contributors, and many others who took the time to raise issues that identified bugs or suggested features.

One of the latest editions by Edgar Ruiz lets you correlate() data frames in databases. To demonstrate (copying Edgar’s vignette), here’s a simple SQLite database with data pointer, db_mtcars:

con <- DBI::dbConnect(RSQLite::SQLite(), path = ":dbname:")
db_mtcars <- copy_to(con, mtcars)
class(db_mtcars)
#> [1] "tbl_dbi"  "tbl_sql"  "tbl_lazy" "tbl"

correlate() detects DB backend, uses tidyeval to calculate correlations in the database, and returns correlation data frame.

db_mtcars %>% correlate(use = "complete.obs")
#> 
#> Correlation method: 'pearson'
#> Missing treated using: 'complete.obs'
#> # A tibble: 11 x 12
#>    rowname     mpg     cyl    disp      hp     drat      wt     qsec
#>    <chr>     <dbl>   <dbl>   <dbl>   <dbl>    <dbl>   <dbl>    <dbl>
#>  1 mpg      NA      -0.852  -0.848  -0.776   0.681   -0.868   0.419 
#>  2 cyl      -0.852  NA       0.902   0.832  -0.700    0.782  -0.591 
#>  3 disp     -0.848   0.902  NA       0.791  -0.710    0.888  -0.434 
#>  4 hp       -0.776   0.832   0.791  NA      -0.449    0.659  -0.708 
#>  5 drat      0.681  -0.700  -0.710  -0.449  NA       -0.712   0.0912
#>  6 wt       -0.868   0.782   0.888   0.659  -0.712   NA      -0.175 
#>  7 qsec      0.419  -0.591  -0.434  -0.708   0.0912  -0.175  NA     
#>  8 vs        0.664  -0.811  -0.710  -0.723   0.440   -0.555   0.745 
#>  9 am        0.600  -0.523  -0.591  -0.243   0.713   -0.692  -0.230 
#> 10 gear      0.480  -0.493  -0.556  -0.126   0.700   -0.583  -0.213 
#> 11 carb     -0.551   0.527   0.395   0.750  -0.0908   0.428  -0.656 
#> # ... with 4 more variables: vs <dbl>, am <dbl>, gear <dbl>, carb <dbl>

Here’s another example using spark:

sc <- sparklyr::spark_connect(master = "local")
#> * Using Spark: 2.1.0
mtcars_tbl <- copy_to(sc, mtcars)
correlate(mtcars_tbl, use = "complete.obs")
#> 
#> Correlation method: 'pearson'
#> Missing treated using: 'complete.obs'
#> # A tibble: 11 x 12
#>    rowname     mpg     cyl    disp      hp     drat      wt     qsec
#>    <chr>     <dbl>   <dbl>   <dbl>   <dbl>    <dbl>   <dbl>    <dbl>
#>  1 mpg      NA      -0.852  -0.848  -0.776   0.681   -0.868   0.419 
#>  2 cyl      -0.852  NA       0.902   0.832  -0.700    0.782  -0.591 
#>  3 disp     -0.848   0.902  NA       0.791  -0.710    0.888  -0.434 
#>  4 hp       -0.776   0.832   0.791  NA      -0.449    0.659  -0.708 
#>  5 drat      0.681  -0.700  -0.710  -0.449  NA       -0.712   0.0912
#>  6 wt       -0.868   0.782   0.888   0.659  -0.712   NA      -0.175 
#>  7 qsec      0.419  -0.591  -0.434  -0.708   0.0912  -0.175  NA     
#>  8 vs        0.664  -0.811  -0.710  -0.723   0.440   -0.555   0.745 
#>  9 am        0.600  -0.523  -0.591  -0.243   0.713   -0.692  -0.230 
#> 10 gear      0.480  -0.493  -0.556  -0.126   0.700   -0.583  -0.213 
#> 11 carb     -0.551   0.527   0.395   0.750  -0.0908   0.428  -0.656 
#> # ... with 4 more variables: vs <dbl>, am <dbl>, gear <dbl>, carb <dbl>

So no data is too big for corrr now! This opens up some nice possibilities. For example, most regression-based modelling packages (like lavaan) cannot operate on large data sets in a database. However, they typically accept a correlation matrix as input. So you can use corrr to extract correlations from large data sets and do more complex modelling in memory.

 Thanks Simon, but I’m not interested.

In case corrr doesn’t float your boat, some other packages you might be interested in are corrplot for rplot() style viz, and widyr for a more general way to handle relational data sets in a tidy framework.

 Sign off

Thanks for reading and I hope this was useful for you.

For updates of recent blog posts, follow @drsimonj on Twitter, or email me at drsimonjackson@gmail.com to get in touch.

If you’d like the code that produced this blog, check out the blogR GitHub repository.

 
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