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Correlation matrices now zap small by default #336

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Jan 4, 2025
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Correlation matrices now zap small by default #336

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8f0646e
Update methods_format.R
DominiqueMakowski Jan 3, 2025
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news, desc
strengejacke Jan 3, 2025
5b3622c
update snapshots
strengejacke Jan 3, 2025
f11f915
add test
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news
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version
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strengejacke Jan 3, 2025
b7e9824
update tests
strengejacke Jan 4, 2025
4af4d7c
fix test
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22bd109
style
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2 changes: 1 addition & 1 deletion DESCRIPTION
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@@ -1,7 +1,7 @@
Type: Package
Package: correlation
Title: Methods for Correlation Analysis
Version: 0.8.6.1
Version: 0.8.6.2
Authors@R:
c(person(given = "Dominique",
family = "Makowski",
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7 changes: 7 additions & 0 deletions NEWS.md
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@@ -1,5 +1,12 @@
# correlation 0.8.6

- The `format()` for objects of class `easycormatrix` gets a `zap_small` argument,
which defaults to `TRUE`, to round very small numbers.

- `cor_sort()` can now deal with non-square matrices.

# correlation 0.8.6

- Fix CRAN check issues.

# correlation 0.8.5
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5 changes: 4 additions & 1 deletion R/methods_format.R
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Expand Up @@ -40,6 +40,7 @@ format.easycormatrix <- function(x,
stars = NULL,
include_significance = NULL,
format = NULL,
zap_small = NULL,
bf_exact = TRUE,
...) {
# If it's a real matrix
Expand All @@ -56,11 +57,13 @@ format.easycormatrix <- function(x,
stars <- .retrieve_arg_from_attr(attri, stars, default = TRUE)
include_significance <- .retrieve_arg_from_attr(attri, include_significance, default = FALSE)
p_digits <- .retrieve_arg_from_attr(attri, p_digits, default = "apa")
zap_small <- .retrieve_arg_from_attr(attri, zap_small, default = TRUE)


# Round and format values
nums <- sapply(as.data.frame(x), is.numeric)
x[, nums] <- sapply(as.data.frame(x)[, nums], insight::format_value, digits = digits)
x[, nums] <- sapply(as.data.frame(x)[, nums], insight::format_value,
digits = digits, zap_small = zap_small, ...)


# Deduct if stars only
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96 changes: 48 additions & 48 deletions tests/testthat/_snaps/as_list.md
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Expand Up @@ -37,18 +37,18 @@

p
---
Parameter | carb | gear | am | vs | qsec | wt | drat | hp | disp | cyl
-----------------------------------------------------------------------------------------------------------------------
mpg | 0.02 | 0.10 | 8.27e-03 | 1.09e-03 | 0.22 | 6.86e-09 | 5.86e-04 | 8.05e-06 | 4.78e-08 | 3.18e-08
cyl | 0.04 | 0.08 | 0.04 | 9.03e-07 | 0.01 | 5.60e-06 | 2.97e-04 | 1.74e-07 | 9.92e-11 |
disp | 0.30 | 0.02 | 0.01 | 2.04e-04 | 0.20 | 6.60e-10 | 2.04e-04 | 3.36e-06 | |
hp | 3.44e-05 | 1.00 | 1.00 | 1.24e-04 | 2.13e-04 | 1.29e-03 | 0.17 | | |
drat | 1.00 | 2.97e-04 | 1.94e-04 | 0.19 | 1.00 | 1.94e-04 | | | |
wt | 0.20 | 0.01 | 3.83e-04 | 0.02 | 1.00 | | | | |
qsec | 1.36e-03 | 1.00 | 1.00 | 4.43e-05 | | | | | |
vs | 0.02 | 1.00 | 1.00 | | | | | | |
am | 1.00 | 2.80e-06 | | | | | | | |
gear | 1.00 | | | | | | | | |
Parameter | carb | gear | am | vs | qsec | wt | drat | hp | disp | cyl
-------------------------------------------------------------------------------
mpg | 0.02 | 0.10 | 0.01 | 0.00 | 0.22 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00
cyl | 0.04 | 0.08 | 0.04 | 0.00 | 0.01 | 0.00 | 0.00 | 0.00 | 0.00 |
disp | 0.30 | 0.02 | 0.01 | 0.00 | 0.20 | 0.00 | 0.00 | 0.00 | |
hp | 0.00 | 1.00 | 1.00 | 0.00 | 0.00 | 0.00 | 0.17 | | |
drat | 1.00 | 0.00 | 0.00 | 0.19 | 1.00 | 0.00 | | | |
wt | 0.20 | 0.01 | 0.00 | 0.02 | 1.00 | | | | |
qsec | 0.00 | 1.00 | 1.00 | 0.00 | | | | | |
vs | 0.02 | 1.00 | 1.00 | | | | | | |
am | 1.00 | 0.00 | | | | | | | |
gear | 1.00 | | | | | | | | |



Expand Down Expand Up @@ -85,13 +85,13 @@

p
---
Group | Parameter | bodywt | brainwt | awake | sleep_cycle | sleep_rem
---------------------------------------------------------------------------
carni | sleep_total | 0.37 | 0.73 | 0.00 | 1.00 | 3.19e-04
carni | sleep_rem | 0.20 | 1.00 | 3.19e-04 | 1.00 |
carni | sleep_cycle | 1.00 | 1.00 | 1.00 | |
carni | awake | 0.37 | 0.73 | | |
carni | brainwt | 0.09 | | | |
Group | Parameter | bodywt | brainwt | awake | sleep_cycle | sleep_rem
------------------------------------------------------------------------
carni | sleep_total | 0.37 | 0.73 | 0.00 | 1.00 | 0.00
carni | sleep_rem | 0.20 | 1.00 | 0.00 | 1.00 |
carni | sleep_cycle | 1.00 | 1.00 | 1.00 | |
carni | awake | 0.37 | 0.73 | | |
carni | brainwt | 0.09 | | | |



Expand Down Expand Up @@ -123,13 +123,13 @@

p
---
Group | Parameter | bodywt | brainwt | awake | sleep_cycle | sleep_rem
------------------------------------------------------------------------------
herbi | sleep_total | 3.42e-06 | 8.71e-06 | 0.00 | 0.35 | 5.00e-09
herbi | sleep_rem | 4.65e-04 | 4.43e-03 | 5.00e-09 | 0.35 |
herbi | sleep_cycle | 0.03 | 0.04 | 0.35 | |
herbi | awake | 3.42e-06 | 8.71e-06 | | |
herbi | brainwt | 5.17e-13 | | | |
Group | Parameter | bodywt | brainwt | awake | sleep_cycle | sleep_rem
------------------------------------------------------------------------
herbi | sleep_total | 0.00 | 0.00 | 0.00 | 0.35 | 0.00
herbi | sleep_rem | 0.00 | 0.00 | 0.00 | 0.35 |
herbi | sleep_cycle | 0.03 | 0.04 | 0.35 | |
herbi | awake | 0.00 | 0.00 | | |
herbi | brainwt | 0.00 | | | |



Expand Down Expand Up @@ -161,13 +161,13 @@

p
---
Group | Parameter | bodywt | brainwt | awake | sleep_cycle | sleep_rem
-------------------------------------------------------------------------------
insecti | sleep_total | 1.00 | 1.00 | 1.46e-22 | 1.00 | 1.00
insecti | sleep_rem | 1.00 | 1.00 | 1.00 | 0.00 |
insecti | sleep_cycle | 1.00 | 1.00 | 1.00 | |
insecti | awake | 1.00 | 1.00 | | |
insecti | brainwt | 5.56e-23 | | | |
Group | Parameter | bodywt | brainwt | awake | sleep_cycle | sleep_rem
--------------------------------------------------------------------------
insecti | sleep_total | 1.00 | 1.00 | 0.00 | 1.00 | 1.00
insecti | sleep_rem | 1.00 | 1.00 | 1.00 | 0.00 |
insecti | sleep_cycle | 1.00 | 1.00 | 1.00 | |
insecti | awake | 1.00 | 1.00 | | |
insecti | brainwt | 0.00 | | | |



Expand Down Expand Up @@ -199,13 +199,13 @@

p
---
Group | Parameter | bodywt | brainwt | awake | sleep_cycle | sleep_rem
---------------------------------------------------------------------------
omni | sleep_total | 1.00 | 1.00 | 0.00 | 1.00 | 1.00
omni | sleep_rem | 1.00 | 1.00 | 1.00 | 1.00 |
omni | sleep_cycle | 0.04 | 7.73e-04 | 1.00 | |
omni | awake | 1.00 | 1.00 | | |
omni | brainwt | 7.64e-06 | | | |
Group | Parameter | bodywt | brainwt | awake | sleep_cycle | sleep_rem
------------------------------------------------------------------------
omni | sleep_total | 1.00 | 1.00 | 0.00 | 1.00 | 1.00
omni | sleep_rem | 1.00 | 1.00 | 1.00 | 1.00 |
omni | sleep_cycle | 0.04 | 0.00 | 1.00 | |
omni | awake | 1.00 | 1.00 | | |
omni | brainwt | 0.00 | | | |



Expand Down Expand Up @@ -237,10 +237,10 @@

p
---
Group | Parameter | hp
----------------------------
0 | cyl | 2.11e-06
0 | wt | 1.11e-05
Group | Parameter | hp
------------------------
0 | cyl | 0.00
0 | wt | 0.00



Expand All @@ -266,10 +266,10 @@

p
---
Group | Parameter | hp
----------------------------
1 | cyl | 9.58e-04
1 | wt | 1.04e-03
Group | Parameter | hp
------------------------
1 | cyl | 0.00
1 | wt | 0.00



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28 changes: 28 additions & 0 deletions tests/testthat/_snaps/windows/correlation.md
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@@ -0,0 +1,28 @@
# correlation output with zap_small

Code
summary(r)
Output
# Correlation Matrix (pearson-method)

Parameter | z | y
-----------------------
x | 0.02 | 0.01
y | 0.00 |

p-value adjustment method: Holm (1979)

---

Code
summary(r, zap_small = FALSE)
Output
# Correlation Matrix (pearson-method)

Parameter | z | y
--------------------------------
x | 0.02 | 6.02e-03
y | -3.07e-03 |

p-value adjustment method: Holm (1979)

13 changes: 13 additions & 0 deletions tests/testthat/test-correlation.R
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Expand Up @@ -198,3 +198,16 @@ test_that("as.data.frame for correlation output", {
set.seed(123)
expect_snapshot(as.data.frame(correlation(ggplot2::msleep)))
})

test_that("correlation output with zap_small", {
set.seed(123)
d <- data.frame(
x = rnorm(10000),
y = rnorm(10000),
z = rnorm(10000)
)
r <- correlation::correlation(d)

expect_snapshot(summary(r), variant = "windows")
expect_snapshot(summary(r, zap_small = FALSE), variant = "windows")
})
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