Fix: testNumeric() function treated the matrix as numeric

[randef1ned]

This PR fixed a bug that testNumeric() function treated the matrix as numeric.

> testNumeric(2)
[1] TRUE
> testNumeric(matrix(2))  # The bug appears
[1] TRUE

[SamGG]

Hi, x being a matrix, my understanding is that testMatrix(x) checks that x has the shape/characteristics of a matrix and testNumeric(x) checks the values of x are in a certain range. I don't understand why you consider testNumeric(matrix(2)) should return FALSE. Could you elaborate? Best.

[randef1ned]

Hello SamGG,

Your understanding is right and reasonable. However, the function testNumeric checks whether an argument is a numeric vector according to the documentation. It is misleading that a user (like me) assumes that the testNumeric function can automatically reject other data types, which would raise errors or yield unwanted results. For example, I would like to add a matrix and a vector. It would raise an error if I input a matrix. Therefore, it is necessary to return false for testNumeric.

> a <- matrix(1:4, nrow = 2); b <- 2
> test_numeric(b, lower = 0)   # b passed the check
[1] TRUE
> a + b    # b is expected to be a numeric vector; no error
     [,1] [,2]
[1,]    3    5
[2,]    4    6
> c <- matrix(2)    # c is a matrix, but it can pass the check
> test_numeric(c, lower = 0)
[1] TRUE
> a + c        # throw error because c is not a numeric vector but a matrix
Error in a + c : non-conformable arrays

According to your understanding, I think it is better to create a new function, e.g., testNumericRange(x), to check the values of x that are in a certain range to avoid any misleading and confoundings.

[tdeenes]

@randef1ned

You shall consider testNumeric as a more powerful alternative to base::is.numeric. Note that is.numeric(matrix(1)) returns TRUE and testNumeric(matrix(1)) does the same, which is the right thing in the current context. If you really need an atomic vector, you shall explicitly test for it, so use testNumeric(x) && testAtomicVector(x). You can easily create your custom check function and then use makeAssertionFunction and makeExpectationFunction to get your own test[check/assert/expect]NumericVector.

[SamGG]

The doc of checkmate::testNumeric says Check that an argument is a vector of type numeric. It should avoid the misleading term vector. Maybe Check that an argument is of type numeric is more in phase with base::is.numeric and what I like it currently performs.

[randef1ned]

Got it. Thanks @tdeenes

It is expected that the checkmate package will behave exactly as base R. Maybe we should inform the users of this information in the documentation.

I agree with the suggestion proposed by @SamGG that the documentation should be modified to avoid any misleading. Dropping the word vector in the documentation seems to break some packages relying on the checkmate package, because a regular user would get to know the packages through the examples and documentation and would never read the source code inside a package. According to the documentation, the testNumeric(x) is a function to check whether x is a numeric vector. Perhaps we need to conduct some surveys to see the understandings of the users.

checkmate is a widely-used R package, so, any changes to the existing function should be thoroughly evaluated.

[randef1ned]

I have just done a quick survey. I searched the testNumeric( function in all R scripts hosted on GitHub. Among the top 40 of the search results, only one repo (MichaelChirico/distr6) checks the input x as a matrix or vector. Therefore, I think it is unsafe to drop the word vector in the testNumeric documentation. Here is the result table:

repo	file	line	type of x
xoopR/distr6	R/Wrapper_MixtureDistribution.R	53	numeric vector
		64	numeric vector
mlr-org/mlr	R/StackedLearner.R	666	numeric vector
emanuelhuber/RGPR	R/checkArgs.R	55	number
		63	number
		72	numeric vector
		80	numeric vector
		96	number
		107	number
		119	number
		133	number
RaphaelS1/Rsmisc	R/makeChecks.R	22	number
nlmixr2/rxode2parse	R/rudf.R	466	number
wpgp/wopr	R/parseFilename.R	48	unknown
		56	unknown
		58	unknown
mlr-org/mlrMBO	R/evalTargetFun.R	52	numeric vector
jakobbossek/smoof	R/makeSingleObjectiveFunction.R	70	numeric vector
bips-hb/innsight	R/Converter.R	1259	integer or vector
SixiangHu/DataMan	R/DataSummary.R	47	numeric vector
		60	numeric vector
		75	numeric vector
rubak/spatstat.revdep	geometr/R/gt_stretch.R	36	number
		38	number
juliedwhite/miamiplot	R/check_miami_input.R	43	number
dimfalk/kostra2010R	R/get_centroid.R	35	numeric vector
aschersleben/cointReg	R/check-arguments.R	235	numeric vector
jakobbossek/netgen	R/autoplotNetwork.R	42	numeric vector
nlmixr2/rxode2	R/rxsolve.R	827	number
yonicd/typeR	data/genthat_extracted_code/checkmate/examples/checkNumeric.Rd.R	11	number
		12	number
mlr-org/mlrCPO	R/FormatCheck.R	626	numeric vector
		684	numeric vector
MichaelChirico/distr6	R/SDistribution_MultivariateNormal.R	217	matrix | vector
		257	matrix | vector
jordansquair/splatter_batch	R/KersplatParams-methods.R	78	unknown
bioc/SNPhood	R/DataClasses.R	924	unknown
		1101	unknown
		1106	unknown
		1121	unknown
		1137	unknown
		1145	unknown
eddelbuettel/checkmate	R/checkNumeric.R	17	number
		18	number
wibeasley/checkmate	R/checkNumeric.R	22	number
		23	number
dimfalk/netatmo.weather	R/get_extent.R	31	numeric vector
aschersleben/NBCD	R/naiveBayes.R	63	numeric vector
rkayastha/RGPR	R/checkArgs.R	55	number
		63	numeric vector
		71	numeric vector
		87	number
		98	number
		110	number
		124	number
thomascherickal/mlr	R/StackedLearner.R	650	numeric vector
cran/triact	R/001_load_methods.R	38	integer vector
mnwright/mlr	R/StackedLearner.R	649	numeric vector
jakob-r/mlr	R/StackedLearner.R	650	numeric vector