Many thanks Ivan

Use is.na() on getValues() outputs, combine the two masks using the | operator 
to get a mask of values that are missing in either raster, then negate the mask 
to choose the non-missing values:

all.equal(getValues(r1)[!mask], getValues(r2)[!mask])

--> what do you mean by use is.na() in getValues(). So I need to call getValues 
a second time? I suppose you mean to first prepare a mask using is.na without 
getValues and then in the second step your code?

Kind regards
Sibylle

-----Original Message-----
From: Ivan Krylov <ikry...@disroot.org> 
Sent: Friday, August 16, 2024 9:28 AM
To: SIBYLLE STÖCKLI via R-help <r-help@r-project.org>
Cc: sibylle.stoec...@gmx.ch
Subject: Re: [R] allequal diff

В Fri, 16 Aug 2024 07:19:38 +0200
SIBYLLE STÖCKLI via R-help <r-help@r-project.org> пишет:

> Is it possible to consider na.rm=TRUE?

> > all.equal(getValues(r1), getValues(r2_resampled), tolerance = 0)
> 
> [1] "'is.NA' value mismatch: 9544032 in current 66532795 in target"

Use is.na() on getValues() outputs, combine the two masks using the | operator 
to get a mask of values that are missing in either raster, then negate the mask 
to choose the non-missing values:

all.equal(getValues(r1)[!mask], getValues(r2)[!mask])

--
Best regards,
Ivan

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