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readDiscreteCharacterData function malfunctioning with Binary and Restriction datatypes #168

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nataliacp opened this issue Sep 6, 2019 · 0 comments

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@nataliacp
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When the datatype in the nexus file is specified as Binary or Restriction, the function loads it into RevBayes as Standard. This causes character datatype mismatches later on.
I have tested this in v.11 and v.12 on a mac. I have not tested it with all datatypes.

>data <- readDiscreteCharacterData("Test.nex")
   Successfully read one character matrix from file 'Test.nex'
> data

   Standard character matrix with 1 taxa and 5 characters
   ======================================================
   Origination:                   Test.nex
   Number of taxa:                1
   Number of included taxa:       1
   Number of characters:          5
   Number of included characters: 5
   Datatype:                      Standard

The contents of Test.nex are:

#NEXUS

BEGIN DATA;
	DIMENSIONS  NTAX=1 NCHAR=5;
	FORMAT DATATYPE = Binary GAP = - MISSING = ? ;
	MATRIX
	Mawe          00001
	;
	END;
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