Hi,
I found an issue with the include.sample.summary argument in the aldex.effect function. When using the argument under R 3.6.2 and the ALDEx2 version 1.16.0 all is good:
But when I try the same under R 4.1.0 and ALDEx2 version 1.24.0 I get a warning and all the median clr values for each sample are the same for each taxon:
Hi, I found an issue with the include.sample.summary argument in the aldex.effect function. When using the argument under R 3.6.2 and the ALDEx2 version 1.16.0 all is good:
[1] ‘1.16.0’
rab.all rab.win.NS rab.win.S rab.sample.X1_ANS rab.sample.X1_BNS rab.sample.X1_CNS A:D:A:D 1.6030007 1.5382122 2.3137897 1.4723764 1.6148116 1.6359866 A:D:A:E 1.9001917 1.7345307 4.0245559 1.7893647 2.0312430 1.8619915 A:E:A:D 3.9435508 1.6312451 10.7664531 1.9402834 1.6978629 1.5823448 A:E:A:E 3.8562343 1.8683216 13.7598065 2.0280768 1.8060024 1.7452067 A:D:C:D 0.5185451 0.6436814 -0.2388991 0.5065450 0.9057612 0.6285314 A:D:C:E 0.5207592 0.6080908 -0.3051005 0.8290245 0.6525141 0.2392668
But when I try the same under R 4.1.0 and ALDEx2 version 1.24.0 I get a warning and all the median clr values for each sample are the same for each taxon:
[1] ‘1.24.0’
There were 15 warnings (use warnings() to see them)
Warning message: In
[<-.data.frame
(*tmp*
, , nm, value = structure(list( ... : provided 400 variables to replace 1 variablesrab.all rab.win.NS rab.win.S rab.sample.X1_ANS rab.sample.X1_BNS rab.sample.X1_CNS A:D:A:D 1.6030007 1.5382122 2.3137897 1.472376 1.614812 1.635987 A:D:A:E 1.9001917 1.7345307 4.0245559 1.472376 1.614812 1.635987 A:E:A:D 3.9435508 1.6312451 10.7664531 1.472376 1.614812 1.635987 A:E:A:E 3.8562343 1.8683216 13.7598065 1.472376 1.614812 1.635987 A:D:C:D 0.5185451 0.6436814 -0.2388991 1.472376 1.614812 1.635987 A:D:C:E 0.5207592 0.6080908 -0.3051005 1.472376 1.614812 1.635987
I haven't found anything online about this and was wondering if you might be able to help me with this.