STA :: Can't fit RCBD with SpATS

I was not able to fix it at this point so I am only adding more precise information concerning the origin of the error.

It occurs for the environment 3177 with any of the 3 traits (PAsp_E_1to5, AleuCol_E_1to5, PH_M_cm). The function SpATS:SpATS() throws the following errors:

The design matrix associated to the random part of the model is not of full rank. Please check that there are no redundant >components in the random part of the model.

The design matrix associated to the fixed part of the model is not of full rank. Please check that there are no redundant >components in the fixed part of the model.

(genotype being fitted successively as fixed then random effect)

I understand that the matrix design is (repId, row, col). For environment 3177, the rank of this matrix is 2 (therefore not full rank) whereas it is 3 for environments 3176 and 3176 (see code below).

@mcrimi @jframi could the rcbd design be wrong for 3177?

> foo$data[studyDbId==3177 & observations.observationVariableName == "PH_M_cm", .(replicate, positionCoordinateX, positionCoordinateY)] %>% as.matrix()
      replicate positionCoordinateX positionCoordinateY
 [1,]         1                   1                   1
 [2,]         1                   1                   2
 [3,]         1                   1                   3
 [4,]         1                   1                   4
 [5,]         1                   1                   5
 [6,]         1                   1                   6
 [7,]         1                   1                   7
 [8,]         1                   1                   8
 [9,]         1                   1                   9
[10,]         1                   1                  10
[11,]         2                   2                   1
[12,]         2                   2                   2
[13,]         2                   2                   3
[14,]         2                   2                   4
[15,]         2                   2                   5
[16,]         2                   2                   6
[17,]         2                   2                   7
[18,]         2                   2                   8
[19,]         2                   2                   9
[20,]         2                   2                  10
> foo$data[studyDbId==3177 & observations.observationVariableName == "PH_M_cm", .(replicate, positionCoordinateX, positionCoordinateY)] %>% as.matrix() %>% rankMatrix()
[1] 2
attr(,"method")
[1] "tolNorm2"
attr(,"useGrad")
[1] FALSE
attr(,"tol")
[1] 4.440892e-15
> foo$data[studyDbId==3176 & observations.observationVariableName == "PH_M_cm", .(replicate, positionCoordinateX, positionCoordinateY)] %>% as.matrix() %>% rankMatrix()
[1] 3
attr(,"method")
[1] "tolNorm2"
attr(,"useGrad")
[1] FALSE
attr(,"tol")
[1] 4.440892e-15
> foo$data[studyDbId==3175 & observations.observationVariableName == "PH_M_cm", .(replicate, positionCoordinateX, positionCoordinateY)] %>% as.matrix() %>% rankMatrix()
[1] 3
attr(,"method")
[1] "tolNorm2"
attr(,"useGrad")
[1] FALSE
attr(,"tol")
[1] 4.440892e-15

IntegratedBreedingPlatform / ShinyBrAPPs

STA :: Can't fit RCBD with SpATS #6