matthewwolak / nadiv Goto Github PK
View Code? Open in Web Editor NEWR package that constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model').
R package that constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model').
Using this lib via OptiSel
Upgrading to 2.17.0 gives this warning loading the Pedigree
Warning messages:
1: In nPed_fixed[] <- numPed(ped_fixed_ord, check = FALSE) :
number of items to replace is not a multiple of replacement length
2: In nPed_fixed[] <- numPed(ped_fixed_ord, check = FALSE) :
number of items to replace is not a multiple of replacement length
Clang throws a warning here:
Line 276 in 71a843a
-=
in order to iterate through j
properly.
In looking for that I also came across this other =-
:
Line 226 in 71a843a
@lmmazur @esscargot
Sometimes the ASReml-R package (asreml
) produces positive log-likelihoods. How should these be handled particularly when doing anything based on the log-likelihood ratio tests (e.g., LRTest()
, proLik()
, and constrainFun()
)?
The assumption normally is that the log-likelihood values are negative. Then the model with the greater log-likelihood (closer to zero) has a better fit to the data.
@matthewwolak needs to construct a reproducible example and then fix the functions
Hi, I am fairly new to R. I am using your alfalfa dataset to learn about computing heritability. I got this error, could you please tell me why I am getting this error and how to fix this. Thank you.
H2 <- nadiv:::pin(model1, tmp ~ V1 / (V1 + V2))
Error in names(pframe) <- paste("V", seq(1, length(pframe)), sep = "") :
'names' attribute [2] must be the same length as the vector [0]
With the update of the Matrix package, I need to ensure that slot @Dimnames for 'Matrix' objects consist of character vectors. Issue is explained in an e-mail to [email protected] from Martin Maechler 05/30/2015.
Additionally, assign the list for slot @Dimnames using the 'dimnames' argument to Matrix() or sparseMatrix() instead of @Dimnames.
constrainFun.R, proLik.R and plot.proLik.R all need to be checked so that consistency of calculations from log-likelihood ratio tests is upheld when log-likelihoods are both negative as well as both positive.
May require some idiosyncracies with asreml-R
plot.proLik.R currently does not display a red line for the 1-alpha CI, because the sign of output from pchisq() does not match the sign of the outcome of the LRT. Reproducible example is in the plot.proLik.Rd examples!
Hello,
I have been trying to run prepPed with my pedigree
ped <- prepPed(am_pedigree_red)
and I get this error:
Error in numPed(ped_fixed_ord[, 1:3]) :
Offspring appearing before their dams: first use the 'prepPed' function
The pedigree is formed by 3 columns ID, Dam and Sire, and I've checked that all the ones in the columns Dam and Sire are also in the column ID. Plus I thought the prepPed function was made for taking care of this.
What could cause the problem?
Thank you very much!
Best wishes,
Giulia Masoero
Hi Matthew,
I am a very happy user of nadiv
, but running into some mysterious issues. After updating some packages, my workstation install of nadiv
creates obviously incorrect A matrices. E.g.:
> makeA(Mrode2)
6 x 6 sparse Matrix of class "dsCMatrix"
1 2 3 4 5 6
1 1.8125000 0.5312500 0.5745243 0.7036456 0.4419417 0.1711633
2 0.5312500 1.7031250 0.5524272 0.2435696 0.3977476 0.4279082
3 0.5745243 0.5524272 0.6562500 0.1913664 0.3125000 0.1210307
4 0.7036456 0.2435696 0.1913664 0.9843750 0.3827328 0.1482318
5 0.4419417 0.3977476 0.3125000 0.3827328 0.6250000 0.2420615
6 0.1711633 0.4279082 0.1210307 0.1482318 0.2420615 0.4687500
(In my own data, full siblings have relatedness coefficients of 0.)
Compare with a version running on our cluster:
> makeA(Mrode2)
6 x 6 sparse Matrix of class "dsCMatrix"
1 2 3 4 5 6
1 1.00 . 0.5000 0.5000 0.5000 0.2500
2 . 1.000 0.5000 . 0.2500 0.6250
3 0.50 0.500 1.0000 0.2500 0.6250 0.5625
4 0.50 . 0.2500 1.0000 0.6250 0.3125
5 0.50 0.250 0.6250 0.6250 1.1250 0.6875
6 0.25 0.625 0.5625 0.3125 0.6875 1.1250
Both machines are running nadiv_2.17.2
. However my workstation is using Matrix_1.6-1
, while the cluster uses Matrix_1.5-3
. Could that be the issue?
Any help much appreciated!
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