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License: Other
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infoCriteria with multiple models
It would be nice if this function would accept multiple objects, similar to the AIC function. For example:
R> AIC(mm1,mm2)
df AIC
mm1 3 46708.52
mm2 4 46654.05
asremlPlus stack usage error
Is this related to asremlPlus?
"
current.asr <- lm
current.asrt <- as.asrtests(current.asr,NULL,NULL)
Error: C stack usage 15922800 is too close to the limit
"
Appreciate feedback.
Thanky you.
jahn
issue infoCriteria
Hello,
it seems that the function infoCriteria from asremlPlus is not compatible with the new asreml package (4.2.0.257).
I get this error:
infoCriteria(mget(model_objects), IClikelihood = "full")
Error: 'vpc.char' is not an exported object from 'namespace:asreml'
Is it possible to solve this issue?
Regards,
Dianne
The argument transform.function in predictPlus seems to not backtransform the predictions
I'm not sure if this is a bug or if I'm making some silly mistake, but seems the argument transform.function in predictPlus is not backtransforming the predictions.
Here is a quick example:
library(asreml)
library(asremlPlus)
# fit a model
mod <- asreml(Yield ~ Variety, data = Oats.dat)
pred <- predictPlus(mod, classify = 'Variety')$predictions
# fit a model but with a transformed target
mod_trans <- asreml(sqrt(Yield) ~ Variety, data = Oats.dat)
pred_trans <- predictPlus(mod, classify = 'Variety', transform.function = 'sqrt')$backtransforms
pred == pred_trans
Variety predicted.value standard.error upper.Confidence.limit lower.Confidence.limit est.status
1 TRUE TRUE NA TRUE TRUE TRUE
2 TRUE TRUE NA TRUE TRUE TRUE
3 TRUE TRUE NA TRUE TRUE TRUE
As you can see, the backtransforms object is equal to the predictions (except for the standard.error column that was set to NA).
My session info:
sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: America/Chicago
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] asremlPlus_4.3.55 asreml_4.1.0.176 Matrix_1.6-0
loaded via a namespace (and not attached):
[1] utf8_1.2.3 generics_0.1.3 qqconf_1.3.2 robustbase_0.99-0 bitops_1.0-7 stringi_1.7.12 lattice_0.21-8 pracma_2.4.2
[9] magrittr_2.0.3 caTools_1.18.2 grid_4.3.1 RColorBrewer_1.1-3 iterators_1.0.14 foreach_1.5.2 doParallel_1.0.17 plyr_1.8.8
[17] jsonlite_1.8.7 opdisDownsampling_0.8.2 httr_1.4.6 fansi_1.0.4 scales_1.2.1 codetools_0.2-19 cli_3.6.1 rlang_1.1.1
[25] munsell_0.5.0 tools_4.3.1 parallel_4.3.1 reshape2_1.4.4 memuse_4.2-3 dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2
[33] dae_3.2.15 benchmarkme_1.0.8 vctrs_0.6.3 R6_2.5.1 lifecycle_1.0.3 stringr_1.5.0 MASS_7.3-60 pkgconfig_2.0.3
[41] pillar_1.9.0 gtable_0.3.3 data.table_1.14.8 glue_1.6.2 sticky_0.5.6.1 Rcpp_1.0.11 benchmarkmeData_1.0.4 DEoptimR_1.1-0
[49] tibble_3.2.1 tidyselect_1.2.0 rstudioapi_0.15.0 qqplotr_0.0.6 compiler_4.3.1 twosamples_2.0.1
C stack usage
Is this related to asremlPlus?
"
current.asr <- lm
current.asrt <- as.asrtests(current.asr,NULL,NULL)
Error: C stack usage 15922800 is too close to the limit
"
Appreciate feedback.
Thanky you.
jahn
estimateV problem with corh variance model
Hi, when trying to use the estimateV.asreml function on a model object I get an error message that Z %*% G are not comformable. Manual says estimate.V can handle cor/corh variance functions - any idea about a workaround?
My model is a fairly simple one:
asreml(myformula, random = ~box+corh(HEXP):boxor, data = myset, maxiter = 200)
(I simplified it from a more complex one with corgh() and some correlations constrained using the vcc option - thought it might be the fault of vcc but the simpler one also does not seem to work).
Any feedback appreciated!
Szymek
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