any(phi >= : missing value where TRUE/FALSE needed

[jvhagey]

Hi @bryandmartin,

I have 4 animals that were sampled different ways on 3 different days. I want to know how the sample types differ. My data for one animal looks like this:

     AnimalID       Sample_Type    Day
1  Animal_2549             Feces  Day_7
2  Animal_2549             Feces  Day_9
3  Animal_2549             Feces Day_11
4  Animal_2549       Grab Sample  Day_7
5  Animal_2549       Grab Sample  Day_9
6  Animal_2549       Grab Sample Day_11
7  Animal_2549   Liquid Strained  Day_7
8  Animal_2549   Liquid Strained  Day_9
9  Animal_2549   Liquid Strained Day_11
10 Animal_2549 Liquid Unstrained Day_11
11 Animal_2549 Liquid Unstrained  Day_9
12 Animal_2549             Solid  Day_7
13 Animal_2549             Solid  Day_9
14 Animal_2549             Solid Day_11
15 Animal_2549      Stomach Tube  Day_9
16 Animal_2549      Stomach Tube Day_11
17 Animal_2549      Stomach Tube  Day_7

I am running the following command to look for deferentially abundant taxa in sample types while controlling for the effects of day and animal sampled.

ps51719 <- readRDS("ps_51719.rds")
set.seed(1)
fullAnalysis_060319 <- differentialTest(formula = ~ Sample_Type + AnimalID + Day, phi.formula = ~ 1,formula_null = ~ AnimalID + Day, phi.formula_null = ~ 1, test="Wald",boot=TRUE, data = ps51719, fdr_cutoff = 0.05)

This produces the following error. Although, I still got a list of significant_taxa so it seems as though it didn't stop differentialTest from running.

Error in if (is.nan(val) || any(phi <= sqrt(.Machine$double.eps)) || any(phi >=  : 
  missing value where TRUE/FALSE needed

Have you seen this error? Do I have to have something in the phi.formula is that why its giving the error? I believe the error started after I set boot=TRUE, but have't been able to track down the line that is causing the problem. Thanks for your help!

I am using the following versions:

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS:   /afs/genomecenter.ucdavis.edu/software/R/3.6.0/lssc0-linux/lib/R/lib/libRblas.so
LAPACK: /afs/genomecenter.ucdavis.edu/software/R/3.6.0/lssc0-linux/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US
 [4] LC_COLLATE=en_US     LC_MONETARY=en_US    LC_MESSAGES=en_US
 [7] LC_PAPER=en_US       LC_NAME=C            LC_ADDRESS=C
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_US LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] corncob_0.1.0   phyloseq_1.24.2

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5      reshape2_1.4.3        purrr_0.3.2
 [4] splines_3.6.0         lattice_0.20-38       rhdf5_2.24.0
 [7] colorspace_1.3-2      stats4_3.6.0          enrichwith_0.2
[10] mgcv_1.8-28           survival_2.44-1.1     rlang_0.3.4
[13] pillar_1.4.0          glue_1.3.1            BiocGenerics_0.26.0
[16] bindrcpp_0.2.2        trust_0.1-7           foreach_1.4.4
[19] plyr_1.8.4            bindr_0.1.1           stringr_1.4.0
[22] zlibbioc_1.26.0       Biostrings_2.48.0     munsell_0.5.0
[25] gtable_0.3.0          VGAM_1.1-1            lpSolveAPI_5.5.2.0-17
[28] codetools_0.2-16      Biobase_2.40.0        permute_0.9-4
[31] IRanges_2.14.12       biomformat_1.8.0      parallel_3.6.0
[34] Rcpp_1.0.1            scales_1.0.0          vegan_2.5-2
[37] S4Vectors_0.18.3      jsonlite_1.6          XVector_0.20.0
[40] ggplot2_3.1.1         stringi_1.4.3         dplyr_0.7.6
[43] numDeriv_2016.8-1     grid_3.6.0            ade4_1.7-13
[46] tools_3.6.0           magrittr_1.5          lazyeval_0.2.2
[49] tibble_2.1.1          cluster_2.0.8         crayon_1.3.4
[52] ape_5.1               pkgconfig_2.0.2       MASS_7.3-51.4
[55] Matrix_1.2-17         data.table_1.11.6     assertthat_0.2.1
[58] brglm2_0.5.1          iterators_1.0.10      Rhdf5lib_1.2.1
[61] R6_2.4.0              multtest_2.36.0       nnet_7.3-12
[64] igraph_1.2.2          nlme_3.1-127          compiler_3.6.0

[bryandmartin]

Hi @jvhagey ,

Something appears to be happening with the initializations here. Would you try setting inits and inits_null and let me know if the problem persists?

Thanks,
Bryan