To recreate - just knit z.Rmd Session Info below... R version 3.3.2 (2016-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS
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
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] MASS_7.3-45 reshape2_1.4.2 geiger_2.0.6 sjmisc_2.2.1 sjPlot_2.2.0 gridExtra_2.2.1 picante_1.6-2 nlme_3.1-128 vegan_2.4-1
[10] lattice_0.20-34 permute_0.9-4 ape_4.0 ggplot2_2.2.1
loaded via a namespace (and not attached):
[1] tidyr_0.6.0 splines_3.3.2 merTools_0.3.0 modelr_0.1.0 shiny_0.14.2 assertthat_0.1 stats4_3.3.2 coin_1.1-3
[9] yaml_2.1.14 backports_1.0.4 quantreg_5.29 digest_0.6.11 RColorBrewer_1.1-2 minqa_1.2.4 colorspace_1.3-2 sandwich_2.3-4
[17] htmltools_0.3.5 httpuv_1.3.3 Matrix_1.2-7.1 plyr_1.8.4 psych_1.6.12 broom_0.4.1 SparseM_1.74 haven_1.0.0
[25] purrr_0.2.2 xtable_1.8-2 mvtnorm_1.0-5 scales_0.4.1 stringdist_0.9.4.4 MatrixModels_0.4-1 lme4_1.1-12 arm_1.9-3
[33] tibble_1.2 effects_3.1-2 mgcv_1.8-16 DT_0.2 TH.data_1.0-7 nnet_7.3-12 lazyeval_0.2.0 mnormt_1.5-5
[41] survival_2.40-1 magrittr_1.5 mime_0.5 evaluate_0.10 foreign_0.8-67 tools_3.3.2 multcomp_1.4-6 stringr_1.1.0
[49] munsell_0.4.3 cluster_2.0.5 blme_1.0-4 nloptr_1.0.4 subplex_1.2-2 htmlwidgets_0.8 labeling_0.3 rmarkdown_1.3
[57] gtable_0.2.0 codetools_0.2-15 deSolve_1.14 abind_1.4-5 sjstats_0.7.1 DBI_0.5-1 R6_2.2.0 zoo_1.7-14
[65] knitr_1.15.1 dplyr_0.5.0 rprojroot_1.1 modeltools_0.2-21 stringi_1.1.2 parallel_3.3.2 Rcpp_0.12.8 coda_0.19-1
[73] lmtest_0.9-34