search

marissalee / tutorials_communityAnalyses

Collection of tutorials to analyze community data in R
6 stars 1 forks source link

boral_withOTUs.R not running on Lab computer #1

Open marissalee opened 6 years ago

marissalee commented 6 years ago

Maybe this is a package version issue?

On the lab Windows 10 computer... R version 3.3.2 tidyr_0.6.0 dplyr_0.5.0 boral_1.5 coda_0.19-1 R2jags_0.5-7 R2WinBUGS_2.1-21 rjags_4-6 fishMod_0.29 mvtnorm_1.0-5

marissalee commented 6 years ago

This is what is working...

R version 3.3.2 (2016-10-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS 10.13.2

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages: [1] bindrcpp_0.2 circlize_0.4.1 ggplot2_2.2.1 tidyr_0.7.0 dplyr_0.7.2 boral_1.3.1 coda_0.19-1

loaded via a namespace (and not attached): [1] Rcpp_0.12.12 bindr_0.1 magrittr_1.5 MASS_7.3-47 R2jags_0.5-7 munsell_0.4.3 colorspace_1.3-2
[8] lattice_0.20-35 R6_2.2.2 rlang_0.1.2 plyr_1.8.4 tools_3.3.2 parallel_3.3.2 grid_3.3.2
[15] gtable_0.2.0 R2WinBUGS_2.1-21 lazyeval_0.2.0 abind_1.4-5 yaml_2.1.14 assertthat_0.2.0 tibble_1.3.3
[22] purrr_0.2.3 GlobalOptions_0.0.12 shape_1.4.3 glue_1.1.1 rjags_4-6 scales_0.4.1 boot_1.3-20
[29] fishMod_0.29 mvtnorm_1.0-6 pkgconfig_2.0.1

marissalee commented 6 years ago

Try changing lab computer... tidyr_0.7.0 dplyr_0.7.2 boral_1.3.1 mvtnorm_1.0-6 ... Ok - I tried to changed the install version (https://support.rstudio.com/hc/en-us/articles/219949047-Installing-older-versions-of-packages), but it didn't work

marissalee commented 6 years ago

8d4425ad9467a6842180dad5cf66fd3cfdfd9cf0

uses matrix() to turn the rowEffs dataframe into a matrix structure that seems to work why is matrix(...) different from as.matrix(rowEffs)... I don't really know.