I’m trying to save the output from tmp <- pairs(my_stanfit)
, however, when I do the plot is drawn to my screen and tmp
remains NULL
. What am I missing?
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Type 'q()' to quit R.
> sessionInfo()
R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 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
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.2.2
> library(rstan, verbose = TRUE)
Loading required package: StanHeaders
rstan version 2.26.13 (Stan version 2.26.1)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
For within-chain threading using `reduce_sum()` or `map_rect()` Stan functions,
change `threads_per_chain` option:
rstan_options(threads_per_chain = 1)
Warning message:
In find.package(package, lib.loc, quiet = TRUE, verbose = verbose) :
package ‘rstan’ found more than once, using the first from
“/usr/local/lib/R/site-library/rstan”,
“/usr/lib/R/site-library/rstan”
> sessionInfo()
R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 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
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rstan_2.26.13 StanHeaders_2.26.13
loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 compiler_4.2.2 pillar_1.8.1 prettyunits_1.1.1
[5] pkgbuild_1.3.1 jsonlite_1.8.3 lifecycle_1.0.3 tibble_3.1.8
[9] gtable_0.3.1 pkgconfig_2.0.3 rlang_1.0.6 DBI_1.1.3
[13] cli_3.4.1 parallel_4.2.2 curl_4.3.3 loo_2.5.1
[17] gridExtra_2.3 dplyr_1.0.99.9000 generics_0.1.3 vctrs_0.5.0
[21] stats4_4.2.2 grid_4.2.2 tidyselect_1.2.0 glue_1.6.2
[25] inline_0.3.19 R6_2.5.1 processx_3.8.0 fansi_1.0.3
[29] ggplot2_3.4.0 callr_3.7.3 magrittr_2.0.3 codetools_0.2-18
[33] matrixStats_0.62.0 scales_1.2.1 ps_1.7.2 colorspace_2.0-3
[37] V8_4.2.1 utf8_1.2.2 RcppParallel_5.1.5 munsell_0.5.0
[41] crayon_1.5.2
> example(read_stan_csv)
rd_st_> csvfiles <- dir(system.file('misc', package = 'rstan'),
rd_st_+ pattern = 'rstan_doc_ex_[0-9].csv', full.names = TRUE)
rd_st_> fit <- read_stan_csv(csvfiles)
> tmp <- pairs(fit, pars = c("mu", "sigma", "alpha", "lp__"), log = TRUE, las = 1)
Warning messages:
1: In par(usr) : argument 1 does not name a graphical parameter
2: In par(usr) : argument 1 does not name a graphical parameter
3: In par(usr) : argument 1 does not name a graphical parameter
4: In par(usr) : argument 1 does not name a graphical parameter
> tmp
NULL
>
Extra question: why do I get the warnings about par(usr)
?