If somebody reads this topic and his/her models do not run, causing R to crash, this thread provides a solution: Stan_surv crashes R repeatedly - #13 by binman
Everything is up-to-date, rstan models and non-survival models of rstanarm run; however, survival functionality of rstanarm is not working. Trying to to run a rstanarm survival model causes R to crash. Haven’t figure it out after 6 hours of trying.
Here’s what I did:
Reinstalled rstan according to the guidelines
https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started
Sample model runs well.
Installed the developer version:
install.packages("rstanarm", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
Installing package into ‘C:/Users/user/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
trying URL ‘https://mc-stan.org/r-packages/bin/windows/contrib/4.0/rstanarm_2.21.2.zip’
Content type ‘application/zip’ length 12617689 bytes (12.0 MB)
downloaded 12.0 MB
package ‘rstanarm’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
- C:\Users\Public\Documents\Wondershare\CreatorTemp\RtmpQ55DeO\downloaded_packages*
>
Loading the package
library(rstanarm)
Loading required package: Rcpp
Registered S3 method overwritten by ‘htmlwidgets’:
- method from *
- print.htmlwidget tools:rstudio*
This is rstanarm version 2.21.2
- See Prior Distributions for rstanarm Models • rstanarm for changes to default priors!
- Default priors may change, so it’s safest to specify priors, even if equivalent to the defaults.
- For execution on a local, multicore CPU with excess RAM we recommend calling - options(mc.cores = parallel::detectCores())*
Trying to find stan_surv function
?stan_surv
No documentation for ‘stan_surv’ in specified packages and libraries:
you could try ‘??stan_surv’
However, I tried to run a stan_glm() model and it worked well.
Testing a survival model
#simulating data
library(simsurv)
set.seed(999111)
N <- 500
covs <- data.frame(id = 1:N,
trt = rbinom(N, 1L, 0.5))
dat = simsurv(dist = "weibull",
lambdas = 0.1,
gammas = 1.5,
betas = c(trt = -0.5),
tde = c(trt = 0.2),
x = covs,
maxt = 5)
dat = merge(dat, covs)
head(dat)
#model
mod3 <- stan_surv(
formula = Surv(eventtime, status) ~ tve(trt, degree = 0, knots = 4),
data = dat,
basehaz = "weibull",
chains = 3,
cores = 3,
seed = 1,
iter = 1000)
Rstudio log file: https://www.dropbox.com/s/pcocm29lr559jz5/rsession-user.log?dl=1
R.Version()
$platform
[1] “x86_64-w64-mingw32”
$arch
[1] “x86_64”
$os
[1] “mingw32”
$system
[1] “x86_64, mingw32”
$status
[1] “”
$major
[1] “4”
$minor
[1] “0.4”
$year
[1] “2021”
$month
[1] “02”
day
[1] "15"
svn rev
[1] “80002”
$language
[1] “R”
$version.string
[1] “R version 4.0.4 (2021-02-15)”
$nickname
[1] “Lost Library Book”
PC configuration
Intel(R) Core™ i5-8250U CPU @ 1.60GHz 1.80 GHz, 16GB of RAM, 64-bit OS, SSD HDD, Windows 10 Enterprise 20H2
session_info(pkgs = NULL, include_base = FALSE)
Packages ------------------------------------------------------------
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.4)
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.3)
bayesplot 1.8.0 2021-01-10 [1] CRAN (R 4.0.4)
boot 1.3-27 2021-02-12 [1] CRAN (R 4.0.4)
cachem 1.0.4 2021-02-13 [1] CRAN (R 4.0.4)
callr 3.5.1 2020-10-13 [1] CRAN (R 4.0.4)
cli 2.3.1 2021-02-23 [1] CRAN (R 4.0.4)
codetools 0.2-18 2020-11-04 [2] CRAN (R 4.0.4)
colorspace 2.0-0 2020-11-11 [1] CRAN (R 4.0.4)
colourpicker 1.1.0 2020-09-14 [1] CRAN (R 4.0.4)
crayon 1.4.1 2021-02-08 [1] CRAN (R 4.0.4)
crosstalk 1.1.1 2021-01-12 [1] CRAN (R 4.0.4)
curl 4.3 2019-12-02 [1] CRAN (R 4.0.4)
DBI 1.1.1 2021-01-15 [1] CRAN (R 4.0.4)
desc 1.3.0 2021-03-05 [1] CRAN (R 4.0.4)
devtools * 2.3.2 2020-09-18 [1] CRAN (R 4.0.4)
digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.4)
dplyr 1.0.5 2021-03-05 [1] CRAN (R 4.0.4)
DT 0.17 2021-01-06 [1] CRAN (R 4.0.4)
dygraphs 1.1.1.6 2018-07-11 [1] CRAN (R 4.0.4)
evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.4)
fansi 0.4.2 2021-01-15 [1] CRAN (R 4.0.4)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.0.4)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.4)
generics 0.1.0 2020-10-31 [1] CRAN (R 4.0.4)
ggplot2 3.3.3 2020-12-30 [1] CRAN (R 4.0.4)
ggridges 0.5.3 2021-01-08 [1] CRAN (R 4.0.4)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.4)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.4)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.4)
gtools 3.8.2 2020-03-31 [1] CRAN (R 4.0.3)
htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.0.4)
htmlwidgets 1.5.3 2020-12-10 [1] CRAN (R 4.0.4)
httpuv 1.5.5 2021-01-13 [1] CRAN (R 4.0.4)
igraph 1.2.6 2020-10-06 [1] CRAN (R 4.0.4)
inline 0.3.17 2020-12-01 [1] CRAN (R 4.0.4)
jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.0.4)
knitr 1.31 2021-01-27 [1] CRAN (R 4.0.4)
later 1.1.0.1 2020-06-05 [1] CRAN (R 4.0.4)
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.4)
lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.4)
lme4 1.1-26 2020-12-01 [1] CRAN (R 4.0.4)
loo 2.4.1 2020-12-09 [1] CRAN (R 4.0.4)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.4)
markdown 1.1 2019-08-07 [1] CRAN (R 4.0.4)
MASS 7.3-53.1 2021-02-12 [1] CRAN (R 4.0.4)
Matrix 1.3-2 2021-01-06 [1] CRAN (R 4.0.4)
matrixStats 0.58.0 2021-01-29 [1] CRAN (R 4.0.4)
mime 0.10 2021-02-13 [1] CRAN (R 4.0.4)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.0.4)
minqa 1.2.4 2014-10-09 [1] CRAN (R 4.0.4)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.4)
nlme 3.1-152 2021-02-04 [1] CRAN (R 4.0.4)
nloptr 1.2.2.2 2020-07-02 [1] CRAN (R 4.0.4)
pillar 1.5.1 2021-03-05 [1] CRAN (R 4.0.4)
pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.0.4)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.4)
pkgload 1.2.0 2021-02-23 [1] CRAN (R 4.0.4)
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.4)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.4)
processx 3.4.5 2020-11-30 [1] CRAN (R 4.0.4)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.0.4)
ps 1.6.0 2021-02-28 [1] CRAN (R 4.0.4)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.4)
R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.4)
Rcpp * 1.0.6 2021-01-15 [1] CRAN (R 4.0.4)
RcppParallel 5.0.3 2021-02-24 [1] CRAN (R 4.0.4)
remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.4)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.0.4)
rlang 0.4.10 2020-12-30 [1] CRAN (R 4.0.4)
rmarkdown 2.7 2021-02-19 [1] CRAN (R 4.0.4)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.4)
rsconnect 0.8.16 2019-12-13 [1] CRAN (R 4.0.4)
rstan 2.21.2 2020-07-27 [1] CRAN (R 4.0.4)
rstanarm * 2.21.2 2020-08-31 [1] local
rstantools 2.1.1 2020-07-06 [1] CRAN (R 4.0.4)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.4)
shiny 1.6.0 2021-01-25 [1] CRAN (R 4.0.4)
shinyjs 2.0.0 2020-09-09 [1] CRAN (R 4.0.4)
shinystan 2.5.0 2018-05-01 [1] CRAN (R 4.0.4)
shinythemes 1.2.0 2021-01-25 [1] CRAN (R 4.0.4)
splines2 0.4.2 2021-02-21 [1] CRAN (R 4.0.4)
StanHeaders 2.21.0-7 2020-12-17 [1] CRAN (R 4.0.4)
statmod 1.4.35 2020-10-19 [1] CRAN (R 4.0.4)
stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.3)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.4)
survival 3.2-10 2021-03-16 [1] CRAN (R 4.0.4)
testthat 3.0.2 2021-02-14 [1] CRAN (R 4.0.4)
threejs 0.3.3 2020-01-21 [1] CRAN (R 4.0.4)
tibble 3.1.0 2021-02-25 [1] CRAN (R 4.0.4)
tidyr 1.1.3 2021-03-03 [1] CRAN (R 4.0.4)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.4)
usethis * 2.0.1 2021-02-10 [1] CRAN (R 4.0.4)
utf8 1.2.1 2021-03-12 [1] CRAN (R 4.0.4)
V8 3.4.0 2020-11-04 [1] CRAN (R 4.0.4)
vctrs 0.3.6 2020-12-17 [1] CRAN (R 4.0.4)
withr 2.4.1 2021-01-26 [1] CRAN (R 4.0.4)
xfun 0.22 2021-03-11 [1] CRAN (R 4.0.4)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.4)
xts 0.12.1 2020-09-09 [1] CRAN (R 4.0.4)
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.3)
zoo 1.8-9 2021-03-09 [1] CRAN (R 4.0.4)
Makevars.win
CXX14FLAGS += -mtune=native -O3 -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2
Makewars.win.bak includes
CXX14FLAGS=-O3 -mtune=native
CXX11FLAGS=-O3 -mtune=native