I think this was pointed out in #585 but I'm not sure if this is expected
pre/post MCMC strangeness?
library(greta)
#>
#> Attaching package: 'greta'
#> The following objects are masked from 'package:stats':
#>
#> binomial, cov2cor, poisson
#> The following objects are masked from 'package:base':
#>
#> %*%, apply, backsolve, beta, chol2inv, colMeans, colSums, diag,
#> eigen, forwardsolve, gamma, identity, rowMeans, rowSums, sweep,
#> tapply
It seems strange that this pre_mcmc and post_mcmc are the same code:
calculate(x, nsim = 1) but depending on whether they are run pre or
post MCMC makes them give different results?
x <- wishart(df = 4, Sigma = diag(3))
#> ℹ Initialising python and checking dependencies, this may take a moment.
#> ✔ Initialising python and checking dependencies ... done!
#>
x
#> greta array (operation following a wishart distribution)
#>
#> [,1] [,2] [,3]
#> [1,] ? ? ?
#> [2,] ? ? ?
#> [3,] ? ? ?
pre_mcmc <- calculate(x, nsim = 1)
m <- model(x)
draws <- mcmc(m, warmup = 1, n_samples = 1)
#> running 4 chains simultaneously on up to 8 CPU cores
#>
#> warmup 0/1 | eta: ?s sampling 0/1 | eta: ?s
now the matrix which should be symmetric looks like a cholesky factor (but
lower triangular, when it should be upper triangular), and cholesky factor
is still coming out as ones
I think this was pointed out in #585 but I'm not sure if this is expected
pre/post MCMC strangeness?
It seems strange that this
pre_mcmcandpost_mcmcare the same code:calculate(x, nsim = 1)but depending on whether they are run pre or post MCMC makes them give different results?now the matrix which should be symmetric looks like a cholesky factor (but lower triangular, when it should be upper triangular), and cholesky factor is still coming out as ones
Created on 2024-05-10 with reprex v2.1.0
Session info
``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.3.3 (2024-02-29) #> os macOS Sonoma 14.3.1 #> system aarch64, darwin20 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 #> tz Australia/Brisbane #> date 2024-05-10 #> pandoc 3.1.13 @ /opt/homebrew/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> abind 1.4-5 2016-07-21 [1] CRAN (R 4.3.0) #> backports 1.4.1 2021-12-13 [1] CRAN (R 4.3.0) #> base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.3.0) #> callr 3.7.6 2024-03-25 [1] CRAN (R 4.3.1) #> cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.1) #> coda 0.19-4.1 2024-01-31 [2] CRAN (R 4.3.1) #> codetools 0.2-20 2024-03-31 [2] CRAN (R 4.3.1) #> crayon 1.5.2 2022-09-29 [1] CRAN (R 4.3.0) #> digest 0.6.35 2024-03-11 [1] CRAN (R 4.3.1) #> evaluate 0.23 2023-11-01 [1] CRAN (R 4.3.1) #> fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0) #> fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.0) #> future 1.33.2 2024-03-26 [1] CRAN (R 4.3.1) #> globals 0.16.3 2024-03-08 [1] CRAN (R 4.3.1) #> glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.1) #> greta * 0.4.5.9000 2024-05-10 [1] local #> hms 1.1.3 2023-03-21 [1] CRAN (R 4.3.0) #> htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.3.1) #> jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.3.1) #> knitr 1.45 2023-10-30 [1] CRAN (R 4.3.1) #> lattice 0.22-6 2024-03-20 [1] CRAN (R 4.3.1) #> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.1) #> listenv 0.9.1 2024-01-29 [2] CRAN (R 4.3.1) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0) #> Matrix 1.6-5 2024-01-11 [1] CRAN (R 4.3.1) #> parallelly 1.37.1 2024-02-29 [1] CRAN (R 4.3.1) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0) #> png 0.1-8 2022-11-29 [1] CRAN (R 4.3.0) #> prettyunits 1.2.0 2023-09-24 [1] CRAN (R 4.3.1) #> processx 3.8.4 2024-03-16 [1] CRAN (R 4.3.1) #> progress 1.2.3 2023-12-06 [1] CRAN (R 4.3.1) #> ps 1.7.6 2024-01-18 [1] CRAN (R 4.3.1) #> purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.0) #> R.cache 0.16.0 2022-07-21 [2] CRAN (R 4.3.0) #> R.methodsS3 1.8.2 2022-06-13 [2] CRAN (R 4.3.0) #> R.oo 1.26.0 2024-01-24 [2] CRAN (R 4.3.1) #> R.utils 2.12.3 2023-11-18 [2] CRAN (R 4.3.1) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.0) #> Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.3.1) #> reprex 2.1.0 2024-01-11 [2] CRAN (R 4.3.1) #> reticulate 1.36.1 2024-04-22 [1] CRAN (R 4.3.1) #> rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.1) #> rmarkdown 2.26 2024-03-05 [1] CRAN (R 4.3.1) #> rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.3.1) #> sessioninfo 1.2.2 2021-12-06 [2] CRAN (R 4.3.0) #> styler 1.10.3 2024-04-07 [2] CRAN (R 4.3.1) #> tensorflow 2.16.0 2024-04-15 [2] CRAN (R 4.3.1) #> tfautograph 0.3.2 2021-09-17 [2] CRAN (R 4.3.0) #> tfruns 1.5.3 2024-04-19 [1] CRAN (R 4.3.1) #> vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.1) #> whisker 0.4.1 2022-12-05 [1] CRAN (R 4.3.0) #> withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.1) #> xfun 0.43 2024-03-25 [1] CRAN (R 4.3.1) #> yaml 2.3.8 2023-12-11 [1] CRAN (R 4.3.1) #> #> [1] /Users/nick/Library/R/arm64/4.3/library #> [2] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library #> #> ─ Python configuration ─────────────────────────────────────────────────────── #> python: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/bin/python #> libpython: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/libpython3.11.dylib #> pythonhome: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2:/Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2 #> version: 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:34:54) [Clang 16.0.6 ] #> numpy: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/python3.11/site-packages/numpy #> numpy_version: 1.26.4 #> tensorflow: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/python3.11/site-packages/tensorflow #> #> NOTE: Python version was forced by use_python() function #> #> ────────────────────────────────────────────────────────────────────────────── ```