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simple and scalable statistical modelling in R
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Calculate fails with TF2 #548

Closed njtierney closed 2 years ago

njtierney commented 2 years ago

Running TF2 branch of greta, we get the following error with calculate

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
greta_sitrep()
#> ℹ checking if python available
#> ✔ python (v3.8) available
#> 
#> ℹ checking if TensorFlow available
#> ✔ TensorFlow (v2.9.2) available
#> 
#> ℹ checking if TensorFlow Probability available
#> ✔ TensorFlow Probability (v0.17.0) available
#> 
#> ℹ checking if greta conda environment available
#> ✔ greta conda environment available
#> 
#> ℹ Initialising python and checking dependencies, this may take a moment.
#> ✔ Initialising python and checking dependencies ... done!
#> 
#> ℹ greta is ready to use!
x <- normal(0, 1, dim = 3)
a <- lognormal(0, 1)
y <- sum(x^2) + a
calculate(y,
          values = list(x = c(0.1, 0.2, 0.3), a = 2))
#> Loaded Tensorflow version 2.9.2
#> Error in py_call_impl(callable, dots$args, dots$keywords): ValueError: Attempt to convert a value (None) with an unsupported type (<class 'NoneType'>) to a Tensor.

Created on 2022-08-10 by the reprex package (v2.0.1)

Session info ``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.2.0 (2022-04-22) #> os macOS Monterey 12.3.1 #> system aarch64, darwin20 #> ui X11 #> language (EN) #> collate en_AU.UTF-8 #> ctype en_AU.UTF-8 #> tz Australia/Perth #> date 2022-08-10 #> pandoc 2.18 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0) #> base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.2.0) #> callr 3.7.0 2021-04-20 [1] CRAN (R 4.2.0) #> cli 3.3.0.9000 2022-06-15 [1] Github (r-lib/cli@31a5db5) #> coda 0.19-4 2020-09-30 [1] CRAN (R 4.2.0) #> codetools 0.2-18 2020-11-04 [1] CRAN (R 4.2.0) #> crayon 1.5.1 2022-03-26 [1] CRAN (R 4.2.0) #> digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.0) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0) #> evaluate 0.15 2022-02-18 [1] CRAN (R 4.2.0) #> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0) #> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0) #> future 1.25.0 2022-04-24 [1] CRAN (R 4.2.0) #> globals 0.15.0 2022-05-09 [1] CRAN (R 4.2.0) #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0) #> greta * 0.4.2.9000 2022-08-10 [1] local #> here 1.0.1 2020-12-13 [1] CRAN (R 4.2.0) #> highr 0.9 2021-04-16 [1] CRAN (R 4.2.0) #> hms 1.1.1 2021-09-26 [1] CRAN (R 4.2.0) #> htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.2.0) #> jsonlite 1.8.0 2022-02-22 [1] CRAN (R 4.2.0) #> knitr 1.39 2022-04-26 [1] CRAN (R 4.2.0) #> lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.0) #> lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.0) #> listenv 0.8.0 2019-12-05 [1] CRAN (R 4.2.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) #> Matrix 1.4-1 2022-03-23 [1] CRAN (R 4.2.0) #> parallelly 1.31.1 2022-04-22 [1] CRAN (R 4.2.0) #> pillar 1.7.0 2022-02-01 [1] CRAN (R 4.2.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0) #> png 0.1-7 2013-12-03 [1] CRAN (R 4.2.0) #> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0) #> processx 3.6.1 2022-06-17 [1] CRAN (R 4.2.0) #> progress 1.2.2 2019-05-16 [1] CRAN (R 4.2.0) #> ps 1.7.1 2022-06-18 [1] CRAN (R 4.2.0) #> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.0) #> R.cache 0.15.0 2021-04-30 [1] CRAN (R 4.2.0) #> R.methodsS3 1.8.1 2020-08-26 [1] CRAN (R 4.2.0) #> R.oo 1.24.0 2020-08-26 [1] CRAN (R 4.2.0) #> R.utils 2.11.0 2021-09-26 [1] CRAN (R 4.2.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0) #> Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.0) #> reprex 2.0.1 2021-08-05 [1] CRAN (R 4.2.0) #> reticulate 1.24-9000 2022-05-11 [1] Github (rstudio/reticulate@451fbff) #> rlang 1.0.4 2022-07-12 [1] CRAN (R 4.2.0) #> rmarkdown 2.14 2022-04-25 [1] CRAN (R 4.2.0) #> rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.0) #> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.2.0) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0) #> stringi 1.7.6 2021-11-29 [1] CRAN (R 4.2.0) #> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.2.0) #> styler 1.7.0 2022-03-13 [1] CRAN (R 4.2.0) #> tensorflow 2.9.0 2022-05-21 [1] CRAN (R 4.2.0) #> tfautograph 0.3.2 2021-09-17 [1] CRAN (R 4.2.0) #> tfruns 1.5.0 2021-02-26 [1] CRAN (R 4.2.0) #> tibble 3.1.7 2022-05-03 [1] CRAN (R 4.2.0) #> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0) #> vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.0) #> whisker 0.4 2019-08-28 [1] CRAN (R 4.2.0) #> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0) #> xfun 0.31 2022-05-10 [1] CRAN (R 4.2.0) #> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0) #> #> [1] /Library/Frameworks/R.framework/Versions/4.2-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/libpython3.8.dylib #> pythonhome: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2:/Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2 #> version: 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:05:16) [Clang 12.0.1 ] #> numpy: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/python3.8/site-packages/numpy #> numpy_version: 1.22.4 #> tensorflow: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/python3.8/site-packages/tensorflow #> #> NOTE: Python version was forced by use_python function #> #> ────────────────────────────────────────────────────────────────────────────── ```

Whereas it passes fine in TF1

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
x <- normal(0, 1, dim = 3)
#> ℹ Initialising python and checking dependencies, this may take a moment.
#> ✔ Initialising python and checking dependencies ... done!
#> 
a <- lognormal(0,1)
y <- sum(x^2) + a
calculate(y,
          values = list(x = c(0.1, 0.2, 0.3),
                        a = 2))
#> $y
#>      [,1]
#> [1,] 2.14

Created on 2022-08-10 by the reprex package (v2.0.1)

Session info ``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.2.0 (2022-04-22) #> os macOS Big Sur/Monterey 10.16 #> system x86_64, darwin17.0 #> ui X11 #> language (EN) #> collate en_AU.UTF-8 #> ctype en_AU.UTF-8 #> tz Australia/Perth #> date 2022-08-10 #> pandoc 2.17.1.1 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> abind 1.4-5 2016-07-21 [1] CRAN (R 4.2.0) #> base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.2.0) #> callr 3.7.1 2022-07-13 [1] CRAN (R 4.2.0) #> cli 3.3.0 2022-04-25 [1] CRAN (R 4.2.0) #> coda 0.19-4 2020-09-30 [1] CRAN (R 4.2.0) #> codetools 0.2-18 2020-11-04 [1] CRAN (R 4.2.0) #> crayon 1.5.1 2022-03-26 [1] CRAN (R 4.2.0) #> digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.0) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0) #> evaluate 0.15 2022-02-18 [1] CRAN (R 4.2.0) #> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0) #> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0) #> future 1.26.1 2022-05-27 [1] CRAN (R 4.2.0) #> globals 0.15.1 2022-06-24 [1] CRAN (R 4.2.0) #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0) #> greta * 0.4.2.9000 2022-08-05 [1] local #> here 1.0.1 2020-12-13 [1] CRAN (R 4.2.0) #> highr 0.9 2021-04-16 [1] CRAN (R 4.2.0) #> hms 1.1.1 2021-09-26 [1] CRAN (R 4.2.0) #> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.0) #> jsonlite 1.8.0 2022-02-22 [1] CRAN (R 4.2.0) #> knitr 1.39 2022-04-26 [1] CRAN (R 4.2.0) #> lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.0) #> lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.0) #> listenv 0.8.0 2019-12-05 [1] CRAN (R 4.2.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) #> Matrix 1.4-1 2022-03-23 [1] CRAN (R 4.2.0) #> parallelly 1.32.0 2022-06-07 [1] CRAN (R 4.2.0) #> pillar 1.8.0 2022-07-18 [1] CRAN (R 4.2.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0) #> png 0.1-7 2013-12-03 [1] CRAN (R 4.2.0) #> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0) #> processx 3.7.0 2022-07-07 [1] CRAN (R 4.2.0) #> progress 1.2.2 2019-05-16 [1] CRAN (R 4.2.0) #> ps 1.7.1 2022-06-18 [1] CRAN (R 4.2.0) #> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.0) #> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.0) #> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0) #> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0) #> R.utils 2.12.0 2022-06-28 [1] CRAN (R 4.2.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0) #> Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.0) #> reprex 2.0.1 2021-08-05 [1] CRAN (R 4.2.0) #> reticulate 1.25 2022-05-11 [1] CRAN (R 4.2.0) #> rlang 1.0.4 2022-07-12 [1] CRAN (R 4.2.0) #> rmarkdown 2.14 2022-04-25 [1] CRAN (R 4.2.0) #> rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.0) #> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.2.0) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0) #> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.0) #> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.2.0) #> styler 1.7.0 2022-03-13 [1] CRAN (R 4.2.0) #> tensorflow 2.9.0 2022-05-21 [1] CRAN (R 4.2.0) #> tfruns 1.5.0 2021-02-26 [1] CRAN (R 4.2.0) #> tibble 3.1.7 2022-05-03 [1] CRAN (R 4.2.0) #> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0) #> vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.0) #> whisker 0.4 2019-08-28 [1] CRAN (R 4.2.0) #> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0) #> xfun 0.31 2022-05-10 [1] CRAN (R 4.2.0) #> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0) #> #> [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library #> #> ─ Python configuration ─────────────────────────────────────────────────────── #> python: /Users/njtierney/Library/r-miniconda/envs/greta-env/bin/python #> libpython: /Users/njtierney/Library/r-miniconda/envs/greta-env/lib/libpython3.7m.dylib #> pythonhome: /Users/njtierney/Library/r-miniconda/envs/greta-env:/Users/njtierney/Library/r-miniconda/envs/greta-env #> version: 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 05:59:23) [Clang 11.1.0 ] #> numpy: /Users/njtierney/Library/r-miniconda/envs/greta-env/lib/python3.7/site-packages/numpy #> numpy_version: 1.16.4 #> tensorflow: /Users/njtierney/Library/r-miniconda/envs/greta-env/lib/python3.7/site-packages/tensorflow #> #> NOTE: Python version was forced by use_python function #> #> ────────────────────────────────────────────────────────────────────────────── ```
njtierney commented 2 years ago

It appears to be failing here in define_tf()

https://github.com/greta-dev/greta/blob/75995cee6fc5f1ae4cfbefd5fe9b6ca7bb4e682c/R/calculate.R#L457

Specifically, it calls self$define_batch_size()

https://github.com/greta-dev/greta/blob/75995cee6fc5f1ae4cfbefd5fe9b6ca7bb4e682c/R/dag_class.R#L428

And this is the part that fails:

https://github.com/greta-dev/greta/blob/75995cee6fc5f1ae4cfbefd5fe9b6ca7bb4e682c/R/dag_class.R#L270-L273

The issue is that we don't have a free_state at this point

names(self$tf_environment)
[1] "all_sampling_data_list" "all_forward_data_list"  "hybrid_data_list"

And some of our notes about TF1/2 around define_tf() seem to indicate we have had thoughts about if this part is even necessary

https://github.com/greta-dev/greta/blob/75995cee6fc5f1ae4cfbefd5fe9b6ca7bb4e682c/R/calculate.R#L454-L457

njtierney commented 2 years ago

Here is the TF1 code for define_tf()

https://github.com/greta-dev/greta/blob/master/R/dag_class.R#L332-L345

njtierney commented 2 years ago

OK so now we can get calculate to work! There are some TF print methods bleeding through that we need to manage, but we can tackle that later.

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
greta_sitrep()
#> ℹ checking if python available
#> ✔ python (v3.8) available
#> 
#> ℹ checking if TensorFlow available
#> ✔ TensorFlow (v2.9.2) available
#> 
#> ℹ checking if TensorFlow Probability available
#> ✔ TensorFlow Probability (v0.17.0) available
#> 
#> ℹ checking if greta conda environment available
#> ✔ greta conda environment available
#> 
#> ℹ Initialising python and checking dependencies, this may take a moment.
#> ✔ Initialising python and checking dependencies ... done!
#> 
#> ℹ greta is ready to use!
x <- normal(0, 1, dim = 3)
a <- lognormal(0, 1)
y <- sum(x^2) + a
calculate(y,
          values = list(x = c(0.1, 0.2, 0.3), a = 2))
#> Loaded Tensorflow version 2.9.2
#> $y
#>      [,1]
#> [1,] 2.14

# ok now try with something more complex
alpha <- normal(0, 1)
beta <- normal(0, 1)
sigma <- lognormal(1, 0.1)
y <- as_data(iris$Petal.Width)
mu <- alpha + iris$Petal.Length * beta
distribution(y) <- normal(mu, sigma)
m <- model(alpha, beta, sigma)

# sample values of the parameters, or different observation data (y), from
# the priors (useful for prior # predictive checking) 
calculate(alpha, beta, sigma, nsim = 10)
#> $alpha
#> tf.Tensor(
#> [[[ 0.1806418 ]]
#> 
#>  [[ 1.4482829 ]]
#> 
#>  [[-1.11619569]]
#> 
#>  [[-0.00959198]]
#> 
#>  [[-0.90302191]]
#> 
#>  [[-1.10670715]]
#> 
#>  [[-0.54173361]]
#> 
#>  [[-0.38892957]]
#> 
#>  [[ 1.3425188 ]]
#> 
#>  [[-0.42507453]]], shape=(10, 1, 1), dtype=float64)
#> 
#> $beta
#> tf.Tensor(
#> [[[ 0.55689267]]
#> 
#>  [[-0.1877545 ]]
#> 
#>  [[-1.04136366]]
#> 
#>  [[ 2.64473685]]
#> 
#>  [[-1.07963292]]
#> 
#>  [[ 0.30969006]]
#> 
#>  [[-0.27217694]]
#> 
#>  [[-0.32732864]]
#> 
#>  [[ 0.14380694]]
#> 
#>  [[-0.73333336]]], shape=(10, 1, 1), dtype=float64)
#> 
#> $sigma
#> tf.Tensor(
#> [[[2.93267488]]
#> 
#>  [[2.66226447]]
#> 
#>  [[3.01775851]]
#> 
#>  [[2.85230994]]
#> 
#>  [[2.97981514]]
#> 
#>  [[2.72624399]]
#> 
#>  [[2.51908717]]
#> 
#>  [[2.37971047]]
#> 
#>  [[2.68252641]]
#> 
#>  [[2.7686491 ]]], shape=(10, 1, 1), dtype=float64)

x <- normal(0, 1)
m <- model(x)
calculate(x, nsim = 10)
#> $x
#> tf.Tensor(
#> [[[ 0.685869  ]]
#> 
#>  [[-0.64783463]]
#> 
#>  [[-1.97278833]]
#> 
#>  [[ 0.08502956]]
#> 
#>  [[ 0.40096284]]
#> 
#>  [[ 0.05948794]]
#> 
#>  [[ 0.60460724]]
#> 
#>  [[-0.31323591]]
#> 
#>  [[-0.30933393]]
#> 
#>  [[ 1.39143724]]], shape=(10, 1, 1), dtype=float64)

Created on 2022-08-17 by the reprex package (v2.0.1)

Session info ``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.2.0 (2022-04-22) #> os macOS Monterey 12.3.1 #> system aarch64, darwin20 #> ui X11 #> language (EN) #> collate en_AU.UTF-8 #> ctype en_AU.UTF-8 #> tz Australia/Perth #> date 2022-08-17 #> pandoc 2.18 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> backports 1.4.1 2021-12-13 [1] CRAN (R 4.2.0) #> base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.2.0) #> callr 3.7.1 2022-07-13 [1] CRAN (R 4.2.0) #> cli 3.3.0.9000 2022-06-15 [1] Github (r-lib/cli@31a5db5) #> coda 0.19-4 2020-09-30 [1] CRAN (R 4.2.0) #> codetools 0.2-18 2020-11-04 [1] CRAN (R 4.2.0) #> crayon 1.5.1 2022-03-26 [1] CRAN (R 4.2.0) #> digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.0) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0) #> evaluate 0.16 2022-08-09 [1] CRAN (R 4.2.0) #> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0) #> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0) #> future 1.27.0 2022-07-22 [1] CRAN (R 4.2.0) #> globals 0.16.0 2022-08-05 [1] CRAN (R 4.2.0) #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0) #> greta * 0.4.2.9000 2022-08-17 [1] local #> here 1.0.1 2020-12-13 [1] CRAN (R 4.2.0) #> highr 0.9 2021-04-16 [1] CRAN (R 4.2.0) #> hms 1.1.1 2021-09-26 [1] CRAN (R 4.2.0) #> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.0) #> jsonlite 1.8.0 2022-02-22 [1] CRAN (R 4.2.0) #> knitr 1.39 2022-04-26 [1] CRAN (R 4.2.0) #> lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.0) #> lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.0) #> listenv 0.8.0 2019-12-05 [1] CRAN (R 4.2.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) #> Matrix 1.4-1 2022-03-23 [1] CRAN (R 4.2.0) #> parallelly 1.32.1 2022-07-21 [1] CRAN (R 4.2.0) #> pillar 1.8.0 2022-07-18 [1] CRAN (R 4.2.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0) #> png 0.1-7 2013-12-03 [1] CRAN (R 4.2.0) #> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0) #> processx 3.7.0 2022-07-07 [1] CRAN (R 4.2.0) #> progress 1.2.2 2019-05-16 [1] CRAN (R 4.2.0) #> ps 1.7.1 2022-06-18 [1] CRAN (R 4.2.0) #> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.0) #> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.0) #> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0) #> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0) #> R.utils 2.12.0 2022-06-28 [1] CRAN (R 4.2.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0) #> Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.0) #> reprex 2.0.1 2021-08-05 [1] CRAN (R 4.2.0) #> reticulate 1.25 2022-05-11 [1] CRAN (R 4.2.0) #> rlang 1.0.4 2022-07-12 [1] CRAN (R 4.2.0) #> rmarkdown 2.14 2022-04-25 [1] CRAN (R 4.2.0) #> rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.0) #> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.2.0) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0) #> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.0) #> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.2.0) #> styler 1.7.0 2022-03-13 [1] CRAN (R 4.2.0) #> tensorflow 2.9.0 2022-05-21 [1] CRAN (R 4.2.0) #> tfautograph 0.3.2 2021-09-17 [1] CRAN (R 4.2.0) #> tfruns 1.5.0 2021-02-26 [1] CRAN (R 4.2.0) #> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0) #> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0) #> vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.0) #> whisker 0.4 2019-08-28 [1] CRAN (R 4.2.0) #> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0) #> xfun 0.32.1 2022-08-11 [1] https://yihui.r-universe.dev (R 4.2.0) #> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0) #> #> [1] /Library/Frameworks/R.framework/Versions/4.2-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/libpython3.8.dylib #> pythonhome: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2:/Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2 #> version: 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:05:16) [Clang 12.0.1 ] #> numpy: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/python3.8/site-packages/numpy #> numpy_version: 1.22.4 #> tensorflow: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/python3.8/site-packages/tensorflow #> #> NOTE: Python version was forced by use_python function #> #> ────────────────────────────────────────────────────────────────────────────── ```
njtierney commented 2 years ago

OK so in the PR https://github.com/greta-dev/greta/pull/534 this is now resolved - see below, print method is now an appropriate array rather than a TF print method

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
greta_sitrep()
#> ℹ checking if python available
#> ✔ python (v3.8) available
#> 
#> ℹ checking if TensorFlow available
#> ✔ TensorFlow (v2.9.2) available
#> 
#> ℹ checking if TensorFlow Probability available
#> ✔ TensorFlow Probability (v0.17.0) available
#> 
#> ℹ checking if greta conda environment available
#> ✔ greta conda environment available
#> 
#> ℹ Initialising python and checking dependencies, this may take a moment.
#> ✔ Initialising python and checking dependencies ... done!
#> 
#> ℹ greta is ready to use!
x <- normal(0, 1, dim = 3)
a <- lognormal(0, 1)
y <- sum(x^2) + a
calculate(y,
          values = list(x = c(0.1, 0.2, 0.3), a = 2))
#> Loaded Tensorflow version 2.9.2
#> $y
#>      [,1]
#> [1,] 2.14

# ok now try with something more complex
alpha <- normal(0, 1)
beta <- normal(0, 1)
sigma <- lognormal(1, 0.1)
y <- as_data(iris$Petal.Width)
mu <- alpha + iris$Petal.Length * beta
distribution(y) <- normal(mu, sigma)
m <- model(alpha, beta, sigma)

# sample values of the parameters, or different observation data (y), from
# the priors (useful for prior # predictive checking) 
calculate(alpha, beta, sigma, nsim = 10)
#> $alpha
#> , , 1
#> 
#>              [,1]
#>  [1,] -0.61108666
#>  [2,] -0.78122184
#>  [3,]  1.04941523
#>  [4,] -0.75608298
#>  [5,]  0.50373025
#>  [6,] -0.03160535
#>  [7,] -0.26621029
#>  [8,] -1.59081045
#>  [9,] -1.25162709
#> [10,] -1.78055759
#> 
#> 
#> $beta
#> , , 1
#> 
#>             [,1]
#>  [1,] -1.5227236
#>  [2,]  0.9011371
#>  [3,] -0.4669596
#>  [4,]  2.7520012
#>  [5,] -1.1530135
#>  [6,]  1.4950297
#>  [7,] -1.8795893
#>  [8,]  1.7380015
#>  [9,]  0.1408232
#> [10,]  1.2259039
#> 
#> 
#> $sigma
#> , , 1
#> 
#>           [,1]
#>  [1,] 2.733376
#>  [2,] 3.597703
#>  [3,] 2.483335
#>  [4,] 2.671506
#>  [5,] 2.593130
#>  [6,] 2.596422
#>  [7,] 2.458442
#>  [8,] 3.061843
#>  [9,] 3.002529
#> [10,] 2.534395

x <- normal(0, 1)
m <- model(x)
calculate(x, nsim = 10)
#> $x
#> , , 1
#> 
#>              [,1]
#>  [1,] -0.92379502
#>  [2,] -1.57630208
#>  [3,]  0.15693283
#>  [4,] -2.77556558
#>  [5,] -0.01648104
#>  [6,] -0.20797487
#>  [7,]  0.18541857
#>  [8,]  0.36728624
#>  [9,]  0.46218441
#> [10,] -1.17776875

Created on 2022-10-10 by the reprex package (v2.0.1)

Session info ``` r sessioninfo::session_info() #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.2.1 (2022-06-23) #> os macOS Monterey 12.3.1 #> system aarch64, darwin20 #> ui X11 #> language (EN) #> collate en_AU.UTF-8 #> ctype en_AU.UTF-8 #> tz Australia/Perth #> date 2022-10-10 #> pandoc 2.19.2 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── #> package * version date (UTC) lib source #> abind 1.4-5 2016-07-21 [1] CRAN (R 4.2.0) #> base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.2.0) #> callr 3.7.2 2022-08-22 [1] CRAN (R 4.2.0) #> cli 3.3.0.9000 2022-06-15 [1] Github (r-lib/cli@31a5db5) #> coda 0.19-4 2020-09-30 [1] CRAN (R 4.2.0) #> codetools 0.2-18 2020-11-04 [1] CRAN (R 4.2.1) #> crayon 1.5.1 2022-03-26 [1] CRAN (R 4.2.0) #> digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.0) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0) #> evaluate 0.16 2022-08-09 [1] CRAN (R 4.2.0) #> fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0) #> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0) #> future 1.27.0 2022-07-22 [1] CRAN (R 4.2.0) #> globals 0.16.0 2022-08-05 [1] CRAN (R 4.2.0) #> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0) #> greta * 0.4.2.9000 2022-10-10 [1] local #> here 1.0.1 2020-12-13 [1] CRAN (R 4.2.0) #> highr 0.9 2021-04-16 [1] CRAN (R 4.2.0) #> hms 1.1.1 2021-09-26 [1] CRAN (R 4.2.0) #> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.0) #> jsonlite 1.8.0 2022-02-22 [1] CRAN (R 4.2.0) #> knitr 1.40 2022-08-24 [1] CRAN (R 4.2.0) #> lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.1) #> lifecycle 1.0.2 2022-09-09 [1] CRAN (R 4.2.0) #> listenv 0.8.0 2019-12-05 [1] CRAN (R 4.2.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0) #> Matrix 1.4-1 2022-03-23 [1] CRAN (R 4.2.1) #> parallelly 1.32.1 2022-07-21 [1] CRAN (R 4.2.0) #> pillar 1.8.1 2022-08-19 [1] CRAN (R 4.2.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0) #> png 0.1-7 2013-12-03 [1] CRAN (R 4.2.0) #> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0) #> processx 3.7.0 2022-07-07 [1] CRAN (R 4.2.0) #> progress 1.2.2 2019-05-16 [1] CRAN (R 4.2.0) #> ps 1.7.1 2022-06-18 [1] CRAN (R 4.2.0) #> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.0) #> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.0) #> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0) #> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0) #> R.utils 2.12.0 2022-06-28 [1] CRAN (R 4.2.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0) #> Rcpp 1.0.9 2022-07-08 [1] CRAN (R 4.2.0) #> reprex 2.0.1 2021-08-05 [1] CRAN (R 4.2.0) #> reticulate 1.25 2022-05-11 [1] CRAN (R 4.2.0) #> rlang 1.0.5 2022-08-31 [1] CRAN (R 4.2.0) #> rmarkdown 2.16 2022-08-24 [1] CRAN (R 4.2.0) #> rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.0) #> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.2.0) #> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0) #> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.0) #> stringr 1.4.1 2022-08-20 [1] CRAN (R 4.2.0) #> styler 1.7.0 2022-03-13 [1] CRAN (R 4.2.0) #> tensorflow 2.9.0 2022-05-21 [1] CRAN (R 4.2.0) #> tfruns 1.5.0 2021-02-26 [1] CRAN (R 4.2.0) #> tibble 3.1.8 2022-07-22 [1] CRAN (R 4.2.0) #> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0) #> vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.0) #> whisker 0.4 2019-08-28 [1] CRAN (R 4.2.0) #> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0) #> xfun 0.33 2022-09-12 [1] CRAN (R 4.2.0) #> yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0) #> #> [1] /Library/Frameworks/R.framework/Versions/4.2-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/libpython3.8.dylib #> pythonhome: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2:/Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2 #> version: 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:05:16) [Clang 12.0.1 ] #> numpy: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/python3.8/site-packages/numpy #> numpy_version: 1.22.4 #> tensorflow: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/python3.8/site-packages/tensorflow #> #> NOTE: Python version was forced by use_python function #> #> ────────────────────────────────────────────────────────────────────────────── ```