greta-dev / greta-dev/greta.dynamics
understand why using `opt` to get MAP estimate in vignette "ode-solve-example.Rmd" fails?
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Description
I can run the example separately here:
``` r
library(greta.dynamics)
#> Loading required package: 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
# priors for the parameters
rIng <- uniform(0, 2) # /day, rate of ingestion
#> ℹ Initialising python and checking dependencies, this may take a moment.
#> ✔ Initialising python and checking dependencies ... done!
#>
rGrow <- uniform(0, 3) # /day, growth rate of prey
rMort <- uniform(0, 1) # /day, mortality rate of predator
assEff <- uniform(0, 1) # -, assimilation efficiency
K <- uniform(0, 30) # mmol/m3, carrying capacity
obs_sd <- uniform(0, 1)
# build the model (takes a few seconds to define the tensorflow graph)
m <- model(rIng, rGrow, rMort, assEff, K, obs_sd)
# compute MAP estimate
o <- opt(
model = m,
initial_values = initials(
rIng = 0.2,
rGrow = 1.0,
rMort = 0.2,
assEff = 0.5,
K = 10.0
)
)
o
#> $par
#> $par$rIng
#> [1] 1
#>
#> $par$rGrow
#> [1] 1.5
#>
#> $par$rMort
#> [1] 0.5
#>
#> $par$assEff
#> [1] 0.5
#>
#> $par$K
#> [1] 15
#>
#> $par$obs_sd
#> [1] 0.5
#>
#>
#> $value
#> [1] 8.317766
#>
#> $iterations
#> [1] 5
#>
#> $convergence
#> [1] 0
```
Created on 2024-11-14 with [reprex v2.1.1](https://reprex.tidyverse.org)
Session info
``` r
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.4.2 (2024-10-31)
#> os macOS Sonoma 14.5
#> system aarch64, darwin20
#> ui X11
#> language (EN)
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz Australia/Hobart
#> date 2024-11-14
#> pandoc 3.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> abind 1.4-8 2024-09-12 [1] CRAN (R 4.4.1)
#> backports 1.5.0 2024-05-23 [1] CRAN (R 4.4.0)
#> base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.4.0)
#> callr 3.7.6 2024-03-25 [1] CRAN (R 4.4.0)
#> cli 3.6.3 2024-06-21 [1] CRAN (R 4.4.0)
#> coda 0.19-4.1 2024-01-31 [1] CRAN (R 4.4.0)
#> codetools 0.2-20 2024-03-31 [2] CRAN (R 4.4.2)
#> crayon 1.5.3 2024-06-20 [1] CRAN (R 4.4.0)
#> digest 0.6.37 2024-08-19 [1] CRAN (R 4.4.1)
#> evaluate 1.0.1 2024-10-10 [1] CRAN (R 4.4.1)
#> fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.0)
#> fs 1.6.5 2024-10-30 [1] CRAN (R 4.4.1)
#> future 1.34.0 2024-07-29 [1] CRAN (R 4.4.0)
#> globals 0.16.3 2024-03-08 [1] CRAN (R 4.4.0)
#> glue 1.8.0 2024-09-30 [1] CRAN (R 4.4.1)
#> greta * 0.5.0 2024-11-06 [1] local
#> greta.dynamics * 0.2.2 2024-11-13 [1] local
#> hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.0)
#> htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
#> jsonlite 1.8.9 2024-09-20 [1] CRAN (R 4.4.1)
#> knitr 1.48 2024-07-07 [1] CRAN (R 4.4.0)
#> lattice 0.22-6 2024-03-20 [2] CRAN (R 4.4.2)
#> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0)
#> listenv 0.9.1 2024-01-29 [1] CRAN (R 4.4.0)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0)
#> Matrix 1.7-1 2024-10-18 [2] CRAN (R 4.4.2)
#> parallelly 1.38.0 2024-07-27 [1] CRAN (R 4.4.0)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0)
#> png 0.1-8 2022-11-29 [1] CRAN (R 4.4.0)
#> prettyunits 1.2.0 2023-09-24 [1] CRAN (R 4.4.0)
#> processx 3.8.4 2024-03-16 [1] CRAN (R 4.4.0)
#> progress 1.2.3 2023-12-06 [1] CRAN (R 4.4.0)
#> ps 1.8.1 2024-10-28 [1] CRAN (R 4.4.1)
#> R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.0)
#> Rcpp 1.0.13-1 2024-11-02 [1] CRAN (R 4.4.1)
#> reprex 2.1.1 2024-07-06 [1] CRAN (R 4.4.0)
#> reticulate 1.39.0 2024-09-05 [1] CRAN (R 4.4.1)
#> rlang 1.1.4 2024-06-04 [1] CRAN (R 4.4.0)
#> rmarkdown 2.29 2024-11-04 [1] CRAN (R 4.4.1)
#> rstudioapi 0.17.1 2024-10-22 [1] CRAN (R 4.4.1)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.4.0)
#> tensorflow 2.16.0 2024-04-15 [1] CRAN (R 4.4.0)
#> tfautograph 0.3.2 2021-09-17 [1] CRAN (R 4.4.0)
#> tfruns 1.5.3 2024-04-19 [1] CRAN (R 4.4.0)
#> vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0)
#> whisker 0.4.1 2022-12-05 [1] CRAN (R 4.4.0)
#> withr 3.0.2 2024-10-28 [1] CRAN (R 4.4.1)
#> xfun 0.49 2024-10-31 [1] CRAN (R 4.4.1)
#> yaml 2.3.10 2024-07-26 [1] CRAN (R 4.4.0)
#>
#> [1] /Users/nick/Library/R/arm64/4.4/library
#> [2] /Library/Frameworks/R.framework/Versions/4.4-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/libpython3.10.dylib
#> pythonhome: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2:/Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2
#> version: 3.10.14 | packaged by conda-forge | (main, Mar 20 2024, 12:51:49) [Clang 16.0.6 ]
#> numpy: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/python3.10/site-packages/numpy
#> numpy_version: 1.26.4
#> tensorflow: /Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/python3.10/site-packages/tensorflow
#>
#> NOTE: Python version was forced by use_python() function
#>
#> ──────────────────────────────────────────────────────────────────────────────
```
But running it inside of the vignette breaks and gives this error:
```
Error in py_call_impl(callable, call_args$unnamed, call_args$named) :
TypeError: is out of scope and cannot be used here. Use return values, explicit Python locals or TensorFlow collections to access it.
Please see https://www.tensorflow.org/guide/function#all_outputs_of_a_tffunction_must_be_return_values for more information.
<...truncated...>in _create_op_internal
File "/Users/nick/Library/r-miniconda-arm64/envs/greta-env-tf2/lib/python3.10/site-packages/tensorflow/python/framework/ops.py", line 1160, in from_node_def
The tensor cannot be accessed from here, because it was defined in FuncGraph(name=fn, id=15414436784), which is out of scope.
```
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