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Examples for Probabilistic System Anglican
Thank you for this beautiful repo!
At linear_regression clj, I see :require [plotting :as plot]
.
https://github.com/probprog/anglican-examples/blob/master/worksheets/linear_regression.clj#L9
Is it supposed to be :require [gorilla-plot.core :as plot]
?
When I run lein gorilla
as instructed in the Readme, I get the following error. I am using a fresh install of clojure verion 1.10.
clojure.lang.Compiler$CompilerException: Syntax error compiling at (org/httpkit/server.clj:1:1).
#:clojure.error{:phase :compile-syntax-check, :line 1, :column 1, :source "org/httpkit/server.clj"}
at clojure.lang.Compiler.load (Compiler.java:7647)
clojure.lang.RT.loadResourceScript (RT.java:381)
clojure.lang.RT.loadResourceScript (RT.java:372)
clojure.lang.RT.load (RT.java:463)
clojure.lang.RT.load (RT.java:428)
clojure.core$load$fn__6824.invoke (core.clj:6126)
clojure.core$load.invokeStatic (core.clj:6125)
clojure.core$load.doInvoke (core.clj:6109)
clojure.lang.RestFn.invoke (RestFn.java:408)
clojure.core$load_one.invokeStatic (core.clj:5908)
clojure.core$load_one.invoke (core.clj:5903)
clojure.core$load_lib$fn__6765.invoke (core.clj:5948)
clojure.core$load_lib.invokeStatic (core.clj:5947)
clojure.core$load_lib.doInvoke (core.clj:5928)
clojure.lang.RestFn.applyTo (RestFn.java:142)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$load_libs.invokeStatic (core.clj:5985)
clojure.core$load_libs.doInvoke (core.clj:5969)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$require.invokeStatic (core.clj:6007)
clojure.core$require.doInvoke (core.clj:6007)
clojure.lang.RestFn.invoke (RestFn.java:703)
gorilla_repl.core$eval668$loading__6706__auto____669.invoke (core.clj:5)
gorilla_repl.core$eval668.invokeStatic (core.clj:5)
gorilla_repl.core$eval668.invoke (core.clj:5)
clojure.lang.Compiler.eval (Compiler.java:7176)
clojure.lang.Compiler.eval (Compiler.java:7165)
clojure.lang.Compiler.load (Compiler.java:7635)
clojure.lang.RT.loadResourceScript (RT.java:381)
clojure.lang.RT.loadResourceScript (RT.java:372)
clojure.lang.RT.load (RT.java:463)
clojure.lang.RT.load (RT.java:428)
clojure.core$load$fn__6824.invoke (core.clj:6126)
clojure.core$load.invokeStatic (core.clj:6125)
clojure.core$load.doInvoke (core.clj:6109)
clojure.lang.RestFn.invoke (RestFn.java:408)
clojure.core$load_one.invokeStatic (core.clj:5908)
clojure.core$load_one.invoke (core.clj:5903)
clojure.core$load_lib$fn__6765.invoke (core.clj:5948)
clojure.core$load_lib.invokeStatic (core.clj:5947)
clojure.core$load_lib.doInvoke (core.clj:5928)
clojure.lang.RestFn.applyTo (RestFn.java:142)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$load_libs.invokeStatic (core.clj:5985)
clojure.core$load_libs.doInvoke (core.clj:5969)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$require.invokeStatic (core.clj:6007)
clojure.core$require.doInvoke (core.clj:6007)
clojure.lang.RestFn.invoke (RestFn.java:436)
leiningen.gorilla$eval662$loading__6706__auto____663.invoke (gorilla.clj:7)
leiningen.gorilla$eval662.invokeStatic (gorilla.clj:7)
leiningen.gorilla$eval662.invoke (gorilla.clj:7)
clojure.lang.Compiler.eval (Compiler.java:7176)
clojure.lang.Compiler.eval (Compiler.java:7165)
clojure.lang.Compiler.load (Compiler.java:7635)
clojure.lang.RT.loadResourceScript (RT.java:381)
clojure.lang.RT.loadResourceScript (RT.java:372)
clojure.lang.RT.load (RT.java:463)
clojure.lang.RT.load (RT.java:428)
clojure.core$load$fn__6824.invoke (core.clj:6126)
clojure.core$load.invokeStatic (core.clj:6125)
clojure.core$load.doInvoke (core.clj:6109)
clojure.lang.RestFn.invoke (RestFn.java:408)
clojure.core$load_one.invokeStatic (core.clj:5908)
clojure.core$load_one.invoke (core.clj:5903)
clojure.core$load_lib$fn__6765.invoke (core.clj:5948)
clojure.core$load_lib.invokeStatic (core.clj:5947)
clojure.core$load_lib.doInvoke (core.clj:5928)
clojure.lang.RestFn.applyTo (RestFn.java:142)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$load_libs.invokeStatic (core.clj:5985)
clojure.core$load_libs.doInvoke (core.clj:5969)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$require.invokeStatic (core.clj:6007)
clojure.core$require.doInvoke (core.clj:6007)
clojure.lang.RestFn.invoke (RestFn.java:408)
leiningen.core.utils$require_resolve.invokeStatic (utils.clj:102)
leiningen.core.utils$require_resolve.invoke (utils.clj:95)
leiningen.core.utils$require_resolve.invokeStatic (utils.clj:105)
leiningen.core.utils$require_resolve.invoke (utils.clj:95)
leiningen.core.main$lookup_task_var.invokeStatic (main.clj:69)
leiningen.core.main$lookup_task_var.invoke (main.clj:65)
leiningen.core.main$pass_through_help_QMARK_.invokeStatic (main.clj:79)
leiningen.core.main$pass_through_help_QMARK_.invoke (main.clj:73)
leiningen.core.main$task_args.invokeStatic (main.clj:82)
leiningen.core.main$task_args.invoke (main.clj:81)
leiningen.core.main$resolve_and_apply.invokeStatic (main.clj:339)
leiningen.core.main$resolve_and_apply.invoke (main.clj:336)
leiningen.core.main$_main$fn__6681.invoke (main.clj:452)
leiningen.core.main$_main.invokeStatic (main.clj:442)
leiningen.core.main$_main.doInvoke (main.clj:439)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.lang.Var.applyTo (Var.java:705)
clojure.core$apply.invokeStatic (core.clj:665)
clojure.main$main_opt.invokeStatic (main.clj:491)
clojure.main$main_opt.invoke (main.clj:487)
clojure.main$main.invokeStatic (main.clj:598)
clojure.main$main.doInvoke (main.clj:561)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.lang.Var.applyTo (Var.java:705)
clojure.main.main (main.java:37)
Caused by: java.lang.ClassNotFoundException: javax.xml.bind.DatatypeConverter
at java.net.URLClassLoader.findClass (URLClassLoader.java:471)
clojure.lang.DynamicClassLoader.findClass (DynamicClassLoader.java:69)
java.lang.ClassLoader.loadClass (ClassLoader.java:588)
clojure.lang.DynamicClassLoader.loadClass (DynamicClassLoader.java:77)
java.lang.ClassLoader.loadClass (ClassLoader.java:521)
java.lang.Class.forName0 (Class.java:-2)
java.lang.Class.forName (Class.java:398)
clojure.lang.RT.classForName (RT.java:2207)
clojure.lang.RT.classForNameNonLoading (RT.java:2220)
org.httpkit.server$eval2688$loading__6706__auto____2689.invoke (server.clj:1)
org.httpkit.server$eval2688.invokeStatic (server.clj:1)
org.httpkit.server$eval2688.invoke (server.clj:1)
clojure.lang.Compiler.eval (Compiler.java:7176)
clojure.lang.Compiler.eval (Compiler.java:7165)
clojure.lang.Compiler.load (Compiler.java:7635)
clojure.lang.RT.loadResourceScript (RT.java:381)
clojure.lang.RT.loadResourceScript (RT.java:372)
clojure.lang.RT.load (RT.java:463)
clojure.lang.RT.load (RT.java:428)
clojure.core$load$fn__6824.invoke (core.clj:6126)
clojure.core$load.invokeStatic (core.clj:6125)
clojure.core$load.doInvoke (core.clj:6109)
clojure.lang.RestFn.invoke (RestFn.java:408)
clojure.core$load_one.invokeStatic (core.clj:5908)
clojure.core$load_one.invoke (core.clj:5903)
clojure.core$load_lib$fn__6765.invoke (core.clj:5948)
clojure.core$load_lib.invokeStatic (core.clj:5947)
clojure.core$load_lib.doInvoke (core.clj:5928)
clojure.lang.RestFn.applyTo (RestFn.java:142)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$load_libs.invokeStatic (core.clj:5985)
clojure.core$load_libs.doInvoke (core.clj:5969)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$require.invokeStatic (core.clj:6007)
clojure.core$require.doInvoke (core.clj:6007)
clojure.lang.RestFn.invoke (RestFn.java:703)
gorilla_repl.core$eval668$loading__6706__auto____669.invoke (core.clj:5)
gorilla_repl.core$eval668.invokeStatic (core.clj:5)
gorilla_repl.core$eval668.invoke (core.clj:5)
clojure.lang.Compiler.eval (Compiler.java:7176)
clojure.lang.Compiler.eval (Compiler.java:7165)
clojure.lang.Compiler.load (Compiler.java:7635)
clojure.lang.RT.loadResourceScript (RT.java:381)
clojure.lang.RT.loadResourceScript (RT.java:372)
clojure.lang.RT.load (RT.java:463)
clojure.lang.RT.load (RT.java:428)
clojure.core$load$fn__6824.invoke (core.clj:6126)
clojure.core$load.invokeStatic (core.clj:6125)
clojure.core$load.doInvoke (core.clj:6109)
clojure.lang.RestFn.invoke (RestFn.java:408)
clojure.core$load_one.invokeStatic (core.clj:5908)
clojure.core$load_one.invoke (core.clj:5903)
clojure.core$load_lib$fn__6765.invoke (core.clj:5948)
clojure.core$load_lib.invokeStatic (core.clj:5947)
clojure.core$load_lib.doInvoke (core.clj:5928)
clojure.lang.RestFn.applyTo (RestFn.java:142)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$load_libs.invokeStatic (core.clj:5985)
clojure.core$load_libs.doInvoke (core.clj:5969)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$require.invokeStatic (core.clj:6007)
clojure.core$require.doInvoke (core.clj:6007)
clojure.lang.RestFn.invoke (RestFn.java:436)
leiningen.gorilla$eval662$loading__6706__auto____663.invoke (gorilla.clj:7)
leiningen.gorilla$eval662.invokeStatic (gorilla.clj:7)
leiningen.gorilla$eval662.invoke (gorilla.clj:7)
clojure.lang.Compiler.eval (Compiler.java:7176)
clojure.lang.Compiler.eval (Compiler.java:7165)
clojure.lang.Compiler.load (Compiler.java:7635)
clojure.lang.RT.loadResourceScript (RT.java:381)
clojure.lang.RT.loadResourceScript (RT.java:372)
clojure.lang.RT.load (RT.java:463)
clojure.lang.RT.load (RT.java:428)
clojure.core$load$fn__6824.invoke (core.clj:6126)
clojure.core$load.invokeStatic (core.clj:6125)
clojure.core$load.doInvoke (core.clj:6109)
clojure.lang.RestFn.invoke (RestFn.java:408)
clojure.core$load_one.invokeStatic (core.clj:5908)
clojure.core$load_one.invoke (core.clj:5903)
clojure.core$load_lib$fn__6765.invoke (core.clj:5948)
clojure.core$load_lib.invokeStatic (core.clj:5947)
clojure.core$load_lib.doInvoke (core.clj:5928)
clojure.lang.RestFn.applyTo (RestFn.java:142)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$load_libs.invokeStatic (core.clj:5985)
clojure.core$load_libs.doInvoke (core.clj:5969)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.core$apply.invokeStatic (core.clj:667)
clojure.core$require.invokeStatic (core.clj:6007)
clojure.core$require.doInvoke (core.clj:6007)
clojure.lang.RestFn.invoke (RestFn.java:408)
leiningen.core.utils$require_resolve.invokeStatic (utils.clj:102)
leiningen.core.utils$require_resolve.invoke (utils.clj:95)
leiningen.core.utils$require_resolve.invokeStatic (utils.clj:105)
leiningen.core.utils$require_resolve.invoke (utils.clj:95)
leiningen.core.main$lookup_task_var.invokeStatic (main.clj:69)
leiningen.core.main$lookup_task_var.invoke (main.clj:65)
leiningen.core.main$pass_through_help_QMARK_.invokeStatic (main.clj:79)
leiningen.core.main$pass_through_help_QMARK_.invoke (main.clj:73)
leiningen.core.main$task_args.invokeStatic (main.clj:82)
leiningen.core.main$task_args.invoke (main.clj:81)
leiningen.core.main$resolve_and_apply.invokeStatic (main.clj:339)
leiningen.core.main$resolve_and_apply.invoke (main.clj:336)
leiningen.core.main$_main$fn__6681.invoke (main.clj:452)
leiningen.core.main$_main.invokeStatic (main.clj:442)
leiningen.core.main$_main.doInvoke (main.clj:439)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.lang.Var.applyTo (Var.java:705)
clojure.core$apply.invokeStatic (core.clj:665)
clojure.main$main_opt.invokeStatic (main.clj:491)
clojure.main$main_opt.invoke (main.clj:487)
clojure.main$main.invokeStatic (main.clj:598)
clojure.main$main.doInvoke (main.clj:561)
clojure.lang.RestFn.applyTo (RestFn.java:137)
clojure.lang.Var.applyTo (Var.java:705)
clojure.main.main (main.java:37)
The branching model in the branching_aistats.clj
file has some non-deterministic error.
(defn fib [n]
"returns the n-th number in the Fibonacci sequence"
(loop [a 0 b 1 m 0]
(if (= m n)
a
(recur b (+ a b) (inc m)))))
(with-primitive-procedures [fib]
(defquery branching
"A simple example illustrating flow control with
dependence on random choices"
[]
(let [count-prior (poisson 4)
r (sample count-prior)
l (if (< 4 r)
6
(+ (fib (* 3 r))
(sample count-prior)))]
(observe (poisson l) 6)
(predict :r r)
(predict :l l))))
If I run it with a lot of particles with SMC sampler, it sometimes give Error during inference: org.apache.commons.math3.exception.NotStrictlyPositiveException: mean (0)
(but sometimes not). If the # of particles is large (say 500,000), it will be broken nearly every time.
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