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failed to run `@example` block in src/input-stan.md:23-45 ```@example stan using Pigeons using Random # We will use this type to make sure our iid sampler (next section) will # be used only for this model struct StanUnidentifiableExample end function stan_unid(n_trials, n_successes) # path to a .stan file (compiled files will be cached in the same directory) stan_file = dirname(dirname(pathof(Pigeons))) * "/examples/stan/unid.stan" # data can be specified either using... # - a path to a json file with suffix .json containing the data to condition on # - the JSON string itself (here via the utility Pigeons.json()) stan_data = Pigeons.json(; n_trials, n_successes) return StanLogPotential(stan_file, stan_data, StanUnidentifiableExample()) end pt = pigeons(target = stan_unid(100, 50), reference = stan_unid(0, 0)) nothing #hide ``` value = MethodError: no method matching StanLogPotential(::String, ::String, ::Main.__atexample__named__stan.StanUnidentifiableExample) Closest candidates are: StanLogPotential(::__T_model, ::__T_stan_file, ::__T_data, !Matched::__T_extra_information) where {__T_model, __T_stan_file, __T_data, __T_extra_information} at ~/work/Pigeons.jl/Pigeons.jl/src/utils/@auto.jl:74

failed to run `@example` block in src/input-stan.md:61-74 ```@example stan using BridgeStan function Pigeons.sample_iid!( log_potential::StanLogPotential{M, S, D, StanUnidentifiableExample}, replica, shared) where {M, S, D} # sample in constrained space constrained = rand(replica.rng, 2) # transform to unconstrained space replica.state.unconstrained_parameters .= BridgeStan.param_unconstrain(log_potential.model, constrained) end pt = pigeons(target = stan_unid(100, 50), reference = stan_unid(0, 0)) nothing # hide ``` value = MethodError: no method matching StanLogPotential(::String, ::String, ::Main.__atexample__named__stan.StanUnidentifiableExample) Closest candidates are: StanLogPotential(::__T_model, ::__T_stan_file, ::__T_data, !Matched::__T_extra_information) where {__T_model, __T_stan_file, __T_data, __T_extra_information} at ~/work/Pigeons.jl/Pigeons.jl/src/utils/@auto.jl:74

failed to run `@example` block in src/input-stan.md:88-102 ```@example stan using MCMCChains using StatsPlots plotlyjs() pt = pigeons( target = stan_unid(100, 50), reference = stan_unid(0, 0), record = [traces]) samples = Chains(sample_array(pt), variable_names(pt)) my_plot = StatsPlots.plot(samples) StatsPlots.savefig(my_plot, "stan_posterior_densities_and_traces.html"); samples ``` value = MethodError: no method matching StanLogPotential(::String, ::String, ::Main.__atexample__named__stan.StanUnidentifiableExample) Closest candidates are: StanLogPotential(::__T_model, ::__T_stan_file, ::__T_data, !Matched::__T_extra_information) where {__T_model, __T_stan_file, __T_data, __T_extra_information} at ~/work/Pigeons.jl/Pigeons.jl/src/utils/@auto.jl:74

failed to run `@example` block in src/input-turing.md:11-23 ```@example turing using Pigeons, Distributions, DistributionsAD, DynamicPPL DynamicPPL.@model function my_turing_model(n_trials, n_successes) p1 ~ Uniform(0, 1) p2 ~ Uniform(0, 1) n_successes ~ Binomial(n_trials, p1*p2) return n_successes end pt = pigeons(target = TuringLogPotential(my_turing_model(100, 50))); nothing # hide ``` value = MethodError: no method matching TuringLogPotential(::DynamicPPL.Model{typeof(Main.__atexample__named__turing.my_turing_model), (:n_trials, :n_successes), (), (), Tuple{Int64, Int64}, Tuple{}, DynamicPPL.DefaultContext}) Closest candidates are: TuringLogPotential(::__T_model, !Matched::Bool) where __T_model at ~/work/Pigeons.jl/Pigeons.jl/src/utils/@auto.jl:74

failed to run `@example` block in src/input-turing.md:42-55 ```@example turing using MCMCChains using StatsPlots plotlyjs() pt = pigeons( target = TuringLogPotential(my_turing_model(100, 50)), record = [traces]) samples = Chains(sample_array(pt), variable_names(pt)) my_plot = StatsPlots.plot(samples) StatsPlots.savefig(my_plot, "turing_posterior_densities_and_traces.html"); samples ``` value = MethodError: no method matching TuringLogPotential(::DynamicPPL.Model{typeof(Main.__atexample__named__turing.my_turing_model), (:n_trials, :n_successes), (), (), Tuple{Int64, Int64}, Tuple{}, DynamicPPL.DefaultContext}) Closest candidates are: TuringLogPotential(::__T_model, !Matched::Bool) where __T_model at ~/work/Pigeons.jl/Pigeons.jl/src/utils/@auto.jl:74

failed to run `@example` block in src/output-mpi-postprocessing.md:39-70 ```@example traces using Pigeons using MCMCChains using StatsPlots plotlyjs() # example target: Binomial likelihood with parameter p = p1 * p2 an_unidentifiable_model = Pigeons.toy_turing_unid_target(100, 50) pt_result = pigeons(target = an_unidentifiable_model, # (*) run in two new MPI processes on = ChildProcess(n_local_mpi_processes = 2), # (*) signal that we want the PT object to be # serialized at the end of each round checkpoint = true, n_rounds = 12, # make sure to record the trace # (each machine keeps its own during sampling) record = [traces; round_trip; record_default()]) # (*) load the result across all machines into this interactive node pt = load(pt_result) # collect the statistics and convert to MCMCChains' Chains # to have axes labels matching variable names in Turing and Stan samples = Chains(sample_array(pt), variable_names(pt)) # create the trace plots my_plot = StatsPlots.plot(samples) StatsPlots.savefig(my_plot, "mpi_posterior_densities_and_traces.html"); nothing # hide ``` value = MethodError: no method matching toy_turing_unid_target(::Int64, ::Int64)

failed to run `@example` block in src/output-normalization.md:27-36 ```@example constants using Pigeons # example target: Binomial likelihood with parameter p = p1 * p2 an_unidentifiable_model = Pigeons.toy_turing_unid_target(100, 50) pt = pigeons(target = an_unidentifiable_model) nothing # hide ``` value = MethodError: no method matching toy_turing_unid_target(::Int64, ::Int64)

failed to run `@example` block in src/output-normalization.md:40-42 ```@example constants stepping_stone(pt) ``` value = UndefVarError: pt not defined

failed to run `@example` block in src/output-numerical.md:25-42 ```@example numerical using Pigeons using MCMCChains # example target: Binomial likelihood with parameter p = p1 * p2 an_unidentifiable_model = Pigeons.toy_turing_unid_target(100, 50) pt = pigeons( target = an_unidentifiable_model, record = [traces; round_trip; record_default()] ) # collect the statistics and convert to MCMCChains' Chains # to have axes labels matching variable names in Turing and Stan samples = Chains(sample_array(pt), variable_names(pt)) samples ``` value = MethodError: no method matching toy_turing_unid_target(::Int64, ::Int64)

failed to run `@example` block in src/output-numerical.md:50-53 ```@example numerical using Statistics m = mean(samples) ``` value = UndefVarError: samples not defined

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