R Under development (unstable) (2026-10-21 r90730) -- "Unsuffered Consequences"
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> pkgname <- "adlaplace"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('adlaplace')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
> nameEx("adlaplace")
> ### * adlaplace
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: adlaplace
> ### Title: Fit a hierarchical model by Laplace-approximate maximum
> ###   likelihood
> ### Aliases: adlaplace
> 
> ### ** Examples
> 
> set.seed(1)
> n <- 80
> g <- factor(sample(4, n, replace = TRUE))
> x <- rbinom(n, 1, 0.5)
> eta <- 0.5 + 0.4 * x + rnorm(4, sd = 0.3)[g]
> nb_sd <- 0.3
> z <- rgamma(n, nb_sd^(-2), nb_sd^(-2))
> dat <- data.frame(y = rpois(n, exp(eta) * z), x = x, g = g)
> md <- model_data(
+   nbinom(y, lower = 1e-9, init = 0.15) ~ x + iid(g, init = 0.3),
+   data = dat
+ )
> config <- list(
+   transform_theta = TRUE,
+   obs_groups = obs_groups(md$term_data$A, num_shards = 5),
+   verbose = FALSE
+ )
> ap <- ad_pack(md, config)
/usr/local/clang23/bin/../include/c++/v1/__utility/swap.h:43:11: runtime error: load of value 10, which is not a valid value for type '__libcpp_remove_reference_t<bool &>' (aka 'bool')
    #0 0x7f721746140d in CppAD::ADFun<double, double>::swap(CppAD::ADFun<double, double>&) (/data/localhost/ripley/R/packages/tests-clang-UBSAN/adlaplace.Rcheck/adlaplace/libs/adlaplace.so+0x6140d)
    #1 0x7f72174f656a in CppAD::ADFun<double, double>::ADFun(CppAD::ADFun<double, double>&&) (/data/localhost/ripley/R/packages/tests-clang-UBSAN/adlaplace.Rcheck/adlaplace/libs/adlaplace.so+0xf656a)
    #2 0x7f72174f5611 in AdTape::AdTape(AdTape&&) (/data/localhost/ripley/R/packages/tests-clang-UBSAN/adlaplace.Rcheck/adlaplace/libs/adlaplace.so+0xf5611)
    #3 0x7f72174f9828 in adlaplace_make_ad_shard(AdTape&&) (/data/localhost/ripley/R/packages/tests-clang-UBSAN/adlaplace.Rcheck/adlaplace/libs/adlaplace.so+0xf9828)
    #4 0x7f721759038f in packs_to_ad_fun(std::__1::vector<AdTape, std::__1::allocator<AdTape>>&&, unsigned long, unsigned long, ad_shard* (*)(AdTape&&)) (/data/localhost/ripley/R/packages/tests-clang-UBSAN/adlaplace.Rcheck/adlaplace/libs/adlaplace.so+0x19038f)
    #5 0x7f7217591c93 in get_ad_pack_raw_obs_h(SEXPREC*, Rcpp::Vector<19, Rcpp::PreserveStorage> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>> const&) (/data/localhost/ripley/R/packages/tests-clang-UBSAN/adlaplace.Rcheck/adlaplace/libs/adlaplace.so+0x191c93)
    #6 0x7f7217419738 in get_ad_pack_raw_obs(SEXPREC*, Rcpp::Vector<19, Rcpp::PreserveStorage>, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char>>) (/data/localhost/ripley/R/packages/tests-clang-UBSAN/adlaplace.Rcheck/adlaplace/libs/adlaplace.so+0x19738)
    #7 0x7f721740769c in _adlaplace_get_ad_pack_raw_obs (/data/localhost/ripley/R/packages/tests-clang-UBSAN/adlaplace.Rcheck/adlaplace/libs/adlaplace.so+0x769c)
    #8 0x55f932921a22 in R_doDotCall (/data/localhost/ripley/R/R-clang/bin/exec/R+0x90a22)
    #9 0x55f93296d44a in bcEval_loop eval.c
    #10 0x55f93295b85b in bcEval eval.c
    #11 0x55f93295b014 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xca014)
    #12 0x55f9329730e8 in R_execClosure eval.c
    #13 0x55f932975eda in R_execMethod (/data/localhost/ripley/R/R-clang/bin/exec/R+0xe4eda)
    #14 0x7f721f67d6ba in R_dispatchGeneric (/data/localhost/ripley/R/R-clang/library/methods/libs/methods.so+0x16ba)
    #15 0x55f9329c2469 in do_standardGeneric (/data/localhost/ripley/R/R-clang/bin/exec/R+0x131469)
    #16 0x55f9329619b2 in bcEval_loop eval.c
    #17 0x55f93295b85b in bcEval eval.c
    #18 0x55f93295b014 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xca014)
    #19 0x55f9329730e8 in R_execClosure eval.c
    #20 0x55f9329725da in applyClosure_core eval.c
    #21 0x55f93295bf26 in Rf_applyClosure (/data/localhost/ripley/R/R-clang/bin/exec/R+0xcaf26)
    #22 0x55f93295b467 in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xca467)
    #23 0x55f932978437 in do_set (/data/localhost/ripley/R/R-clang/bin/exec/R+0xe7437)
    #24 0x55f93295b23f in Rf_eval (/data/localhost/ripley/R/R-clang/bin/exec/R+0xca23f)
    #25 0x55f9329a87d7 in Rf_ReplIteration (/data/localhost/ripley/R/R-clang/bin/exec/R+0x1177d7)
    #26 0x55f9329aa2ce in run_Rmainloop (/data/localhost/ripley/R/R-clang/bin/exec/R+0x1192ce)
    #27 0x55f9329aa33a in Rf_mainloop (/data/localhost/ripley/R/R-clang/bin/exec/R+0x11933a)
    #28 0x55f932892db7 in main (/data/localhost/ripley/R/R-clang/bin/exec/R+0x1db7)
    #29 0x7f721f90b680 in __libc_start_call_main (/lib64/libc.so.6+0x3680) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c)
    #30 0x7f721f90b797 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3797) (BuildId: 85075e2ae2e13352a1413d41c327dacf6461526c)
    #31 0x55f932892cd4 in _start (/data/localhost/ripley/R/R-clang/bin/exec/R+0x1cd4)

SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior /usr/local/clang23/bin/../include/c++/v1/__utility/swap.h:43:11 
> cache <- new.env(parent = emptyenv())
> x0 <- md$term_data$info$parameters$init
> outer_fn(x = x0, config = config, cache = cache, ad_pack = ap)
[1] 153.8755
> outer_gr(x = x0, config = config, cache = cache, ad_pack = ap)
[1] -25.3846648 -23.3412463  -0.4940207 -11.3119746
> 
> 
> 
> cleanEx()
> nameEx("by_group")
> ### * by_group
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: by_group
> ### Title: By-Group Classes and Functions
> ### Aliases: by_group
> 
> ### ** Examples
> 
> # Create with explicit levels
> bg <- by_group(term = "group", levels = c("A", "B", "C"))
> 
> # Create from data
> dat <- data.frame(group = c("A", "B", "A", "C"))
> bg <- by_group(term = "group", data = dat)
> 
> 
> 
> cleanEx()
> nameEx("fpoly-class")
> ### * fpoly-class
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: fpoly-class
> ### Title: Fixed Polynomial Model Term
> ### Aliases: fpoly-class fpoly design,fpoly-method beta_info,fpoly-method
> 
> ### ** Examples
> 
> # Create a fixed polynomial term
> fpoly_term <- fpoly(x = "temp", p = 3, ref_value = 15)
> 
> 
> 
> cleanEx()
> nameEx("gamm")
> ### * gamm
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: gamm
> ### Title: Example GAMM simulation data
> ### Aliases: gamm dat
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data("gamm", package = "adlaplace")
> exists("dat")
[1] TRUE
> nrow(dat)
[1] 500
> 
> 
> 
> cleanEx()
> nameEx("intercept-class")
> ### * intercept-class
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: intercept-class
> ### Title: intercept Model Term
> ### Aliases: intercept-class intercept design,intercept-method
> ###   beta_info,intercept-method precision,intercept-method
> ###   random_info,intercept-method
> 
> ### ** Examples
> 
> # Create a intercept term
> intercept_term <- intercept(init=2)
> 
> 
> 
> cleanEx()
> nameEx("iwp")
> ### * iwp
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: iwp
> ### Title: Integrated Wiener Process Term Constructor
> ### Aliases: iwp
> 
> ### ** Examples
> 
> knots <- seq(0, 1, length.out = 5)
> iwp_term <- iwp(x = "age", knots = knots)
> iwp_term
$age_iwp
An object of class "iwp"
Slot "name":
[1] "age"

Slot "label":
[1] "age_iwp"

Slot "formula":
~0 + age
<environment: 0x55f957549be8>

Slot "knots":
[1] 0.00 0.25 0.50 0.75 1.00

Slot "ref_value":
[1] 0

Slot "p.order":
[1] 2

Slot "init":
[1] 0.02

Slot "lower":
[1] 1e-09

Slot "upper":
[1] Inf

Slot "parscale":
[1] 1

Slot "log":
[1] TRUE

Slot "model_role":
[1] random
Levels: fixed random response

Slot "density":
[1] "random_diagonal"

Slot "ad_kind":
[1] "random"

Slot "package":
[1] "adlaplace"


$age_rpoly
An object of class "rpoly"
Slot "sd":
[1] Inf

Slot "basis_scale":
[1] 0.25

Slot "name":
[1] "age"

Slot "label":
[1] "age_rpoly"

Slot "formula":
~0 + age
<environment: 0x55f9576a6d48>

Slot "knots":
numeric(0)

Slot "ref_value":
[1] 0

Slot "p.order":
[1] 1

Slot "init":
numeric(0)

Slot "lower":
numeric(0)

Slot "upper":
numeric(0)

Slot "parscale":
numeric(0)

Slot "log":
[1] TRUE

Slot "model_role":
[1] random
Levels: fixed random response

Slot "density":
[1] "random_diagonal"

Slot "ad_kind":
[1] "random"

Slot "package":
[1] "adlaplace"


> 
> 
> 
> cleanEx()
> nameEx("linear-class")
> ### * linear-class
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: linear-class
> ### Title: Linear Model Term
> ### Aliases: linear-class linear design,linear-method
> ###   beta_info,linear-method precision,linear-method
> ###   random_info,linear-method
> 
> ### ** Examples
> 
> # Create a linear term
> linear_term <- linear(x = "temperature")
> 
> 
> 
> cleanEx()
> nameEx("london")
> ### * london
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: london
> ### Title: London daily mortality and PM10 (case-crossover example)
> ### Aliases: london
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data("london", package = "adlaplace")
> head(london)
    city       date year month day dow all       tmean      rh     pm10
1 London 2002-01-01 2002   Jan   1 Tue 199 -0.22500001 75.6783 71.70000
2 London 2002-01-02 2002   Jan   2 Wed 231  0.08749995 77.5250 40.20000
3 London 2002-01-03 2002   Jan   3 Thu 210  0.85000002 81.3250 41.80000
4 London 2002-01-04 2002   Jan   4 Fri 203  0.53750002 85.4500 50.40000
5 London 2002-01-05 2002   Jan   5 Sat 224  4.25000000 93.5250 49.36429
6 London 2002-01-06 2002   Jan   6 Sun 198  7.06874990 96.4000 31.10000
> 
> 
> 
> cleanEx()
> nameEx("model_data")
> ### * model_data
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: model_data
> ### Title: Assemble model terms and per-shard 'density_data' objects
> ### Aliases: model_data
> 
> ### ** Examples
> 
> set.seed(1)
> dat <- data.frame(
+   y = rpois(30, 2),
+   x1 = rnorm(30),
+   x2 = runif(30)
+ )
> md <- model_data(
+   y ~ x1 + iwp(x2, p = 2, knots = seq(0, 1, length.out = 5)),
+   data = dat
+ )
> names(md$terms)
[1] "gaussian_y" "linear_x1"  "x2_iwp"     "x2_rpoly"   "intercept" 
> 
> 
> 
> cleanEx()
> nameEx("obs_groups")
> ### * obs_groups
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: obs_groups
> ### Title: Partition observations into AD shards by sparsity pattern
> ### Aliases: obs_groups
> 
> ### ** Examples
> 
> set.seed(1)
> A <- matrix(rnorm(100), 20, 5)
> G <- obs_groups(A, num_shards = 3)
> G
20 x 3 sparse Matrix of class "ngCMatrix"
           
 [1,] | . .
 [2,] | . .
 [3,] . . |
 [4,] | . .
 [5,] . | .
 [6,] . | .
 [7,] . | .
 [8,] | . .
 [9,] . | .
[10,] | . .
[11,] | . .
[12,] . | .
[13,] . . |
[14,] . | .
[15,] . | .
[16,] . . |
[17,] . . |
[18,] . . |
[19,] | . .
[20,] . . |
> 
> 
> 
> cleanEx()
> nameEx("outer_optim_wrappers")
> ### * outer_optim_wrappers
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: outer_optim_wrappers
> ### Title: Outer objective and gradient wrappers
> ### Aliases: outer_optim_wrappers outer_fn outer_gr
> 
> ### ** Examples
> 
> set.seed(1)
> n <- 80
> g <- factor(sample(4, n, replace = TRUE))
> x <- rbinom(n, 1, 0.5)
> eta <- 0.5 + 0.4 * x + rnorm(4, sd = 0.3)[g]
> nb_sd <- 0.3
> z <- rgamma(n, nb_sd^(-2), nb_sd^(-2))
> dat <- data.frame(y = rpois(n, exp(eta) * z), x = x, g = g)
> md <- model_data(
+   nbinom(y, lower = 1e-9, init = 0.15) ~ x + iid(g, init = 0.3),
+   data = dat
+ )
> config <- list(
+   transform_theta = TRUE,
+   obs_groups = obs_groups(md$term_data$A, num_shards = 5),
+   verbose = FALSE
+ )
> ap <- ad_pack(md, config)
> cache <- new.env(parent = emptyenv())
> x0 <- md$term_data$info$parameters$init
> outer_fn(x = x0, config = config, cache = cache, ad_pack = ap)
[1] 153.8755
> outer_gr(x = x0, config = config, cache = cache, ad_pack = ap)
[1] -25.3846648 -23.3412463  -0.4940207 -11.3119746
> 
> 
> 
> 
> cleanEx()
> nameEx("ref_align")
> ### * ref_align
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: ref_align
> ### Title: Align Reference Value to Nearest Knot
> ### Aliases: ref_align
> ### Keywords: internal
> 
> ### ** Examples
> 
> # Align reference value to nearest knot
> knots <- c(10, 20, 30, 40, 50)
> adlaplace::ref_align(23, knots) # Returns 20
[1] 20
> 
> 
> 
> 
> cleanEx()
> nameEx("replace_vars")
> ### * replace_vars
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: replace_vars
> ### Title: Replace data-column names in model terms
> ### Aliases: replace_vars replace_vars,model_term-method
> ###   replace_vars,dirichlet_multinom-method replace_vars,formula-method
> ###   replace_vars,list-method
> 
> ### ** Examples
> 
> terms <- collect_terms(nbinom(y) ~ fpoly(sqrt_pm, p = 1))
> replace_vars(terms, c(sqrt_pm = "sqrt_pm_s1"))
$y_nbinom_sd
An object of class "nbinom"
Slot "name":
[1] "y"

Slot "label":
[1] "y_nbinom_sd"

Slot "formula":
y ~ .
<environment: 0x55f959ef1b20>

Slot "knots":
numeric(0)

Slot "ref_value":
numeric(0)

Slot "p.order":
[1] 1

Slot "init":
[1] 0.02

Slot "lower":
[1] 1e-09

Slot "upper":
[1] Inf

Slot "parscale":
[1] 1

Slot "log":
[1] TRUE

Slot "model_role":
[1] response
Levels: fixed random response

Slot "density":
[1] "nbinom_obs"

Slot "ad_kind":
[1] "observations"

Slot "package":
[1] "adlaplace"


$sqrt_pm_s1_fpoly
An object of class "fpoly"
Slot "init":
[1] 0

Slot "lower":
[1] -Inf

Slot "upper":
[1] Inf

Slot "parscale":
[1] 1

Slot "basis_scale":
[1] 1

Slot "name":
[1] "sqrt_pm_s1"

Slot "label":
[1] "sqrt_pm_s1_fpoly"

Slot "formula":
~0 + sqrt_pm_s1
<environment: 0x55f959f41a58>

Slot "knots":
numeric(0)

Slot "ref_value":
[1] 0

Slot "p.order":
[1] 1

Slot "log":
[1] TRUE

Slot "model_role":
[1] fixed
Levels: fixed random response

Slot "density":
[1] NA

Slot "ad_kind":
[1] NA

Slot "package":
[1] "adlaplace"


$intercept
An object of class "intercept"
Slot "sd":
[1] Inf

Slot "name":
[1] "intercept"

Slot "label":
[1] "intercept"

Slot "formula":
. ~ 1
<environment: namespace:adlaplace>

Slot "knots":
numeric(0)

Slot "ref_value":
numeric(0)

Slot "p.order":
integer(0)

Slot "init":
[1] 0

Slot "lower":
[1] -Inf

Slot "upper":
[1] Inf

Slot "parscale":
[1] 1

Slot "log":
[1] TRUE

Slot "model_role":
[1] fixed
Levels: fixed random response

Slot "density":
[1] NA

Slot "ad_kind":
[1] NA

Slot "package":
[1] "adlaplace"


> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  2.874 0.114 3.649 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')