miniLNM

Miniature Logistic-Normal Multinomial Models

v0.1.0 · Sep 13, 2024 · CC0

Description

Logistic-normal Multinomial (LNM) models are common in problems with multivariate count data. This package gives a simple implementation with a 30 line 'Stan' script. This lightweight implementation makes it an easy starting point for other projects, in particular for downstream tasks that require analysis of "compositional" data. It can be applied whenever a multinomial probability parameter is thought to depend linearly on inputs in a transformed, log ratio space. Additional utilities make it easy to inspect, create predictions, and draw samples using the fitted models. More about the LNM can be found in Xia et al. (2013) "A Logistic Normal Multinomial Regression Model for Microbiome Compositional Data Analysis" <doi:10.1111/biom.12079> and Sankaran and Holmes (2023) "Generative Models: An Interdisciplinary Perspective" <doi:10.1146/annurev-statistics-033121-110134>.

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r-devel-linux-x86_64-debian-clang	ERROR	281.3s
r-devel-linux-x86_64-debian-gcc	ERROR	238.5s
r-devel-linux-x86_64-fedora-clang	ERROR	232.5s
r-devel-linux-x86_64-fedora-gcc	ERROR	527.1s
r-devel-windows-x86_64	ERROR	324s
r-oldrel-macos-arm64	NOTE
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r-oldrel-windows-x86_64	ERROR	439s
r-patched-linux-x86_64	NOTE	298.5s
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r-release-windows-x86_64	NOTE	345s

Check details (27 non-OK)

NOTE r-devel-linux-x86_64-debian-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

ERROR r-devel-linux-x86_64-debian-clang

examples

Running examples in ‘miniLNM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: beta_mean
> ### Title: LNM Posterior Mean
> ### Aliases: beta_mean
> 
> ### ** Examples
> 
> example_data <- lnm_data(N = 50, K = 10)
> xy <- dplyr::bind_cols(example_data[c("X", "y")])
> fit <- lnm(
+     starts_with("y") ~ starts_with("x"), xy, 
+     iter = 25, output_samples = 25
+ )
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1:   This procedure has not been thoroughly tested and may be unstable
Chain 1:   or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1: 
Chain 1: 
Chain 1: 
Chain 1: Gradient evaluation took 0.000439 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 4.39 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Begin eta adaptation.
Chain 1: Iteration:   1 / 250 [  0%]  (Adaptation)
Chain 1: Iteration:  50 / 250 [ 20%]  (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%]  (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%]  (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%]  (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1: 
Chain 1: Begin stochastic gradient ascent.
Chain 1:   iter             ELBO   delta_ELBO_mean   delta_ELBO_med   notes 
Chain 1: Informational Message: The maximum number of iterations is reached! The algorithm may not have converged.
Chain 1: This variational approximation is not guaranteed to be meaningful.
Chain 1: 
Chain 1: Drawing a sample of size 25 from the approximate posterior... 
Chain 1: COMPLETED.
Error in if (p$diagnostics$pareto_k > 1) { : 
  missing value where TRUE/FALSE needed
Calls: lnm ... new -> initialize -> initialize -> vb -> vb -> .local
Execution halted

ERROR r-devel-linux-x86_64-debian-clang

tests

Running ‘testthat.R’ [10s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(miniLNM)
  > 
  > test_check("miniLNM")
  Chain 1: ------------------------------------------------------------
  Chain 1: EXPERIMENTAL ALGORITHM:
  Chain 1:   This procedure has not been thoroughly tested and may be unstable
  Chain 1:   or buggy. The interface is subject to change.
  Chain 1: ------------------------------------------------------------
  Chain 1: 
  Chain 1: 
  Chain 1: 
  Chain 1: Gradient evaluation took 0.000228 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per 
...[truncated]...
   warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is disabled.", " Decreasing tol_rel_obj may help if variational algorithm has terminated prematurely.", " Otherwise consider using sampling instead.", call. = FALSE, immediate. = TRUE) } else if (p$diagnostics$pareto_k > 0.7) {     warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is unreliable.", " Increasing the number of draws or decreasing tol_rel_obj may help.", call. = FALSE, immediate. = TRUE) }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. └─miniLNM::lnm(...) at test-sample.R:4:1
   2.   ├─methods::new(...)
   3.   │ ├─methods::initialize(value, ...)
   4.   │ └─methods::initialize(value, ...)
   5.   ├─rstan::vb(stanmodels$lnm, data_list, ...)
   6.   └─rstan::vb(stanmodels$lnm, data_list, ...)
   7.     └─rstan (local) .local(object, ...)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted

NOTE r-devel-linux-x86_64-debian-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

ERROR r-devel-linux-x86_64-debian-gcc

examples

Running examples in ‘miniLNM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: beta_mean
> ### Title: LNM Posterior Mean
> ### Aliases: beta_mean
> 
> ### ** Examples
> 
> example_data <- lnm_data(N = 50, K = 10)
> xy <- dplyr::bind_cols(example_data[c("X", "y")])
> fit <- lnm(
+     starts_with("y") ~ starts_with("x"), xy, 
+     iter = 25, output_samples = 25
+ )
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1:   This procedure has not been thoroughly tested and may be unstable
Chain 1:   or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1: 
Chain 1: 
Chain 1: 
Chain 1: Gradient evaluation took 0.00036 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 3.6 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Begin eta adaptation.
Chain 1: Iteration:   1 / 250 [  0%]  (Adaptation)
Chain 1: Iteration:  50 / 250 [ 20%]  (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%]  (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%]  (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%]  (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1: 
Chain 1: Begin stochastic gradient ascent.
Chain 1:   iter             ELBO   delta_ELBO_mean   delta_ELBO_med   notes 
Chain 1: Informational Message: The maximum number of iterations is reached! The algorithm may not have converged.
Chain 1: This variational approximation is not guaranteed to be meaningful.
Chain 1: 
Chain 1: Drawing a sample of size 25 from the approximate posterior... 
Chain 1: COMPLETED.
Error in if (p$diagnostics$pareto_k > 1) { : 
  missing value where TRUE/FALSE needed
Calls: lnm ... new -> initialize -> initialize -> vb -> vb -> .local
Execution halted

ERROR r-devel-linux-x86_64-debian-gcc

tests

Running ‘testthat.R’ [7s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(miniLNM)
  > 
  > test_check("miniLNM")
  Chain 1: ------------------------------------------------------------
  Chain 1: EXPERIMENTAL ALGORITHM:
  Chain 1:   This procedure has not been thoroughly tested and may be unstable
  Chain 1:   or buggy. The interface is subject to change.
  Chain 1: ------------------------------------------------------------
  Chain 1: 
  Chain 1: 
  Chain 1: 
  Chain 1: Gradient evaluation took 0.000189 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per tr
...[truncated]...
   warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is disabled.", " Decreasing tol_rel_obj may help if variational algorithm has terminated prematurely.", " Otherwise consider using sampling instead.", call. = FALSE, immediate. = TRUE) } else if (p$diagnostics$pareto_k > 0.7) {     warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is unreliable.", " Increasing the number of draws or decreasing tol_rel_obj may help.", call. = FALSE, immediate. = TRUE) }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. └─miniLNM::lnm(...) at test-sample.R:4:1
   2.   ├─methods::new(...)
   3.   │ ├─methods::initialize(value, ...)
   4.   │ └─methods::initialize(value, ...)
   5.   ├─rstan::vb(stanmodels$lnm, data_list, ...)
   6.   └─rstan::vb(stanmodels$lnm, data_list, ...)
   7.     └─rstan (local) .local(object, ...)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted

NOTE r-devel-linux-x86_64-fedora-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

ERROR r-devel-linux-x86_64-fedora-clang

examples

Running examples in ‘miniLNM-Ex.R’ failed
The error most likely occurred in:

> ### Name: beta_mean
> ### Title: LNM Posterior Mean
> ### Aliases: beta_mean
> 
> ### ** Examples
> 
> example_data <- lnm_data(N = 50, K = 10)
> xy <- dplyr::bind_cols(example_data[c("X", "y")])
> fit <- lnm(
+     starts_with("y") ~ starts_with("x"), xy, 
+     iter = 25, output_samples = 25
+ )
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1:   This procedure has not been thoroughly tested and may be unstable
Chain 1:   or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1: 
Chain 1: 
Chain 1: 
Chain 1: Gradient evaluation took 0.000424 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 4.24 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Begin eta adaptation.
Chain 1: Iteration:   1 / 250 [  0%]  (Adaptation)
Chain 1: Iteration:  50 / 250 [ 20%]  (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%]  (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%]  (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%]  (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1: 
Chain 1: Begin stochastic gradient ascent.
Chain 1:   iter             ELBO   delta_ELBO_mean   delta_ELBO_med   notes 
Chain 1: Informational Message: The maximum number of iterations is reached! The algorithm may not have converged.
Chain 1: This variational approximation is not guaranteed to be meaningful.
Chain 1: 
Chain 1: Drawing a sample of size 25 from the approximate posterior... 
Chain 1: COMPLETED.
Error in if (p$diagnostics$pareto_k > 1) { : 
  missing value where TRUE/FALSE needed
Calls: lnm ... new -> initialize -> initialize -> vb -> vb -> .local
Execution halted

ERROR r-devel-linux-x86_64-fedora-clang

tests

Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(miniLNM)
  > 
  > test_check("miniLNM")
  Chain 1: ------------------------------------------------------------
  Chain 1: EXPERIMENTAL ALGORITHM:
  Chain 1:   This procedure has not been thoroughly tested and may be unstable
  Chain 1:   or buggy. The interface is subject to change.
  Chain 1: ------------------------------------------------------------
  Chain 1: 
  Chain 1: 
  Chain 1: 
  Chain 1: Gradient evaluation took 0.00054 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition 
...[truncated]...
   warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is disabled.", " Decreasing tol_rel_obj may help if variational algorithm has terminated prematurely.", " Otherwise consider using sampling instead.", call. = FALSE, immediate. = TRUE) } else if (p$diagnostics$pareto_k > 0.7) {     warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is unreliable.", " Increasing the number of draws or decreasing tol_rel_obj may help.", call. = FALSE, immediate. = TRUE) }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. └─miniLNM::lnm(...) at test-sample.R:4:1
   2.   ├─methods::new(...)
   3.   │ ├─methods::initialize(value, ...)
   4.   │ └─methods::initialize(value, ...)
   5.   ├─rstan::vb(stanmodels$lnm, data_list, ...)
   6.   └─rstan::vb(stanmodels$lnm, data_list, ...)
   7.     └─rstan (local) .local(object, ...)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted

NOTE r-devel-linux-x86_64-fedora-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

ERROR r-devel-linux-x86_64-fedora-gcc

examples

Running examples in ‘miniLNM-Ex.R’ failed
The error most likely occurred in:

> ### Name: beta_mean
> ### Title: LNM Posterior Mean
> ### Aliases: beta_mean
> 
> ### ** Examples
> 
> example_data <- lnm_data(N = 50, K = 10)
> xy <- dplyr::bind_cols(example_data[c("X", "y")])
> fit <- lnm(
+     starts_with("y") ~ starts_with("x"), xy, 
+     iter = 25, output_samples = 25
+ )
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1:   This procedure has not been thoroughly tested and may be unstable
Chain 1:   or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1: 
Chain 1: 
Chain 1: 
Chain 1: Gradient evaluation took 0.001765 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 17.65 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Begin eta adaptation.
Chain 1: Iteration:   1 / 250 [  0%]  (Adaptation)
Chain 1: Iteration:  50 / 250 [ 20%]  (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%]  (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%]  (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%]  (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1: 
Chain 1: Begin stochastic gradient ascent.
Chain 1:   iter             ELBO   delta_ELBO_mean   delta_ELBO_med   notes 
Chain 1: Informational Message: The maximum number of iterations is reached! The algorithm may not have converged.
Chain 1: This variational approximation is not guaranteed to be meaningful.
Chain 1: 
Chain 1: Drawing a sample of size 25 from the approximate posterior... 
Chain 1: COMPLETED.
Error in if (p$diagnostics$pareto_k > 1) { : 
  missing value where TRUE/FALSE needed
Calls: lnm ... new -> initialize -> initialize -> vb -> vb -> .local
Execution halted

ERROR r-devel-linux-x86_64-fedora-gcc

tests

Running ‘testthat.R’ [13s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(miniLNM)
  > 
  > test_check("miniLNM")
  Chain 1: ------------------------------------------------------------
  Chain 1: EXPERIMENTAL ALGORITHM:
  Chain 1:   This procedure has not been thoroughly tested and may be unstable
  Chain 1:   or buggy. The interface is subject to change.
  Chain 1: ------------------------------------------------------------
  Chain 1: 
  Chain 1: 
  Chain 1: 
  Chain 1: Gradient evaluation took 0.000784 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per 
...[truncated]...
   warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is disabled.", " Decreasing tol_rel_obj may help if variational algorithm has terminated prematurely.", " Otherwise consider using sampling instead.", call. = FALSE, immediate. = TRUE) } else if (p$diagnostics$pareto_k > 0.7) {     warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is unreliable.", " Increasing the number of draws or decreasing tol_rel_obj may help.", call. = FALSE, immediate. = TRUE) }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. └─miniLNM::lnm(...) at test-sample.R:4:1
   2.   ├─methods::new(...)
   3.   │ ├─methods::initialize(value, ...)
   4.   │ └─methods::initialize(value, ...)
   5.   ├─rstan::vb(stanmodels$lnm, data_list, ...)
   6.   └─rstan::vb(stanmodels$lnm, data_list, ...)
   7.     └─rstan (local) .local(object, ...)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted

NOTE r-devel-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'

ERROR r-devel-windows-x86_64

examples

Running examples in 'miniLNM-Ex.R' failed
The error most likely occurred in:

> ### Name: beta_mean
> ### Title: LNM Posterior Mean
> ### Aliases: beta_mean
> 
> ### ** Examples
> 
> example_data <- lnm_data(N = 50, K = 10)
> xy <- dplyr::bind_cols(example_data[c("X", "y")])
> fit <- lnm(
+     starts_with("y") ~ starts_with("x"), xy, 
+     iter = 25, output_samples = 25
+ )
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1:   This procedure has not been thoroughly tested and may be unstable
Chain 1:   or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1: 
Chain 1: 
Chain 1: 
Chain 1: Gradient evaluation took 0.000701 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 7.01 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Begin eta adaptation.
Chain 1: Iteration:   1 / 250 [  0%]  (Adaptation)
Chain 1: Iteration:  50 / 250 [ 20%]  (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%]  (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%]  (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%]  (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1: 
Chain 1: Begin stochastic gradient ascent.
Chain 1:   iter             ELBO   delta_ELBO_mean   delta_ELBO_med   notes 
Chain 1: Informational Message: The maximum number of iterations is reached! The algorithm may not have converged.
Chain 1: This variational approximation is not guaranteed to be meaningful.
Chain 1: 
Chain 1: Drawing a sample of size 25 from the approximate posterior... 
Chain 1: COMPLETED.
Error in if (p$diagnostics$pareto_k > 1) { : 
  missing value where TRUE/FALSE needed
Calls: lnm ... new -> initialize -> initialize -> vb -> vb -> .local
Execution halted

ERROR r-devel-windows-x86_64

tests

Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(miniLNM)
  > 
  > test_check("miniLNM")
  Chain 1: ------------------------------------------------------------
  Chain 1: EXPERIMENTAL ALGORITHM:
  Chain 1:   This procedure has not been thoroughly tested and may be unstable
  Chain 1:   or buggy. The interface is subject to change.
  Chain 1: ------------------------------------------------------------
  Chain 1: 
  Chain 1: 
  Chain 1: 
  Chain 1: Gradient evaluation took 0.000456 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per tran
...[truncated]...
   warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is disabled.", " Decreasing tol_rel_obj may help if variational algorithm has terminated prematurely.", " Otherwise consider using sampling instead.", call. = FALSE, immediate. = TRUE) } else if (p$diagnostics$pareto_k > 0.7) {     warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is unreliable.", " Increasing the number of draws or decreasing tol_rel_obj may help.", call. = FALSE, immediate. = TRUE) }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. └─miniLNM::lnm(...) at test-sample.R:4:1
   2.   ├─methods::new(...)
   3.   │ ├─methods::initialize(value, ...)
   4.   │ └─methods::initialize(value, ...)
   5.   ├─rstan::vb(stanmodels$lnm, data_list, ...)
   6.   └─rstan::vb(stanmodels$lnm, data_list, ...)
   7.     └─rstan (local) .local(object, ...)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted

NOTE r-oldrel-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-oldrel-macos-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-oldrel-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'

ERROR r-oldrel-windows-x86_64

examples

Running examples in 'miniLNM-Ex.R' failed
The error most likely occurred in:

> ### Name: beta_mean
> ### Title: LNM Posterior Mean
> ### Aliases: beta_mean
> 
> ### ** Examples
> 
> example_data <- lnm_data(N = 50, K = 10)
> xy <- dplyr::bind_cols(example_data[c("X", "y")])
> fit <- lnm(
+     starts_with("y") ~ starts_with("x"), xy, 
+     iter = 25, output_samples = 25
+ )
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1:   This procedure has not been thoroughly tested and may be unstable
Chain 1:   or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1: 
Chain 1: 
Chain 1: 
Chain 1: Gradient evaluation took 0.000506 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 5.06 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Begin eta adaptation.
Chain 1: Iteration:   1 / 250 [  0%]  (Adaptation)
Chain 1: Iteration:  50 / 250 [ 20%]  (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%]  (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%]  (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%]  (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1: 
Chain 1: Begin stochastic gradient ascent.
Chain 1:   iter             ELBO   delta_ELBO_mean   delta_ELBO_med   notes 
Chain 1: Informational Message: The maximum number of iterations is reached! The algorithm may not have converged.
Chain 1: This variational approximation is not guaranteed to be meaningful.
Chain 1: 
Chain 1: Drawing a sample of size 25 from the approximate posterior... 
Chain 1: COMPLETED.
Error in if (p$diagnostics$pareto_k > 1) { : 
  missing value where TRUE/FALSE needed
Calls: lnm ... new -> initialize -> initialize -> vb -> vb -> .local
Execution halted

ERROR r-oldrel-windows-x86_64

tests

Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(miniLNM)
  > 
  > test_check("miniLNM")
  Chain 1: ------------------------------------------------------------
  Chain 1: EXPERIMENTAL ALGORITHM:
  Chain 1:   This procedure has not been thoroughly tested and may be unstable
  Chain 1:   or buggy. The interface is subject to change.
  Chain 1: ------------------------------------------------------------
  Chain 1: 
  Chain 1: 
  Chain 1: 
  Chain 1: Gradient evaluation took 0.000467 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per tran
...[truncated]...
   warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is disabled.", " Decreasing tol_rel_obj may help if variational algorithm has terminated prematurely.", " Otherwise consider using sampling instead.", call. = FALSE, immediate. = TRUE) } else if (p$diagnostics$pareto_k > 0.7) {     warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is unreliable.", " Increasing the number of draws or decreasing tol_rel_obj may help.", call. = FALSE, immediate. = TRUE) }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. └─miniLNM::lnm(...) at test-sample.R:4:1
   2.   ├─methods::new(...)
   3.   │ ├─methods::initialize(value, ...)
   4.   │ └─methods::initialize(value, ...)
   5.   ├─rstan::vb(stanmodels$lnm, data_list, ...)
   6.   └─rstan::vb(stanmodels$lnm, data_list, ...)
   7.     └─rstan (local) .local(object, ...)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted

NOTE r-patched-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

ERROR r-release-linux-x86_64

examples

Running examples in ‘miniLNM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: beta_mean
> ### Title: LNM Posterior Mean
> ### Aliases: beta_mean
> 
> ### ** Examples
> 
> example_data <- lnm_data(N = 50, K = 10)
> xy <- dplyr::bind_cols(example_data[c("X", "y")])
> fit <- lnm(
+     starts_with("y") ~ starts_with("x"), xy, 
+     iter = 25, output_samples = 25
+ )
Chain 1: ------------------------------------------------------------
Chain 1: EXPERIMENTAL ALGORITHM:
Chain 1:   This procedure has not been thoroughly tested and may be unstable
Chain 1:   or buggy. The interface is subject to change.
Chain 1: ------------------------------------------------------------
Chain 1: 
Chain 1: 
Chain 1: 
Chain 1: Gradient evaluation took 0.000421 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 4.21 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Begin eta adaptation.
Chain 1: Iteration:   1 / 250 [  0%]  (Adaptation)
Chain 1: Iteration:  50 / 250 [ 20%]  (Adaptation)
Chain 1: Iteration: 100 / 250 [ 40%]  (Adaptation)
Chain 1: Iteration: 150 / 250 [ 60%]  (Adaptation)
Chain 1: Iteration: 200 / 250 [ 80%]  (Adaptation)
Chain 1: Success! Found best value [eta = 1] earlier than expected.
Chain 1: 
Chain 1: Begin stochastic gradient ascent.
Chain 1:   iter             ELBO   delta_ELBO_mean   delta_ELBO_med   notes 
Chain 1: Informational Message: The maximum number of iterations is reached! The algorithm may not have converged.
Chain 1: This variational approximation is not guaranteed to be meaningful.
Chain 1: 
Chain 1: Drawing a sample of size 25 from the approximate posterior... 
Chain 1: COMPLETED.
Error in if (p$diagnostics$pareto_k > 1) { : 
  missing value where TRUE/FALSE needed
Calls: lnm ... new -> initialize -> initialize -> vb -> vb -> .local
Execution halted

ERROR r-release-linux-x86_64

tests

Running ‘testthat.R’ [10s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(miniLNM)
  > 
  > test_check("miniLNM")
  Chain 1: ------------------------------------------------------------
  Chain 1: EXPERIMENTAL ALGORITHM:
  Chain 1:   This procedure has not been thoroughly tested and may be unstable
  Chain 1:   or buggy. The interface is subject to change.
  Chain 1: ------------------------------------------------------------
  Chain 1: 
  Chain 1: 
  Chain 1: 
  Chain 1: Gradient evaluation took 0.000279 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per 
...[truncated]...
   warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is disabled.", " Decreasing tol_rel_obj may help if variational algorithm has terminated prematurely.", " Otherwise consider using sampling instead.", call. = FALSE, immediate. = TRUE) } else if (p$diagnostics$pareto_k > 0.7) {     warning("Pareto k diagnostic value is ", round(p$diagnostics$pareto_k, 2), ". Resampling is unreliable.", " Increasing the number of draws or decreasing tol_rel_obj may help.", call. = FALSE, immediate. = TRUE) }`: missing value where TRUE/FALSE needed
  Backtrace:
      ▆
   1. └─miniLNM::lnm(...) at test-sample.R:4:1
   2.   ├─methods::new(...)
   3.   │ ├─methods::initialize(value, ...)
   4.   │ └─methods::initialize(value, ...)
   5.   ├─rstan::vb(stanmodels$lnm, data_list, ...)
   6.   └─rstan::vb(stanmodels$lnm, data_list, ...)
   7.     └─rstan (local) .local(object, ...)
  
  [ FAIL 3 | WARN 0 | SKIP 0 | PASS 0 ]
  Error:
  ! Test failures.
  Execution halted

NOTE r-release-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-macos-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'

Check History

ERROR 0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 27, 2026

NOTE r-devel-linux-x86_64-debian-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

ERROR r-devel-linux-x86_64-debian-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-linux-x86_64-fedora-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-linux-x86_64-fedora-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'

NOTE r-patched-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-macos-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'

NOTE r-oldrel-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-oldrel-macos-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-oldrel-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'

NOTE 0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026

NOTE r-devel-linux-x86_64-debian-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-linux-x86_64-debian-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-linux-x86_64-fedora-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-linux-x86_64-fedora-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'

NOTE r-patched-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-macos-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'

NOTE r-oldrel-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-oldrel-macos-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-oldrel-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'

ERROR 0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026

NOTE r-devel-linux-x86_64-debian-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

ERROR r-devel-linux-x86_64-debian-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-linux-x86_64-fedora-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-linux-x86_64-fedora-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'

NOTE r-patched-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-macos-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'

NOTE r-oldrel-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-oldrel-macos-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-oldrel-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'

NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 22, 2026

NOTE r-devel-linux-x86_64-debian-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-linux-x86_64-debian-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-linux-x86_64-fedora-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-linux-x86_64-fedora-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'

NOTE r-patched-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-macos-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'

NOTE r-oldrel-macos-arm64

installed package size

installed size is 42.4Mb
  sub-directories of 1Mb or more:
    libs  41.9Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is 43.3Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb

NOTE r-oldrel-windows-x86_64

for GNU extensions in Makefiles

GNU make is a SystemRequirements.

ERROR 0 OK · 13 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 18, 2026

NOTE r-devel-linux-x86_64-debian-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-linux-x86_64-debian-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-linux-x86_64-fedora-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-linux-x86_64-fedora-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

ERROR r-devel-windows-x86_64

whether package can be installed

Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.6/miniLNM.Rcheck/00install.out' for details.

NOTE r-patched-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-macos-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'

NOTE r-oldrel-macos-arm64

installed package size

installed size is 42.4Mb
  sub-directories of 1Mb or more:
    libs  41.9Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is 43.3Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb

NOTE r-oldrel-windows-x86_64

for GNU extensions in Makefiles

GNU make is a SystemRequirements.

NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026

NOTE r-devel-linux-x86_64-debian-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-linux-x86_64-debian-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-linux-x86_64-fedora-clang

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-linux-x86_64-fedora-gcc

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-devel-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'

NOTE r-patched-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-linux-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-macos-arm64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-macos-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    ‘estimate.R’ ‘formula.R’ ‘toy_data.R’

NOTE r-release-windows-x86_64

DESCRIPTION meta-information

Missing dependency on R >= 4.1.0 because package code uses the pipe
  |> or function shorthand \(...) syntax added in R 4.1.0.
  File(s) using such syntax:
    'estimate.R' 'formula.R' 'toy_data.R'

NOTE r-oldrel-macos-arm64

installed package size

installed size is 42.4Mb
  sub-directories of 1Mb or more:
    libs  41.9Mb

NOTE r-oldrel-macos-x86_64

installed package size

installed size is 43.3Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb

NOTE r-oldrel-windows-x86_64

for GNU extensions in Makefiles

GNU make is a SystemRequirements.

Reverse Dependencies (1)

imports

multimedia

Dependency Network

Version History

1 tracked

new 0.1.0 Mar 10, 2026

R Observatory began tracking this package on Mar 10, 2026; it first appeared on CRAN Sep 13, 2024. Releases before tracking aren’t shown.

People

Kris Sankaran author maintainer

Available on

CRAN r2u Bioconductor autoCRAN COPR

Dependencies

Depends

R (>= 4.0.0)

Imports

Rcpp (>= 0.12.0)RcppParallel (>= 5.0.1)cli dplyr fansi formula.tools gluemethodsposterior rstan (>= 2.18.1)rstantools (>= 2.4.0)tidyselect

Suggests

knitr rmarkdown testthat (>= 3.0.0)

Compilation

Needs compilation

First Published

Sep 13, 2024

First appeared in R 4.4.1 · current R 4.6.1

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CRAN Checks

View on CRAN →