R Observatory: Metrics for spsurv version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

spsurv

1.1.0Package record

Bernstein Polynomial Based Semiparametric Survival Analysis

0packages depend

1.6Kdownloads / year

88.7%test coverage

10/13flavors OK

Overview

About

Maintained by Renato PanaroCRAN page ↗GitHub ↗Website ↗Issues ↗

Semiparametric survival analysis based on Bernstein polynomials. 'spsurv' includes proportional hazards, proportional odds and accelerated failure time frameworks for right-censored data. RV Panaro (2020) doi:10.48550/arXiv.2003.10548.

Changes in 1.1.0

**CRAN resubmission:** Maintainer contact updated to rvpanaro@gmail.com; license is GPL-3 (removed the bundled LICENSE copy of the GPL); Authors@R roles reviewed (single maintainer; thesis advisors listed as ths, with rev for code review feedback); package Description citation updated to <doi:10.48550/arXiv.2003.10548>; set Config/rstantools/auto_config: FALSE and ship committed Stan C++ exports (no install-time configure/rstan_config(), avoiding Windows R-devel rstan.dll load failures); added RcppParallel and synced src/Makevars.win TBB flags with Unix Makevars; restored covr, rsample, and rsurv in Suggests for optional tests referenced in tests/.
**Inference robustness:** .spbp_gamma_information_diagnostics() no longer calls qr() on non-finite gamma information matrices; vcov()/survfit() return NA uncertainty with a warning when that block is unavailable.

Show all changes in 1.1.0Hide the rest of the changes in 1.1.0

**tidymodels:** parsnip engines spsurv (MLE) and spsurv_bayes for proportional_hazards(), new proportional_odds(), and survival_reg(); bp_survival_reg() convenience constructor; workflow / predict(type = "survival") support.
**tidybayes:** as_draws_df.spbp(), spread_surv_draws.spbp(), and S3 hooks for tidy_draws / spread_draws / gather_draws on Bayes fits; posterior draw indices (.chain, .iteration, .draw).
**Prediction:** censored-style predict.spbp() types (survival, time, linear_pred); augment.spbp().
**Vignette:** vignette("tidymodels").
**Inference:** vcov.spbp() no longer applies a diagonal ridge (polish removed); beta standard errors are unchanged when the Bernstein block is stable and no longer inflated when it is ill-conditioned.
**Summary:** summary.spbp() now includes a coef_interval component (Wald for MLE, HPD for Bayes) and prints it when show_intervals = TRUE.
**Repository:** paper workflow moved from inst/ to paper/ (excluded from the package tarball).
**Dependencies:** trimmed Suggests to packages used in vignettes, tests, or optional integrations. devtools and roxygen2 are not listed in Suggests.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("spsurv", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("rvpanaro/spsurv")

Development version from rvpanaro/spsurv. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-spsurv

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-spsurv

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-spsurv

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

3ERROR10OK

Check messages

ERRORtestsr-oldrel-macos-x86_64, r-oldrel-windows-x86_64, r-release-macos-x86_64

r-oldrel-macos-x86_64

Running ‘testthat.R’ [33s/94s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(parsnip)
  > library(generics)
  
  Attaching package: 'generics'
  
  The following objects are masked from 'package:base':
  
      as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
      setequal, union
  
  > library(spsurv)
  Loading required package: survival
  Loading required package: coda
  > veteran <- survival::veteran
  > 
  > test_check("spsurv")
  
  SAMPLING FOR MODEL 'spbp' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 9e-05 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.9 seconds.
  Chain 1: Adjust your expectations accordingly!
  Chain 1: 
  Chain 1: 
  Chain 1: WARNING: No variance estimation is
  Chain 1:          performed for num_warmup < 20
  Chain 1: 
  Chain 1: Iteration: 1 / 10 [ 10%]  (Warmup)
  Chain 1: Iteration: 2 / 10 [ 20%]  (Warmup)
  Chain 1: Iterati
...[truncated]...
. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. ├─stats::vcov(fit, bp.param = TRUE)
   10. └─spsurv:::vcov.spbp(fit, bp.param = TRUE)
   11.   └─spsurv:::.spbp_sym_inv(Schur_A)
  ── Error ('test-vcov.R:166:3'): ill-conditioned gamma warning appears only for survfit, not after fit ──
  Error: symmetric inverse requires a finite numeric matrix
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(vcov(fit)) at test-vcov.R:166:3
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. ├─stats::vcov(fit)
   10. └─spsurv:::vcov.spbp(fit)
   11.   └─spsurv:::.spbp_sym_inv(Schur_A)
  
  [ FAIL 3 | WARN 46 | SKIP 1 | PASS 672 ]
  Error:
  ! Test failures.
  Execution halted

r-oldrel-windows-x86_64

Running 'testthat.R' [57s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(parsnip)
  > library(generics)
  
  Attaching package: 'generics'
  
  The following objects are masked from 'package:base':
  
      as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
      setequal, union
  
  > library(spsurv)
  Loading required package: survival
  Loading required package: coda
  > veteran <- survival::veteran
  > 
  > test_check("spsurv")
  
  SAMPLING FOR MODEL 'spbp' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 0.00011 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.1 seconds.
  Chain 1: Adjust your expectations accordingly!
  Chain 1: 
  Chain 1: 
  Chain 1: WARNING: No variance estimation is
  Chain 1:          performed for num_warmup < 20
  Chain 1: 
  Chain 1: Iteration: 1 / 10 [ 10%]  (Warmup)
  Chain 1: Iteration: 2 / 10 [ 20%]  (Warmup)
  Chain 1: Iteration
...[truncated]...
0
  factor(celltype)large        0.097 0.097   0.1
  
  --- 
  DIC = 2885   WAIC = -1443 
  [ FAIL 1 | WARN 52 | SKIP 1 | PASS 685 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • Set SPSURV_RUN_COVERAGE=true to run coverage check (1): 'test-coverage.R:6:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-interval.R:18:3'): confint with custom level ───────────────────
  Error in `array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), NULL) else NULL)`: 'data' must be of a vector type, was 'NULL'
  Backtrace:
      ▆
   1. ├─stats::confint(fit, level = 0.9) at test-interval.R:18:3
   2. └─spsurv:::confint.spbp(fit, level = 0.9)
   3.   ├─base::diag(as.matrix(vcov(object)))
   4.   ├─base::as.matrix(vcov(object))
   5.   └─base::as.matrix.default(vcov(object))
   6.     └─base::array(...)
  
  [ FAIL 1 | WARN 52 | SKIP 1 | PASS 685 ]
  Error:
  ! Test failures.
  Execution halted

r-release-macos-x86_64

Running ‘testthat.R’ [32s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(parsnip)
  > library(generics)
  
  Attaching package: 'generics'
  
  The following objects are masked from 'package:base':
  
      as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
      setequal, union
  
  > library(spsurv)
  Loading required package: survival
  Loading required package: coda
  > veteran <- survival::veteran
  > 
  > test_check("spsurv")
  
  SAMPLING FOR MODEL 'spbp' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 6.3e-05 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.63 seconds.
  Chain 1: Adjust your expectations accordingly!
  Chain 1: 
  Chain 1: 
  Chain 1: WARNING: No variance estimation is
  Chain 1:          performed for num_warmup < 20
  Chain 1: 
  Chain 1: Iteration: 1 / 10 [ 10%]  (Warmup)
  Chain 1: Iteration: 2 / 10 [ 20%]  (Warmup)
  Chain 1: Iter
...[truncated]...
. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. ├─stats::vcov(fit, bp.param = TRUE)
   10. └─spsurv:::vcov.spbp(fit, bp.param = TRUE)
   11.   └─spsurv:::.spbp_sym_inv(Schur_A)
  ── Error ('test-vcov.R:166:3'): ill-conditioned gamma warning appears only for survfit, not after fit ──
  Error: symmetric inverse requires a finite numeric matrix
  Backtrace:
       ▆
    1. ├─testthat::expect_silent(vcov(fit)) at test-vcov.R:166:3
    2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise)
    3. │   ├─testthat (local) .capture(...)
    4. │   │ ├─withr::with_output_sink(...)
    5. │   │ │ └─base::force(code)
    6. │   │ ├─base::withCallingHandlers(...)
    7. │   │ └─base::withVisible(code)
    8. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    9. ├─stats::vcov(fit)
   10. └─spsurv:::vcov.spbp(fit)
   11.   └─spsurv:::.spbp_sym_inv(Schur_A)
  
  [ FAIL 3 | WARN 46 | SKIP 1 | PASS 672 ]
  Error:
  ! Test failures.
  Execution halted

CRAN check page ↗

Slowest check: 15.7 min · r-oldrel-macos-x86_64

Status changes

ERROR10 OK, 3 ERRORNow
ERROR4 OK, 2 ERROR2026-09-29
OK6 OK2026-09-28
NOTE9 OK, 4 NOTE2026-06-09
ERROR9 OK, 3 NOTE, 1 ERROR2026-06-08
NOTE7 OK, 7 NOTE2026-04-22

Show 2 earlier changesHide 2 earlier changes

ERROR6 OK, 7 NOTE, 1 ERROR2026-04-18
NOTE7 OK, 7 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.0

READMEYes · 426 wordsVignettesYes · 8 · evaluation depends on the environmentNEWSYes · 100% structured · mentions 1.1.0Citation fileNoWebsiteYes · pkgdown

Help pages: 54 (10 internal)includes a package overview page
Examples that run: 83%10 run in a plain check · 2 never run
Exported functions with examples: 32%
Documented parameters: 71%
Return-value docs: 73%
Help pages citing references: 2%

Vignettes (8)

How these are measured

Downloads

1.6K

CRAN downloads in the past year

Rank #25,287 · ~4/day · ~136/mo

Releases R versions

Daily download trend is not available in this view yet.

31730 days

31790 days

1.6K1 year

Compare downloads with other packages →

Also on500 r2u7 autocran

How downloads are counted

Repository

rvpanaro/spsurv ↗Account: rvpanaro

5Stars

0Forks

0Open issues

0Open PRs

0Releases

133Commits

8Commit identities

survival-analysisr-packagebernstein-polynomialrstansurvival-regressionrstats-packagecran-r

133 commits · Last activity 2026-10-04

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 508
Median days to close, 50 most recently updated closed PRs: 0

Issues over time

2026-09-28 · 12026-09-30 · 0

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/rvpanaro/spsurv on 2026-10-11.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-04 · The repository has a site deploy workflow

pkgdown site last built 2026-10-04

Coverage (1)

Coverage reporting (Codecov)

CRAN release process (2)

cran-comments.mdrevdep/

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

26 external dependencies (excludes base and recommended)

Installing spsurv adds 49 packages (22 with compiled code, 46 MB of source tarballs). Heaviest: BH 14 MB, ggplot2 6.0 MB, viridis 2.9 MB.

Depends (3)

R >= 4.1.0survivalcoda

Imports (6)

methodsRcpp RcppParallel rstan (>= 2.18.1)generics viridis

LinkingTo (6)

BH Rcpp RcppEigen RcppParallel rstan StanHeaders (>= 2.18.0)

Suggests (14)

testthat knitr rmarkdown ggplot2 (>= 3.3.0)KMsurv parsnip censored workflows tidybayes posterior (>= 1.4.0)covr rsample rsurv rstantools

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (3)

Renato Panaro

https://rvpanaro.github.io/

Fábio Demarqui

Thesis advisor, Reviewer

http://www.est.ufmg.br/~fndemarqui/

Vinicius Mayrink

Thesis advisor · added in 1.1.0

http://www.est.ufmg.br/~vdinizm/

Listed in earlier versions (1)

Vinícius Mayrink

no longer listed · 1.0.0

Releases (2)

Pick two releases to compare their code metrics.

unarchivedReturned to CRAN
2026-09-28
1.1.0Latest
record
2026-09-28 · current release · diff ↗ ·
removed 9 exports
coef, confint, extract, itsamp, mode, stan_dens, survivor, traceplot, vcov

added 17 exports
as_draws_df.spbp, bernstein, bp_survival_reg, credint, estimates, ggresiduals, proportional_odds, pw.basis, rank_models, se, spread_surv_draws.spbp, spsurv_fit_proportional_hazards, spsurv_fit_proportional_odds, spsurv_fit_survival_reg, spsurv_pred_linear_pred, spsurv_pred_survival, spsurv_pred_time
archivedRemoved from CRAN
2026-06-11
email to the maintainer is undeliverable
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
1.0.0
record
2020-03-31
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-03-31
Total releases: 2 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.1.0
Download size: 1.1 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("spsurv")

Format

Panaro, R., Demarqui, F., & Mayrink, V. (2026). spsurv: Bernstein Polynomial Based Semiparametric Survival Analysis (Version 1.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.spsurv

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for spsurv version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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