Package ipd updated to version 0.4.0 with previous version 0.1.4 dated 2025-01-07

Fri, 06 Mar 2026 09:02:00 CDT

Title: Inference on Predicted Data
Description: Performs valid statistical inference on predicted data (IPD) using recent methods, where for a subset of the data, the outcomes have been predicted by an algorithm. Provides a wrapper function with specified defaults for the type of model and method to be used for estimation and inference. Further provides methods for tidying and summarizing results. Salerno et al., (2025) <doi:10.1093/bioinformatics/btaf055>.
Author: Stephen Salerno [aut, cre, cph] , Jiacheng Miao [aut], Awan Afiaz [aut], Kentaro Hoffman [aut], Jesse Gronsbell [aut], Jianhui Gao [aut], David Cheng [aut], Anna Neufeld [aut], Qiongshi Lu [aut], Tyler H McCormick [aut], Jeffrey T Leek [aut]
Maintainer: Stephen Salerno <ssalerno@fredhutch.org>

Diff between ipd versions 0.1.4 dated 2025-01-07 and 0.4.0 dated 2026-03-06

 ipd-0.1.4/ipd/R/helpers.R                      |only
 ipd-0.1.4/ipd/man/figures                      |only
 ipd-0.4.0/ipd/DESCRIPTION                      |   34
 ipd-0.4.0/ipd/MD5                              |  202 +-
 ipd-0.4.0/ipd/NAMESPACE                        |   39
 ipd-0.4.0/ipd/NEWS.md                          |  116 +
 ipd-0.4.0/ipd/R/chen_logistic.R                |only
 ipd-0.4.0/ipd/R/chen_ols.R                     |only
 ipd-0.4.0/ipd/R/chen_poisson.R                 |only
 ipd-0.4.0/ipd/R/ipd-package.R                  |   75
 ipd-0.4.0/ipd/R/ipd.R                          |  493 +----
 ipd-0.4.0/ipd/R/methods.R                      |  690 +++----
 ipd-0.4.0/ipd/R/pdc_logistic.R                 |only
 ipd-0.4.0/ipd/R/pdc_ols.R                      |only
 ipd-0.4.0/ipd/R/pdc_poisson.R                  |only
 ipd-0.4.0/ipd/R/postpi_analytic_ols.R          |  107 -
 ipd-0.4.0/ipd/R/postpi_boot_logistic.R         |  110 -
 ipd-0.4.0/ipd/R/postpi_boot_ols.R              |  201 +-
 ipd-0.4.0/ipd/R/ppi_a_ols.R                    |only
 ipd-0.4.0/ipd/R/ppi_logistic.R                 |   74
 ipd-0.4.0/ipd/R/ppi_mean.R                     |   43
 ipd-0.4.0/ipd/R/ppi_ols.R                      |  103 -
 ipd-0.4.0/ipd/R/ppi_plusplus_logistic.R        |  216 +-
 ipd-0.4.0/ipd/R/ppi_plusplus_mean.R            |  148 -
 ipd-0.4.0/ipd/R/ppi_plusplus_ols.R             |  174 -
 ipd-0.4.0/ipd/R/ppi_plusplus_quantile.R        |  130 -
 ipd-0.4.0/ipd/R/ppi_quantile.R                 |   71
 ipd-0.4.0/ipd/R/pspa_logistic.R                |   48
 ipd-0.4.0/ipd/R/pspa_mean.R                    |   40
 ipd-0.4.0/ipd/R/pspa_ols.R                     |   48
 ipd-0.4.0/ipd/R/pspa_poisson.R                 |   48
 ipd-0.4.0/ipd/R/pspa_quantile.R                |   45
 ipd-0.4.0/ipd/R/simdat.R                       |  702 +++----
 ipd-0.4.0/ipd/R/utils_chen.R                   |only
 ipd-0.4.0/ipd/R/utils_ipd.R                    |only
 ipd-0.4.0/ipd/R/utils_ppi.R                    |only
 ipd-0.4.0/ipd/R/utils_pspa.R                   |only
 ipd-0.4.0/ipd/README.md                        |  478 +++-
 ipd-0.4.0/ipd/build/partial.rdb                |binary
 ipd-0.4.0/ipd/build/vignette.rds               |binary
 ipd-0.4.0/ipd/inst/CITATION                    |only
 ipd-0.4.0/ipd/inst/doc/ipd.R                   |  386 ++-
 ipd-0.4.0/ipd/inst/doc/ipd.Rmd                 |  609 +++---
 ipd-0.4.0/ipd/inst/doc/ipd.html                | 2457 +++++++++++++++----------
 ipd-0.4.0/ipd/inst/paper.R                     | 1248 ++++++------
 ipd-0.4.0/ipd/man/A.Rd                         |   10
 ipd-0.4.0/ipd/man/Sigma_cal.Rd                 |   24
 ipd-0.4.0/ipd/man/augment.ipd.Rd               |   33
 ipd-0.4.0/ipd/man/calc_lhat_glm.Rd             |   27
 ipd-0.4.0/ipd/man/chen_logistic.Rd             |only
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 ipd-0.4.0/ipd/man/est_ini.Rd                   |   11
 ipd-0.4.0/ipd/man/glance.ipd.Rd                |   26
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 ipd-0.4.0/ipd/man/ipd-package.Rd               |   80
 ipd-0.4.0/ipd/man/ipd.Rd                       |  130 -
 ipd-0.4.0/ipd/man/link_Hessian.Rd              |    4
 ipd-0.4.0/ipd/man/link_grad.Rd                 |    4
 ipd-0.4.0/ipd/man/log1pexp.Rd                  |   45
 ipd-0.4.0/ipd/man/logistic_get_stats.Rd        |   23
 ipd-0.4.0/ipd/man/mean_psi.Rd                  |   10
 ipd-0.4.0/ipd/man/mean_psi_pop.Rd              |   24
 ipd-0.4.0/ipd/man/ols.Rd                       |   13
 ipd-0.4.0/ipd/man/ols_get_stats.Rd             |   23
 ipd-0.4.0/ipd/man/optim_est.Rd                 |   24
 ipd-0.4.0/ipd/man/optim_weights.Rd             |   25
 ipd-0.4.0/ipd/man/pdc_logistic.Rd              |only
 ipd-0.4.0/ipd/man/pdc_ols.Rd                   |only
 ipd-0.4.0/ipd/man/pdc_poisson.Rd               |only
 ipd-0.4.0/ipd/man/postpi_analytic_ols.Rd       |   26
 ipd-0.4.0/ipd/man/postpi_boot_logistic.Rd      |  127 -
 ipd-0.4.0/ipd/man/postpi_boot_ols.Rd           |   24
 ipd-0.4.0/ipd/man/ppi_a_ols.Rd                 |only
 ipd-0.4.0/ipd/man/ppi_logistic.Rd              |  146 -
 ipd-0.4.0/ipd/man/ppi_mean.Rd                  |   97
 ipd-0.4.0/ipd/man/ppi_ols.Rd                   |   18
 ipd-0.4.0/ipd/man/ppi_plusplus_logistic.Rd     |  202 +-
 ipd-0.4.0/ipd/man/ppi_plusplus_logistic_est.Rd |  164 -
 ipd-0.4.0/ipd/man/ppi_plusplus_mean.Rd         |  152 -
 ipd-0.4.0/ipd/man/ppi_plusplus_mean_est.Rd     |  134 -
 ipd-0.4.0/ipd/man/ppi_plusplus_ols.Rd          |  194 +
 ipd-0.4.0/ipd/man/ppi_plusplus_ols_est.Rd      |  156 -
 ipd-0.4.0/ipd/man/ppi_plusplus_quantile.Rd     |  136 -
 ipd-0.4.0/ipd/man/ppi_plusplus_quantile_est.Rd |  126 -
 ipd-0.4.0/ipd/man/ppi_quantile.Rd              |  106 -
 ipd-0.4.0/ipd/man/print.ipd.Rd                 |   31
 ipd-0.4.0/ipd/man/print.summary.ipd.Rd         |   33
 ipd-0.4.0/ipd/man/psi.Rd                       |   12
 ipd-0.4.0/ipd/man/pspa_logistic.Rd             |   15
 ipd-0.4.0/ipd/man/pspa_mean.Rd                 |   13
 ipd-0.4.0/ipd/man/pspa_ols.Rd                  |   15
 ipd-0.4.0/ipd/man/pspa_poisson.Rd              |   15
 ipd-0.4.0/ipd/man/pspa_quantile.Rd             |   11
 ipd-0.4.0/ipd/man/pspa_y.Rd                    |   43
 ipd-0.4.0/ipd/man/rectified_cdf.Rd             |   15
 ipd-0.4.0/ipd/man/rectified_p_value.Rd         |   15
 ipd-0.4.0/ipd/man/reexports.Rd                 |   84
 ipd-0.4.0/ipd/man/show-ipd-method.Rd           |only
 ipd-0.4.0/ipd/man/sim_data_y.Rd                |    2
 ipd-0.4.0/ipd/man/simdat.Rd                    |   49
 ipd-0.4.0/ipd/man/summary.ipd.Rd               |   45
 ipd-0.4.0/ipd/man/tidy.ipd.Rd                  |   27
 ipd-0.4.0/ipd/man/wls.Rd                       |   15
 ipd-0.4.0/ipd/man/zconfint_generic.Rd          |   13
 ipd-0.4.0/ipd/man/zstat_generic.Rd             |   77
 ipd-0.4.0/ipd/tests/spelling.R                 |    9
 ipd-0.4.0/ipd/vignettes/ipd.Rmd                |  609 +++---
 ipd-0.4.0/ipd/vignettes/ipd.md                 |only
 115 files changed, 6797 insertions(+), 5854 deletions(-)

More information about ipd at CRAN