Package: pcpr 1.0.0.9000

Lawrence G. Chillrud

pcpr: Principal Component Pursuit for Environmental Epidemiology

Implementation of the pattern recognition technique Principal Component Pursuit tailored to environmental health data, as described in Gibson et al (2022) <doi:10.1289/EHP10479>.

Authors:Lawrence G. Chillrud [aut, cre, cph], Jaime Benavides [aut], Elizabeth A. Gibson [aut], Junhui Zhang [aut], Jingkai Yan [aut], John N. Wright [aut], Jeff Goldsmith [aut], Marianthi-Anna Kioumourtzoglou [aut], Columbia University [fnd]

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pcpr.pdf |pcpr.html✨
pcpr/json (API)
NEWS

# Install 'pcpr' in R:

install.packages('pcpr', repos = c('https://columbia-prime.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/columbia-prime/pcpr/issues

Pkgdown site:https://columbia-prime.github.io

Datasets:

queens - Daily chemical concentrations of 26 PM2.5 species from Queens, NYC

On CRAN:

dimensionality-reduction environmental-health environmental-mixtures epidemiology machine-learning pattern-recognition public-health statistical-modeling

5.65 score 5 stars 103 downloads 13 exports 29 dependencies

Last updated 6 hours agofrom:d4543329c8. Checks:9 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Apr 02 2025
R-4.5-win	OK	Apr 02 2025
R-4.5-mac	OK	Apr 02 2025
R-4.5-linux	OK	Apr 02 2025
R-4.4-win	OK	Apr 02 2025
R-4.4-mac	OK	Apr 02 2025
R-4.4-linux	OK	Apr 02 2025
R-4.3-win	OK	Apr 02 2025
R-4.3-mac	OK	Apr 02 2025

Exports:get_pcp_defaults grid_search_cv hard_threshold impute_matrix matrix_rank proj_rank_r root_pcp rrmc sim_data sim_lod sim_na sing sparsity

Dependencies:backports checkmate cli codetools digest dplyr fansi foreach furrr future generics globals glue iterators lifecycle listenv magrittr parallelly pillar pkgconfig progressr purrr R6 rlang tibble tidyselect utf8 vctrs withr

Air pollution source apportionment with PCP

Rendered frompcp-applied.Rmdusingknitr::rmarkdownon Apr 02 2025.

Last update: 2025-04-02
Started: 2025-03-20

Quickstart: applying PCP to a simulated environmental mixture

Rendered frompcp-quickstart.Rmdusingknitr::rmarkdownon Apr 02 2025.

Last update: 2025-04-02
Started: 2025-03-20

Theory crash course

Rendered fromtheory-crash-course.Rmdusingknitr::rmarkdownon Apr 02 2025.

Last update: 2025-03-25
Started: 2025-03-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Retrieve default PCP parameter settings for given matrix	get_pcp_defaults
Cross-validated grid search for PCP models	grid_search_cv
Hard-thresholding operator	hard_threshold
Impute missing values in given matrix	impute_matrix
Estimate rank of a given matrix	matrix_rank
Project matrix to rank r	proj_rank_r
Daily chemical concentrations of 26 PM2.5 species from Queens, NYC (2001-2021)	queens
Square root principal component pursuit (convex PCP)	root_pcp
Rank-based robust matrix completion (non-convex PCP)	rrmc
Simulate simple mixtures data	sim_data
Simulate limit of detection data	sim_lod
Simulate random missingness in a given matrix	sim_na
Compute singular values of given matrix	sing
Estimate sparsity of given matrix	sparsity