Package: excessmort 0.8.0

Rafael A. Irizarry

excessmort: Excess Mortality

Implementation of method for estimating excess mortality and other health related outcomes from weekly or daily count data described in Acosta and Irizarry (2021) "A Flexible Statistical Framework for Estimating Excess Mortality".

Authors:Rafael A. Irizarry [aut, cre], Rolando Acosta [aut], Mónica Robles-Fontán [aut], Ferenci Tamás [ctb]

excessmort_0.8.0.tar.gz
excessmort_0.8.0.tar.gz(r-4.5-noble)excessmort_0.8.0.tar.gz(r-4.4-noble)
excessmort_0.8.0.tgz(r-4.4-emscripten)excessmort_0.8.0.tgz(r-4.3-emscripten)
excessmort.pdf |excessmort.html✨
excessmort/json (API)

# Install 'excessmort' in R:

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

Datasets:

cdc_state_counts - Weekly death counts for each USA state
cook_demographics - Cook County Medical Examiner Records
cook_records - Cook County Medical Examiner Records
icd - Puerto Rico daily mortality by cause of death
louisiana_counts - Louisiana daily mortality
new_jersey_counts - New Jersey daily mortality
puerto_rico_counts - Puerto Rico daily mortality
puerto_rico_icd - Puerto Rico daily mortality by cause of death
world_counts - Weekly death counts for several countries

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.70 score 25 scripts 692 downloads 12 exports 38 dependencies

Last updated 4 months agofrom:7f8a693392. Checks:2 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 23 2025
R-4.5-linux	OK	Feb 23 2025

Exports:approx_demographics collapse_age_dist collapse_counts_by_age compute_counts compute_expected excess_cumulative excess_model excess_plot expected_diagnostic expected_plot get_demographics group_age

Dependencies:cli colorspace cpp11 dplyr fansi farver generics ggplot2 glue gtable isoband labeling lattice lifecycle lubridate magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig purrr R6 RColorBrewer rlang scales stringi stringr tibble tidyr tidyselect timechange utf8 vctrs viridisLite withr

Introduction to excessmort

Rafael Irizarry and Rolando Acosta

Rendered fromexcessmort.Rmdusingknitr::rmarkdownon Feb 23 2025.

Last update: 2021-10-11
Started: 2021-10-11

Citation

Readme and manuals

Help Manual

Help page	Topics
Interpolate demographic data	approx_demographics
Weekly death counts for each USA state	cdc_state_counts
Callapse age groups into broader ones	collapse_age_dist collapse_counts_by_age
Compute counts	compute_counts
Compute expected counts for each day	compute_expected
Cook County Medical Examiner Records	cook_demographics cook_records
Compute cumulative excess deaths	excess_cumulative
Fit excess count model	excess_model
Plot results from fitted excess count model	excess_plot
Excess counts in an interval	excess_stats
Diagnostic Plots for Model Fit	expected_diagnostic
Plot Expected Counts	expected_plot
Fit an ar model to residuals from expected counts	fit_ar
Get demographic data from Census	get_demographics
Assign age to group	group_age
Louisiana daily mortality	louisiana_counts
New Jersey daily mortality	new_jersey_counts
Compute year of the day ingoring Feb 29	noleap_yday
Puerto Rico daily mortality	puerto_rico_counts
Puerto Rico daily mortality by cause of death	icd puerto_rico_icd
Weekly death counts for several countries	world_counts