Package: phenomix 1.0.5

Eric J. Ward

phenomix: Fit Density Curves to Peak Timing Data that Varies over Time

The 'phenomix' package fits time-varying density curves to run timing type data commonly encountered in fisheries and ecology. Example applications include to peak run timing curves collected for juvenile or adult Pacific salmon, though could also be applied to other kinds of data such as hydrographs, plant phenology (flowering, leaf out).

Authors:Eric J. Ward [aut, cre], Samantha M. Wilson [ctb], Joseph H. Anderson [ctb]

phenomix_1.0.5.tar.gz
phenomix_1.0.5.zip(r-4.7)phenomix_1.0.5.zip(r-4.6)phenomix_1.0.5.zip(r-4.5)
phenomix_1.0.5.tgz(r-4.6-any)phenomix_1.0.5.tgz(r-4.5-any)
phenomix_1.0.5.tar.gz(r-4.7-any)phenomix_1.0.5.tar.gz(r-4.6-any)
phenomix_1.0.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
phenomix/json (API)

# Install 'phenomix' in R:
install.packages('phenomix', repos = c('https://nmfs-opensci.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nwfsc-cb/phenomix/issues

Pkgdown/docs site:https://nwfsc-cb.github.io

On CRAN:

Conda:

4.61 score 6 stars 34 scripts 11 exports 34 dependencies

Last updated from:361b04dbb0. Checks:7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE257
source / vignettesOK208
linux-release-x86_64NOTE256
macos-release-arm64NOTE219
macos-oldrel-arm64NOTE151
windows-develNOTE228
windows-releaseNOTE211
windows-oldrelNOTE187
wasm-releaseOK109

Exports:create_dataextract_allextract_annualextract_lowerextract_meansextract_sigmaextract_thetaextract_upperfitparsplot_diagnostics

Dependencies:clicpp11dplyrfarvergenericsggplot2gluegnormgtableisobandlabelinglatticelifecyclemagrittrMASSMatrixnlmepillarpkgconfigR6RColorBrewerRcppRcppEigenrlangRTMBS7scalestibbletidyselectTMButf8vctrsviridisLitewithr

Extracting estimated and derived parameters
Extracting parameters manually | Helper functions | Annual summaries
Rendered froma4_derived.Rmdusingknitr::rmarkdown

Last update: 2026-01-14
Started: 2023-05-03

Fitting time varying phenology models with the phenomix package
Overview | Manipulating data for estimation | Fitting the model | Getting coefficients | Getting predicted values | Plotting results | Additional examples | Diagnosing lack of convergence
Rendered froma1_examples.Rmdusingknitr::rmarkdown

Last update: 2026-01-14
Started: 2022-03-03

Including covariates
Covariates
Rendered froma2_covariates.Rmdusingknitr::rmarkdown

Last update: 2026-01-14
Started: 2022-03-03

Troubleshooting
Using initial values | Specifying limits
Rendered froma3_troubleshooting.Rmdusingknitr::rmarkdown

Last update: 2026-01-14
Started: 2022-03-03