incidence v1.7.0
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Compute, Handle, Plot and Model Incidence of Dated Events
Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<http://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Functions in incidence
| Name | Description | |
| dim.incidence | Access various elements of an incidence object | |
| fit | Fit exponential models to incidence data | |
| get_counts | Get counts from an incidence object | |
| as.data.frame.incidence | Conversion of incidence objects | |
| incidence_pal1 | Color palettes used in incidence | |
| plot.incidence | Plot function for incidence objects | |
| cumulate | Compute cumulative 'incidence' | |
| group_names | extract and set group names | |
| incidence | Compute incidence of events from a vector of dates. | |
| estimate_peak | Estimate the peak date of an incidence curve using bootstrap | |
| find_peak | Find the peak date of an incidence curve | |
| pool | Pool 'incidence' across groups | |
| subset.incidence | Subsetting 'incidence' objects | |
| get_dates | Retrieve dates from an incidence object | |
| get_fit | Accessors for incidence_fit objects | |
| bootstrap | Bootstrap incidence time series | |
| No Results! | ||
Vignettes of incidence
| Name | ||
| conversions.Rmd | ||
| customize_plot.Rmd | ||
| incidence_class.Rmd | ||
| incidence_fit_class.Rmd | ||
| overview.Rmd | ||
| No Results! | ||
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Details
| Type | Package |
| Date | 2019-03-14 |
| Encoding | UTF-8 |
| License | MIT + file LICENSE |
| URL | http://www.repidemicsconsortium.org/incidence/ |
| BugReports | http://github.com/reconhub/incidence/issues |
| RoxygenNote | 6.1.1 |
| VignetteBuilder | knitr |
| NeedsCompilation | no |
| Packaged | 2019-03-14 16:04:52 UTC; zkamvar |
| Repository | CRAN |
| Date/Publication | 2019-03-14 16:30:10 UTC |
| imports | aweek (>= 0.2.0) , ggplot2 |
| suggests | covr , cowplot , knitr , magrittr , outbreaks , rmarkdown , scales , testthat , vdiffr |
| Contributors | Jun Cai, Rich FitzJohn, Thibaut Jombart, Sangeeta Bhatia, Jakob Schumacher, Juliet R.C. Pulliam |
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