diff --git a/404.html b/404.html index ca01cff0..1e68d621 100644 --- a/404.html +++ b/404.html @@ -6,11 +6,18 @@ Page not found (404) • epichains + + + + + + + Contributing to bpmodels • epichainsContributing to bpmodels • epichainsLicense • epichainsMIT License • epichains + + + + + + + Articles • epichainsArticles • epichains + + + + + + + + + + + + + Authors and Citation • epichainsAuthors and Citation • epichains @@ -23,6 +29,7 @@ can be used, for example, to analyse the distribution of chain sizes or length of infectious disease outbreaks, as discussed in Farrington et al. (2003) <doi:10.1093/biostatistics/4.2.279>."> +

epichains is an R package to simulate, analyse, and visualize the size and length of branching processes with a given offspring distribution. These models are often used in infectious disease epidemiology, where the chains represent chains of transmission, and the offspring distribution represents the distribution of secondary infections caused by an infected individual.

diff --git a/logo.svg b/logo.svg new file mode 100644 index 00000000..3d9f2d4a --- /dev/null +++ b/logo.svg @@ -0,0 +1,833 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/news/index.html b/news/index.html index 2b329a0d..0f0e0f59 100644 --- a/news/index.html +++ b/news/index.html @@ -1,5 +1,5 @@ -Changelog • epichainsChangelog • epichainsAggregate cases in <epichains> objects by "time" or "generation" — aggregate.epichains • epichainsCheck that nchains is greater than 0 and not infinity — check_nchains_valid • epichainsCheck if constructed random number generator for offspring exists — check_offspring_func_valid • epichainsCheck if offspring argument is specified as a character string — check_offspring_valid • epichainsCheck if the serials_dist argument is specified as a function — check_serial_valid • epichainsCalculates the complementary log-probability — complementary_logprob • epichainsCOVID-19 Data Repository for South Africa — covid19_sa • epichainsDensity of the Borel distribution — dborel • epichainsFormat method for epichains class — format.epichains • epichainsLog-likelihood of the size of chains with gamma-Borel offspring distribution — gborel_size_ll • epichainsLog-likelihood of the length of chains with geometric offspring distribution — geom_length_ll • epichainsReturn a function for calculating chain statistics — get_statistic_func • epichainshead method for epichains class — head.epichains • epichainsFunction reference • epichainsCheck if an epichains object has the chains_summary attribute — is_chains_summary • epichainsCheck if an epichains object has the chains_tree attribute — is_chains_tree • epichainsReports whether x is an epichains object — is_epichains • epichainsReports whether x is an "epichains_aggregate_df" object — is_epichains_aggregate_df • epichainsEstimate the log-likelihood/likelihood for observed branching processes — likelihood • epichainsLog-likelihood of the length of chains with Poisson offspring distribution — pois_length_ll • epichainsLog-likelihood of the size of chains with Poisson offspring distribution — pois_size_ll • epichainsPrint an epichains object — print.epichains • epichainsGenerate random numbers from the Borel distribution — rborel • epichainsSamples chain lengths with given observation probabilities — rgen_length • epichainsSimulate transmission chains sizes/lengths — simulate_summary • epichainsSimulate transmission trees from an initial number of infections — simulate_tree • epichainsSummary method for epichains class — summary.epichains • epichainstail method for epichains class — tail.epichains • epichainsDetermine and update the chain statistic being tracked — update_chain_stat • epichainsepichains class validator — validate_epichains • epichains