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Created with Raphaël 2.2.015Apr13128763131Mar3029272625244324Feb21201411430Jan2822212013Dec29Oct2320181611109126Sep241917929Aug2221201413817Jul161113Jun6546May218Apr171515Jan6Dec17Nov230Oct292237Sep6330Aug201627Jun20122May30Apr251918131227Mar31Jan30323Nov22212030Oct1312542129Sep13871remove set_paramS3 methods in progress: summary, plot (times, models)S3 in progress: control_seiqhrf, init_seiqhrf, param_seiqhrf, as.data.frame.seiqhrf, print(control, init, param, model), usage in vignette v2add quantile 95% CI in summaryclear function names: icm.seiqhrf -> seiqhrfclear function names: control.icm -> control_seiqhrfdebug summaryadd summary_seiqhrfmake default values consistent with previous versionadd from E to R: arec.rand, arec.rate, arec.dist.shape, arec.dist.scaleMerge branch 'master' of https://gitlab.svi.edu.au/biocellgen-private/sirplusclear structure of update status, allow .rand to be FALSE for all steps in recovery.FUNfix bug with plotting known counts in all experiment facetsfix bug with plotting known counts in all experiment facetsremove redundant codeMerge branch 'master' of https://gitlab.svi.edu.au/biocellgen-private/sirplustrivial changeexported new functions by cbaadd code for setting up time sensitive experiments where parameter values change over timeadd code for setting up time sensitive experiments where parameter values change over timeminor change in documentconfirm all changed functions return identical values as the originalsfinish clean up arrivals.FUNorganize file namesdeparture.FUNfinish clean up departures.FUNfinish clean up recovery.FUNMerge branch 'master' of https://gitlab.svi.edu.au/biocellgen-private/sirplusget rid of <<-debugclean up recovery.FUN: till line 117 in revised (recovery.FUN) and line 192 in original (progress.seiqhrf.icm)clean up initialize.FUNFixing description and docsfix conflictfix devtools::check()Add testthat: infection.FUN returns identical output as Churches' infection.seiqhrf.icmdebug infection.FUNmake x-axis finer tuned... showing each weekCopy-editing in vignette; tweaks for R CMD checkadded hosp plots to vignette