egfR0

to get up and running...

To run code in this repo using the Makefile, use shellpipes remotes::install_github("dushoff/shellpipes") https://dushoff.github.io/shellpipes/

To pull and push (on git) idiomatically, simply run in terminal make sync.

I think I installed epiGrowthFit manually/outside the make file, but don't recall -MER 20240130

TODO.md contains some long-term desiderata from JD
notes.md contains meeting notes from meetings primarily between JD, KH, and ML
README.md (this document) is where MR is writing user notes as he gets to know the project...
Makefile describes workflows.
Not in this repo, but to understand the make workflows, it may help to see the shellpipes package documentation: https://dushoff.github.io/shellpipes/. for more, https://github.com/mac-theobio/useMakestuff
makestuff/README.md has lots of make documentation

Name		Name	Last commit message	Last commit date
Latest commit History 180 Commits
outputs		outputs
slow		slow
KH_R0.R		KH_R0.R
Makefile		Makefile
R0combo.R		R0combo.R
R0est_funs.R		R0est_funs.R
R0plot.R		R0plot.R
README.md		README.md
TODO.md		TODO.md
base.R		base.R
bitten.R		bitten.R
calcs.R		calcs.R
check.R		check.R
comp.R		comp.R
compare.R		compare.R
compare.md		compare.md
conflicts.R		conflicts.R
conflicts.Rout.args		conflicts.Rout.args
content.mk		content.mk
convert.R		convert.R
dathack.R		dathack.R
delphi.R		delphi.R
doc.Rnw		doc.Rnw
draft.tex		draft.tex
egf.R		egf.R
egf_R0.R		egf_R0.R
egf_fit.R		egf_fit.R
egf_plot.R		egf_plot.R
egf_sample.R		egf_sample.R
egf_single.R		egf_single.R
egf_single_old.R		egf_single_old.R
exp.R		exp.R
fake.tex		fake.tex
fakedoc.Rnw		fakedoc.Rnw
generations.mk		generations.mk
hardPars.R		hardPars.R
incubation.R		incubation.R
incubationPlot.R		incubationPlot.R
interval.png		interval.png
intervalPlots.R		intervalPlots.R
intervals.R		intervals.R
knitr.tex		knitr.tex
linked.R		linked.R
logistic.R		logistic.R
lowPeaks.R		lowPeaks.R
mexico.R		mexico.R
mm_plot.R		mm_plot.R
mm_plot.md		mm_plot.md
mm_windows.R		mm_windows.R
monthly.R		monthly.R
monthly_phase.R		monthly_phase.R
notes.md		notes.md
once.R		once.R
pars.R		pars.R
rabies.bib		rabies.bib
rplot.R		rplot.R
rplot_combo.R		rplot_combo.R
series.tsv		series.tsv
simR0_funs.R		simR0_funs.R
simparams.R		simparams.R
softClimb.R		softClimb.R
softDecline.R		softDecline.R
varnames.tsv		varnames.tsv
version.R		version.R