Various problems with examples introduced by ip_devel merge

[matthewcso]

Currently done: Added make_betavec back, fixed problems with compiling vignettes

• vis_model(method="diagram") is broken, switched to igraph for now Error in .local(x, i, j, ..., value) : not-yet-implemented 'Matrix[<-' method
• make_ratemat breaks with this error Error in .local(x, i, j, ..., value) : not-yet-implemented 'Matrix[<-' method
• rExp: Error in if (return_val == "r0" && var(r0_values) > 1e-08) warning("the exponential simulation has not converged: please iterate for more steps.") : missing value where TRUE/FALSE needed
• vis_model: Error in .local(x, i, j, ..., value) : not-yet-implemented 'Matrix[<-' method

Additional R CMD Check Warnings Warning messages: 1: In tools::parse_Rd(path, macros = macros) : C:/Users/somat/Documents/GitHub/McMasterPandemic/man/expand_params_variant.Rd:22: unknown macro '\item' 2: In tools::parse_Rd(path, macros = macros) : C:/Users/somat/Documents/GitHub/McMasterPandemic/man/expand_params_variant.Rd:24: unknown macro '\item' 3: In tools::parse_Rd(path, macros = macros) : C:/Users/somat/Documents/GitHub/McMasterPandemic/man/expand_params_variant.Rd:26: unexpected section header '\description' 4: In tools::parse_Rd(path, macros = macros) : C:/Users/somat/Documents/GitHub/McMasterPandemic/man/expand_params_variant.Rd:29: unexpected section header '\examples' 5: In tools::parse_Rd(path, macros = macros) : C:/Users/somat/Documents/GitHub/McMasterPandemic/man/expand_params_variant.Rd:33: unexpected END_OF_INPUT '

[bbolker]

The unknown macro/unexpected END_OF_INPUT stuff was caused by an unescaped % in the documentation, that's fixed now.

[bbolker]

vis_model and make_ratemat stuff should be fixed now.

[bbolker]

rExp example is fixed (sort of, although rExp should probably still be examined: see also #51 ). There is still an error withtests/test_calibrate.R (not tested via devtools::test()) and a bunch of undocumented arguments and undefined symbols (unimported or used via non-standard evaluations)

[bbolker]

@matthewcso , I guess you're working on this; let me know if I can help

[matthewcso]

@bbolker You solved all the bullet points in this issue (examples breaking), so I'll close this and open a new issue for the other rcmdcheck issues.