visualize rate (per-capita flow) matrix

visualize rate (per-capita flow) matrix

show_ratemat(
  M,
  method = c("Matrix", "diagram", "igraph"),
  subset = NULL,
  xlab = "to",
  ylab = "from",
  sub = "",
  zlim = c(0, 1),
  aspect = "iso",
  block_size = NULL,
  block_col = 2,
  axlabs = TRUE,
  const_width = (method == "igraph"),
  colour_palette = viridis::magma(n = 50, direction = -1),
  do_symbols = NULL,
  box.size = 0.02,
  ...
)

Arguments

M

rate matrix

method

visualization method

subset

list of two regular expressions, the first to subset rate matrix rows (based on rownames) and the second to subset columns (based on colnames)

xlab

label on x axis

ylab

label on y axis

sub

subtitle for plot

zlim

appears to be unused (!!)

aspect

aspect ratio ("iso", "fill" are the sensible options)

block_size

numeric vector of number of compartments per block; if NA, try to guess from number of epidemiological compartments

block_col

each element in block_col controls the color of the corresponding grid overlay added by block_size (if add_blocks==TRUE)

axlabs

for flow matrices, show axis tick labels?

const_width

set flows to constant value of 1?

colour_palette

vector of colours for rate matrix heatmap

do_symbols

plot symbolic values for flows?

box.size

box size for diagram

...

arguments to pass to lower level functions (plotmat::diagram/image/igraph)

See also

Other classic_macpan: add_d_log(), add_updated_vaxrate(), aggregate_agecats(), calibrate_comb(), calibrate(), check_age_cat_compatibility(), check_contact_rate_setting(), col_multiply(), condense_age(), condense_params_vax(), condense_state(), condense_vax(), dev_is_tikz(), do_step(), expand_params_age(), expand_params_desc_age(), expand_params_desc_variant(), expand_params_desc_vax(), expand_params_mistry(), expand_params_variant(), expand_params_vax(), expand_state_age(), expand_state_vax(), expand_stateval_testing(), fix_pars(), fix_stored(), forecast_ensemble(), forecast_sim(), getData(), get_GI_moments(), get_Gbar(), get_R0(), get_doses_per_day(), get_evec(), get_kernel_moments(), get_opt_pars(), get_r(), invlink_trans(), make_betavec(), make_beta(), make_jac(), make_ratemat(), make_state(), make_test_wtsvec(), make_vaxrate(), mk_Nvec(), mk_agecats(), mk_contact_rate_setting(), mk_mistry_Nvec(), mk_pmat(), mk_vaxcats(), mle_fun(), non_expanded_states, rExp(), read_params(), repair_names_age(), restore(), run_sim_ageify(), run_sim_break(), run_sim_loglin(), run_sim_mobility(), run_sim_range(), run_sim(), testify(), texify(), trans_state_vars(), update_contact_rate_setting(), update_foi(), update_params_mistry(), vis_model(), write_params()

Examples

params <- read_params("ICU1.csv")
state <- make_state(params[["N"]],E0=params[["E0"]], use_eigvec=FALSE)
M <- make_ratemat(state, params)
show_ratemat(M)

## silly but shows we can do multiple block types in different colours
show_ratemat(M, block_size=c(3,5), block_col=c(2,4))
#> Loading required namespace: latticeExtra