show_ratemat | R Documentation |
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,
...
)
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) |
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()
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))
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