change I,Q,H->R to I,Q->R

R/FIN_plot.R

@@ -213,7 +213,7 @@ plot_sirplus <- function(x, comp_remove,
         theme_bw() + theme(axis.text.x = element_text(angle = 90))
     
     if(length(unique(plot_df$experiment)) > 1){
-        p <- p + facet_grid(reo_exp(experiment) ~ ., scale = 'free')
+        p <- p + facet_grid(reo_exp(experiment) ~ ., scales = 'free')
     }
     
     if(sep_compartments){

R/MOD_recovery.R

@@ -114,7 +114,7 @@ recovery.FUN <- function(dat, at, seed = NULL) {
                        rand = dat$control$rec.rand, 
                        active, 
                        status = dat$attr$status, 
-                       label = c("i", "q", "h"), 
+                       label = c("i", "q"), 
                        state = recovState, 
                        at, 
                        expTime = dat$attr$expTime, 

R/original_plot_models.R

@@ -87,7 +87,7 @@ plot_models <- function(sims = baseline_sim,
         } else (
             plot_df %>% ggplot(aes(x = Date, y = count, colour = compartment,
                                    linetype = sim)) + 
-                facet_grid(reo_exp(experiment) ~ ., scale = 'free') + 
+                facet_grid(reo_exp(experiment) ~ ., scales = 'free') + 
                 scale_x_date(date_breaks = "1 week", date_labels = "%m-%d") + 
                 geom_line(size = 1.5, alpha = 0.8) + 
                 scale_colour_manual(values = compcols, labels = complabels) + 
@@ -109,7 +109,7 @@ plot_models <- function(sims = baseline_sim,
         } else (
             plot_df %>% ggplot(aes(x = Date, y = count+1, colour = compartment, 
                                    linetype = sim)) + 
-                facet_grid(reo_exp(experiment) ~ ., scale = 'free') + 
+                facet_grid(reo_exp(experiment) ~ ., scales = 'free') + 
                 scale_y_continuous(trans = trans) +
                 scale_x_date(date_breaks = "1 week", date_labels = "%m-%d") + 
                 geom_line(size = 1.5, alpha = 0.8) + 

tests/testthat/test-all-modules.R

-test_that("All modules(MOD) produce the same result as Churches' modules (.seiqhrf.icm)", {
-    
-    param <- param_seiqhrf(arec.rate = 0)
-    init <- init_seiqhrf(s.num = 1000)
-    
-    #### default functions: initialize.FUN, infection.FUN, recovery.FUN, departures.FUN, arrivals.FUN
-    control1 <- control_seiqhrf(nsteps = 10)
-    ### Churches' original function:
-    control2 <- control1
-    control2$initialize.FUN <- "initialize.icm"
-    control2$infection.FUN <- "infection.seiqhrf.icm"
-    control2$recovery.FUN <- "progress.seiqhrf.icm"
-    control2$departures.FUN <- "departures.seiqhrf.icm"
-    control2$arrivals.FUN <- "arrivals.seiqhrf.icm"
-    
-    No_seeds <- 10
-    seed_list <- sample(1:1000, No_seeds)
-    comp <- rep(NA, No_seeds)
-    i <- 1
-    for(seed in seed_list){
-        sim1 <- seiqhrf(param = param, init = init, control = control1, seed)
-        sim2 <- seiqhrf(param = param, init = init, control = control2, seed)
-        comp[i] <- identical(sim1, sim2)
-        i <- i + 1
-    }
-    
-    expect_equal(sum(comp), No_seeds)
-})

tests/testthat/test-recovery.R

-test_that("Identical output as Churches' original function: recovery.FUN", {
-    
-    control <- control_seiqhrf()
-    param <- param_seiqhrf(arec.rate = 0)
-    init <- init_seiqhrf()
-    
-    at <- 2
-    dat <- do.call(initialize.FUN, list(param, init, control))
-    dat <- do.call(infection.FUN, list(dat, at))   
-    
-    No_seeds <- 10
-    seed_list <- sample(1:1000, No_seeds)
-    comp <- rep(NA, No_seeds)
-    i <- 1
-    for(seed in seed_list){
-        dat1 <- do.call(recovery.FUN, list(dat, at, seed))
-        dat2 <- do.call(progress.seiqhrf.icm, list(dat, at, seed))
-        comp[i] <- identical(dat1, dat2)
-        i <- i + 1
-    }
-    
-    expect_equal(sum(comp), No_seeds)
-})
\ No newline at end of file

tests/testthat/test-seiqhrf-simulate.R

-test_that("seiqhrf and simulate_seiqhrf produce identical output", {
-    
-    s.num = 1000
-    q.num = 10
-    nsteps = 10
-    nsims = 3
-    arec.rate = 0  ### has to be fixed 0 for comparison
-    
-    No_seeds <- 10
-    seed_list <- sample(1:1000, No_seeds)
-    comp <- rep(NA, No_seeds)
-    i <- 1
-    for(seed in seed_list){
-        Churhes_res <- simulate_seiqhrf(nsteps = nsteps, nsims = nsims,
-                                        arec.rate = arec.rate, s.num = s.num, q.num = q.num,
-                                        infection.FUN = infection.seiqhrf.icm, 
-                                        recovery.FUN = progress.seiqhrf.icm, 
-                                        departures.FUN = departures.seiqhrf.icm, 
-                                        arrivals.FUN = arrivals.seiqhrf.icm, seed = seed)$sim
-        class(Churhes_res) <- "seiqhrf"
-        
-        param <- param_seiqhrf(arec.rate = arec.rate)
-        init <- init_seiqhrf(s.num = s.num, q.num = q.num)
-        control <- control_seiqhrf(nsteps = nsteps, nsims = nsims)
-        sirplus_res <- seiqhrf(init, control, param, seed)
-        
-        comp[i] <- identical(Churhes_res[3:4], sirplus_res[3:4]) # Due to $usr.specified in control and param, can only compare "epi" and "times
-        i <- i + 1
-    }
-    
-    expect_equal(sum(comp), No_seeds)
-})