From e41e58a204d7f79858ea4e238470801e2d355679 Mon Sep 17 00:00:00 2001
From: pqiao29 <pqiao@student.unimelb.edu.au>
Date: Thu, 16 Apr 2020 18:55:24 +1000
Subject: [PATCH] change I,Q,H->R to I,Q->R
---
R/FIN_plot.R | 2 +-
R/MOD_recovery.R | 2 +-
R/original_plot_models.R | 4 ++--
tests/testthat/.DS_Store | Bin 6148 -> 6148 bytes
tests/testthat/test-all-modules.R | 28 ----------------------
tests/testthat/test-recovery.R | 23 ------------------
tests/testthat/test-seiqhrf-simulate.R | 32 -------------------------
7 files changed, 4 insertions(+), 87 deletions(-)
delete mode 100644 tests/testthat/test-all-modules.R
delete mode 100644 tests/testthat/test-recovery.R
delete mode 100644 tests/testthat/test-seiqhrf-simulate.R
diff --git a/R/FIN_plot.R b/R/FIN_plot.R
index 508b8a6..6c46abf 100644
--- a/R/FIN_plot.R
+++ b/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$experiment)) > 1){
- p <- p + facet_grid(reo_exp(experiment) ~ ., scale = 'free')
+ p <- p + facet_grid(reo_exp(experiment) ~ ., scales = 'free')
}
if(sep_compartments){
diff --git a/R/MOD_recovery.R b/R/MOD_recovery.R
index dfce50a..5d93feb 100644
--- a/R/MOD_recovery.R
+++ b/R/MOD_recovery.R
@@ -114,7 +114,7 @@ recovery.FUN <- function(dat, at, seed = NULL) {
rand = dat$control$rec.rand,
active,
status = dat$attr$status,
- label = c("i", "q", "h"),
+ label = c("i", "q"),
state = recovState,
at,
expTime = dat$attr$expTime,
diff --git a/R/original_plot_models.R b/R/original_plot_models.R
index 049b888..016b614 100644
--- a/R/original_plot_models.R
+++ b/R/original_plot_models.R
@@ -87,7 +87,7 @@ plot_models <- function(sims = baseline_sim,
} else (
plot_df %>% ggplot(aes(x = Date, y = count, colour = compartment,
linetype = sim)) +
- facet_grid(reo_exp(experiment) ~ ., scale = 'free') +
+ facet_grid(reo_exp(experiment) ~ ., scales = 'free') +
scale_x_date(date_breaks = "1 week", date_labels = "%m-%d") +
geom_line(size = 1.5, alpha = 0.8) +
scale_colour_manual(values = compcols, labels = complabels) +
@@ -109,7 +109,7 @@ plot_models <- function(sims = baseline_sim,
} else (
plot_df %>% ggplot(aes(x = Date, y = count+1, colour = compartment,
linetype = sim)) +
- facet_grid(reo_exp(experiment) ~ ., scale = 'free') +
+ facet_grid(reo_exp(experiment) ~ ., scales = 'free') +
scale_y_continuous(trans = trans) +
scale_x_date(date_breaks = "1 week", date_labels = "%m-%d") +
geom_line(size = 1.5, alpha = 0.8) +
diff --git a/tests/testthat/.DS_Store b/tests/testthat/.DS_Store
index c75274b698af4eb48b88f2e123d3eb21760bb0ce..83ee8de8d1227601f3384dd2fcf93d92c9374316 100644
GIT binary patch
delta 53
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IIsWnk05K5_hX4Qo
delta 255
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zLn%-xNJft#$TKHDIVmSU38)@u4udiftN#ZB28PW%OstIc{7A+W0ktIqjVJ@sMGTdg
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E0N*V=u>b%7
diff --git a/tests/testthat/test-all-modules.R b/tests/testthat/test-all-modules.R
deleted file mode 100644
index 1c7107f..0000000
--- a/tests/testthat/test-all-modules.R
+++ /dev/null
@@ -1,28 +0,0 @@
-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)
-})
diff --git a/tests/testthat/test-recovery.R b/tests/testthat/test-recovery.R
deleted file mode 100644
index 527a3e3..0000000
--- a/tests/testthat/test-recovery.R
+++ /dev/null
@@ -1,23 +0,0 @@
-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
diff --git a/tests/testthat/test-seiqhrf-simulate.R b/tests/testthat/test-seiqhrf-simulate.R
deleted file mode 100644
index 9581007..0000000
--- a/tests/testthat/test-seiqhrf-simulate.R
+++ /dev/null
@@ -1,32 +0,0 @@
-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)
-})
--
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