context("tests for agents_to_aggregate")
(dplyr)
(tidyr)
test_that("checking agents_to_aggregate works for SI model",{
agents <- (agent_id = 1:5,
S = (1, 1, 1, 1, ),
= (, , , 6, 10))
exp_agg_df <- (agents,
states = "I")
expect_equal((exp_agg_df), (11, 3))
})
test_that("check_min_max_time", {
# correct formats
mm_t <- (0, 1)
testthat::expect_true((mm_t))
mm_t <- (1, )
testthat::expect_true((mm_t))
# incorrect formats
mm_t <- (, 1)
testthat::expect_error((mm_t))
mm_t <- (1, 0)
testthat::expect_error((mm_t))
mm_t <- 1
testthat::expect_error((mm_t))
mm_t <- 1:3
testthat::expect_error((mm_t))
})
test_that("check_ordered", {
# error in ordering
df_not_ordered <- (group1 = 1:5,
group2 = (2:5,1))
states <- ("group1", "group2")
testthat::expect_error((df_not_ordered, states))
output <- (df_not_ordered, states,assert_error = F)
testthat::expect_equivalent(output$summary_df,
(ordering = ("group1 <= group2",
"group2 <= group1"),
error = (F, T),
count = (4L, 1L)))
<- (id = (1:5),
error = ((, 4), ),
ordering = (("group1 <= group2", 4),
"group2 <= group1"))
testthat::expect_equal(output$ordering_df,
)
# no error in ordering
df_ordered <- (group1 = 1:5,
group2 = (2:6))
states <- ("group1", "group2")
testthat::expect_true((df_ordered, states))
testthat::expect_true((df_ordered, states,
assert_error = F))
})
test_that("check_ordered, dealing with NAs", {
# NAs and an error inside
test_na <- (sim = 1, agent_id = 1:5,
S1 = (1,5),
I1 = ( 4, 10, 9, 2, 9),
R1 = ( 6, 11, 12, 3, 18),
S2 = (16, 13, 48, 57, 46),
I2 = (85, 15, 92, 84, 48),
R2 = (88, 22, 94, 87, 50),
= (, 50, , 91, 65),
I3 = (, , , , 96),
R3 = (, , , , 100),
= (, , , 90, )
)
test_na_co_output <- (test_na,
states = (("S", "I", "R"),
((1:3, each = 3),4)),
assert_error = F)
# this should error
testthat::expect_true((test_na_co_output))
# ordering df errors have no NAs
testthat::expect_equal(test_na_co_output$ordering_df$error,
(F,F,F,T,F))
testthat::expect_true(((test_na_co_output$ordering_df$error)) == 0)
# summary_df errors have no NAs
error_same <- test_na_co_output$summary_df %>%
dplyr::left_join((count = (4,1),
error = (F, T)),
= "count")
testthat::expect_equal(error_same$error.x, error_same$error.y)
testthat::expect_true(((error_same$error.x)) == 0)
# NAs and a completely NA individual
test_na_full_row <- (sim = 1, agent_id = 1:6,
S1 = ((1,5), ),
I1 = ( 4, 10, 9, 2, 9, ),
R1 = ( 6, 11, 12, 3, 18, ),
S2 = (16, 13, 48, 57, 46, ),
I2 = (85, 15, 92, 84, 48, ),
R2 = (88, 22, 94, 87, 50, ),
= (, 50, , 91, 65, ),
I3 = (, , , , 96, ),
R3 = (, , , , 100, ),
= (, , , 90, , )
)
test_na_full_row_co_output <-
(test_na_full_row,
states = (("S", "I", "R"),
((1:3, each = 3),4)),
assert_error = F)
testthat::expect_true((test_na_full_row_co_output$ordering_df[6,]$error))
#^ if NAs we want ordering to be NA
})
test_that(("check_ordered works with NAs in tibbles,",
"data.frames and grouped_df"),{
test_df <- (agent_id = (1:5),
sim = 1,
tI = (19, 18, , , ),
tR = (35, 27, , , ))
testthat::expect_true((test_df, ("tI", "tR")))
## tbl_df version
test_df <- (agent_id = (1:5),
sim = 1,
tI = (19, 18, , , ),
tR = (35, 27, , , ))
if (::("dplyr") >= '1.0.0'){
test_tbl <- tibble::as_tibble(test_df)
} {
test_tbl <- dplyr::tbl_df(test_df)
}
testthat::expect_true((test_tbl, ("tI", "tR")))
## grouped_df version
test_df <- (agent_id = (1:5),
sim = (((1:2)), each = 5),
tI = (19, 18, , , ),
tR = (35, 27, , , ))
if (::("dplyr") >= '1.0.0'){
test_tbl <- tibble::as_tibble(test_df) %>% dplyr::group_by(sim)
} {
test_tbl <- dplyr::tbl_df(test_df) %>% dplyr::group_by(sim)
}
testthat::expect_true((test_tbl, ("tI", "tR")))
})
test_that("expanding_info", {
# standard case
<- ( = (1:3, each = 2),
= (-1,0,2,3,3,4),
count = (2,1,1,2,1,2))
t_min <- -1
t_max <- 4
K <- 3
expanded_df <- expanding_info( ,t_min, t_max, K)
testthat::expect_equal(((expanded_df$)),
((expanded_df$)))
%>% dplyr::left_join(expanded_df %>% dplyr::mutate( = ()),
= ("t", "state")) %>%
dplyr::mutate(similar = count.x == count.y) %>%
dplyr::pull(similar) %>% %>%
testthat::expect_true()
# special case when only 1 time point
<- ( = 1:2,
= (0,2),
count = (12,2))
testthat::expect_equivalent(expanding_info(, t_min = 0, t_max = 0, K = 2),
%>% dplyr::select(, , count) %>%
dplyr::mutate( = (),
= ()))
})
test_that("distinct_time", {
# something interesting
<- ( = 1:100, x = ((1,1,2,2,3,3),
= 100),
y = ((1,1,1,2,2,2,3,3,3),
= 100))
df_filtered <- (, 1)
testthat::expect_equal((df_filtered), (67,3))
testthat::expect_equal(df_filtered,
!(1:100 %in% (((2,4), = 33))),])
df_all <- (, )
testthat::expect_equal(df_all, )
df_x <- (, (1,3))
testthat::expect_equal(df_x, [1:100 %% 2 == 1,])
df_y <- (, (1,2))
testthat::expect_equal(df_y, [1:100 %% 3 == 1,])
# nothing interesting
<- ( =1:100, x = (1:3, = 100),
y = (1:4, = 100))
df_filtered <- (, 1)
testthat::expect_equal(df_filtered, )
df_all <- (, )
testthat::expect_equal(df_all, )
df_x <- (, (1,3))
testthat::expect_equal(df_x, )
df_y <- (, (1,2))
testthat::expect_equal(df_y, )
df_single <- (, 1:3)
testthat::expect_equal((df_single), 1)
testthat::expect_equal(df_single, [1,])
})
test_that("agents_to_aggregate.data.frame, data_example_s example",{
data_example_s <- (group1 = (.1,0),
group2 = (2.1,2),
group3 = (3.1,3))
## three classes
s_output3 <- (agents = data_example_s,
states = (group2, group3))
# if start time is 0, should start with 2 group1, and non of the other groups
testthat::expect_equivalent(s_output3 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 2, X1 = 0, X2 = 0))
t_start <- (s_output3$,size = 1)
s_output3.1 <- (agents = data_example_s,
states = (group2, group3),
min_max_time = (t_start,))
testthat::expect_equal(s_output3.1, s_output3[s_output3$ >= t_start,])
## four classes
s_output4 <- (agents = data_example_s,
states = (group1, group2, group3))
# if start time is 0, should start with 1 group0, and 1 in group1
testthat::expect_equivalent(s_output4 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 1, X1 = 1, X2 = 0, X3 = 0))
t_start <- (s_output4$,size = 1)
s_output4.1 <- (agents = data_example_s,
states = (group1, group2, group3),
min_max_time = (t_start,))
testthat::expect_equal(s_output4.1, s_output4[s_output4$ >= t_start,])
s_output4._neg1 <- (agents = data_example_s,
states = (group1, group2 ,
group3),
min_max_time = (-1L,))
# if start time is -1, should start with 2 in group1
testthat::expect_equivalent(s_output4._neg1 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 2, X1 = 0, X2 = 0, X3 = 0))
testthat::expect_equal(s_output4._neg1[2:(s_output4._neg1),],
s_output4)
})
test_that("agents_to_aggregate.data.frame - string, data_example_s example",{
data_example_s <- (group1 = (.1,0),
group2 = (2.1,2),
group3 = (3.1,3))
## three classes
s_output3 <- (agents = data_example_s,
states = ("group2", "group3"))
# if start time is 0, should start with 2 group1, and non of the other groups
testthat::expect_equivalent(s_output3 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 2, X1 = 0, X2 = 0))
t_start <- (s_output3$,size = 1)
s_output3.1 <- (agents = data_example_s,
states = ("group2", "group3"),
min_max_time = (t_start,))
testthat::expect_equal(s_output3.1, s_output3[s_output3$ >= t_start,])
## four classes
s_output4 <- (agents = data_example_s,
states = ("group1","group2", "group3"))
# if start time is 0, should start with 1 group0, and 1 in group1
testthat::expect_equivalent(s_output4 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 1, X1 = 1, X2 = 0, X3 = 0))
t_start <- (s_output4$,size = 1)
s_output4.1 <- (agents = data_example_s,
states = ("group1", "group2", "group3"),
min_max_time = (t_start,))
testthat::expect_equal(s_output4.1, s_output4[s_output4$ >= t_start,])
s_output4._neg1 <- (agents = data_example_s,
states = ("group1", "group2",
"group3"),
min_max_time = (-1L,))
# if start time is -1, should start with 2 in group1
testthat::expect_equivalent(s_output4._neg1 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 2, X1 = 0, X2 = 0, X3 = 0))
testthat::expect_equal(s_output4._neg1[2:(s_output4._neg1),],
s_output4)
})
test_that("agents_to_aggregate.data.frame, data_example_e example", {
data_example_e <- (group1 = (-1.1, -.1,-1),
group2 = (2.1,2.1,2),
group3 = (3.1,3.1,3))
## three classes
s_output3 <- (agents = data_example_e,
states = (group2, group3))
# if start time is 0, should start with 3 group0,
testthat::expect_equivalent(s_output3 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 3, X1 = 0, X2 = 0))
testthat::expect_equivalent(s_output3[s_output3$ == 2,] %>%
dplyr::select(dplyr::matches("X")),
(X0 = 2, X1 = 1, X2 = 0))
testthat::expect_equivalent(s_output3[s_output3$ == 3,] %>%
dplyr::select(dplyr::matches("X")),
(X0 = 0, X1 = 2, X2 = 1))
t_start <- (s_output3$,size = 1)
s_output3.1 <- (agents = data_example_e,
states = (group2, group3),
min_max_time = (t_start,))
testthat::expect_equal(s_output3.1, s_output3[s_output3$ >= t_start,])
# four classes
s_output4 <- (agents = data_example_e,
states = (group1, group2, group3),
min_max_time = (0,))
# if start time is 0, should start with 3 group1,
testthat::expect_equivalent(s_output4 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 0, X1 = 3, X2 = 0, X3 = 0))
t_start <- (s_output4$,size = 1)
s_output4.1 <- (agents = data_example_e,
states = (group1, group2,
group3),
min_max_time = (t_start,))
testthat::expect_equal(s_output4.1, s_output4[s_output4$ >= t_start,])
#if start time is -1, start with 2 group1, 1 group0
s_output4._neg1 <- (agents = data_example_e,
states = (group1, group2,
group3),
min_max_time = (-1,))
testthat::expect_equivalent(s_output4._neg1 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 1, X1 = 2, X2 = 0, X3 = 0))
testthat::expect_equal(s_output4._neg1[s_output4._neg1$ > -1,],
s_output4)
})
test_that("agents_to_aggregate.data.frame - string, data_example_e example", {
data_example_e <- (group1 = (-1.1, -.1,-1),
group2 = (2.1,2.1,2),
group3 = (3.1,3.1,3))
## three classes
s_output3 <- (agents = data_example_e,
states = ("group2", "group3"))
# if start time is 0, should start with 3 group0,
testthat::expect_equivalent(s_output3 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 3, X1 = 0, X2 = 0))
testthat::expect_equivalent(s_output3[s_output3$ == 2,] %>%
dplyr::select(dplyr::matches("X")),
(X0 = 2, X1 = 1, X2 = 0))
testthat::expect_equivalent(s_output3[s_output3$ == 3,] %>%
dplyr::select(dplyr::matches("X")),
(X0 = 0, X1 = 2, X2 = 1))
t_start <- (s_output3$,size = 1)
s_output3.1 <- (agents = data_example_e,
states = ("group2", "group3"),
min_max_time = (t_start,))
testthat::expect_equal(s_output3.1, s_output3[s_output3$ >= t_start,])
# four classes
s_output4 <- (agents = data_example_e,
states = ("group1","group2","group3"),
min_max_time = (0,))
# if start time is 0, should start with 3 group1,
testthat::expect_equivalent(s_output4 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 0, X1 = 3, X2 = 0, X3 = 0))
t_start <- (s_output4$,size = 1)
s_output4.1 <- (agents = data_example_e,
states = ("group1", "group2",
"group3"),
min_max_time = (t_start,))
testthat::expect_equal(s_output4.1, s_output4[s_output4$ >= t_start,])
#if start time is -1, start with 2 group1, 1 group0
s_output4._neg1 <- (agents = data_example_e,
states = ("group1","group2",
"group3"),
min_max_time = (-1,))
testthat::expect_equivalent(s_output4._neg1 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 1, X1 = 2, X2 = 0, X3 = 0))
testthat::expect_equal(s_output4._neg1[s_output4._neg1$ > -1,],
s_output4)
})
test_that("agents_to_aggregate.data.frame, data_example_i example", {
data_example_i <- (group1 = (, -2.1, , -2.1, , -2),
group2 = (-1.1,-1.1,-.1,-.1,-1,-1),
group3 = (3.1,3.1,3.1,3.1,3,3))
## three classes
s_output3 <- (agents = data_example_i,
states = (group2, group3))
# if start time is 0, should start with all 6 X1,
testthat::expect_equivalent(s_output3 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 0, X1 = 6, X2 = 0))
testthat::expect_equivalent(s_output3[s_output3$ == 3,] %>%
dplyr::select(dplyr::matches("X")),
(X0 = 0, X1 = 4, X2 = 2))
t_start <- (s_output3$,size = 1)
s_output3.1 <- (agents = data_example_i,
states = (group2, group3),
min_max_time = (t_start,))
testthat::expect_equal(s_output3.1, s_output3[s_output3$ >= t_start,])
# four classes
s_output4 <- (agents = data_example_i,
states = (group1, group2, group3),
min_max_time = (0,))
# if start time is 0, should start with 6 X2,
testthat::expect_equivalent(s_output4 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 0, X1 = 0, X2 = 6, X3 = 0))
# t == 3: 4 X2, 2 X3
testthat::expect_equivalent(s_output4[s_output4$ == 3,] %>%
dplyr::select(dplyr::matches("X")),
(X0 = 0, X1 = 0, X2 = 4, X3 = 2))
# t == 4: 6 X3
testthat::expect_equivalent(s_output4[s_output4$ == 4,] %>%
dplyr::select(dplyr::matches("X")),
(X0 = 0, X1 = 0, X2 = 0, X3 = 6))
t_start <- (s_output4$,size = 1)
s_output4.1 <- (agents = data_example_i,
states = (group1, group2,
group3),
min_max_time = (t_start,))
testthat::expect_equal(s_output4.1, s_output4[s_output4$ >= t_start,])
# if start time is -1, start with 2 X2, 2 X1, 2 X0
# as data_example_i[3,] => X0
# [4,] => X1
# rest X2
s_output4._neg1 <- (agents = data_example_i,
states = (group1, group2,
group3),
min_max_time = (-1,))
testthat::expect_equivalent(s_output4._neg1 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 1, X1 = 1, X2 = 4, X3 = 0))
testthat::expect_equal(s_output4._neg1[s_output4._neg1$ > -1,],
s_output4)
})
test_that("agents_to_aggregate.data.frame - string, data_example_i example", {
data_example_i <- (group1 = (, -2.1, , -2.1, , -2),
group2 = (-1.1,-1.1,-.1,-.1,-1,-1),
group3 = (3.1,3.1,3.1,3.1,3,3))
## three classes
s_output3 <- (agents = data_example_i,
states = ("group2", "group3"))
# if start time is 0, should start with all 6 X1,
testthat::expect_equivalent(s_output3 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 0, X1 = 6, X2 = 0))
testthat::expect_equivalent(s_output3[s_output3$ == 3,] %>%
dplyr::select(dplyr::matches("X")),
(X0 = 0, X1 = 4, X2 = 2))
t_start <- (s_output3$,size = 1)
s_output3.1 <- (agents = data_example_i,
states = ("group2", "group3"),
min_max_time = (t_start,))
testthat::expect_equal(s_output3.1, s_output3[s_output3$ >= t_start,])
# four classes
s_output4 <- (agents = data_example_i,
states = ("group1","group2","group3"),
min_max_time = (0,))
# if start time is 0, should start with 6 X2,
testthat::expect_equivalent(s_output4 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 0, X1 = 0, X2 = 6, X3 = 0))
# t == 3: 4 X2, 2 X3
testthat::expect_equivalent(s_output4[s_output4$ == 3,] %>%
dplyr::select(dplyr::matches("X")),
(X0 = 0, X1 = 0, X2 = 4, X3 = 2))
# t == 4: 6 X3
testthat::expect_equivalent(s_output4[s_output4$ == 4,] %>%
dplyr::select(dplyr::matches("X")),
(X0 = 0, X1 = 0, X2 = 0, X3 = 6))
t_start <- (s_output4$,size = 1)
s_output4.1 <- (agents = data_example_i,
states = ("group1", "group2",
"group3"),
min_max_time = (t_start,))
testthat::expect_equal(s_output4.1, s_output4[s_output4$ >= t_start,])
# if start time is -1, start with 2 X2, 2 X1, 2 X0
# as data_example_i[3,] => X0
# [4,] => X1
# rest X2
s_output4._neg1 <- (agents = data_example_i,
states = ("group1","group2",
"group3"),
min_max_time = (-1,))
testthat::expect_equivalent(s_output4._neg1 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 1, X1 = 1, X2 = 4, X3 = 0))
testthat::expect_equal(s_output4._neg1[s_output4._neg1$ > -1,],
s_output4)
})
test_that("agents_to_aggregate.data.frame, data_example_r example", {
data_example_r_cont <- (group1 = (-3.1, -3.1, , , -3.1, -3.1, , ),
group2 = (-2.1, -2.1,-2.1, -2.1, , , , ),
group3 = (-1.1, -.1, -1.1, -.1 , -1.1, -.1 , -1.1, -.1))
data_example_r_disc <- (group1 = (-3, , -3, ),
group2 = (-2, -2, , ),
group3 = (-1, -1, -1, -1))
data_example_r <- (data_example_r_cont, data_example_r_disc)
## three classes
s_output3 <- (agents = data_example_r,
states = (group2, group3))
# if start time is 0, should start with all 12 X2,
testthat::expect_equivalent(s_output3 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 0, X1 = 0, X2 = 12))
testthat::expect_equivalent((s_output3),1)
# four classes
s_output4 <- (agents = data_example_r,
states = (group1, group2, group3),
min_max_time = (0,))
# if start time is 0, should start with 6 X2,
testthat::expect_equivalent(s_output4 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 0, X1 = 0, X2 = 0, X3 = 12))
# if start time is -1, start with 8 X3, 2 X2, 1 X1, 1 X0
# rest in X3
# data_example([c(1,3,5,7,9:12),]) => X3
# data_example_r[c(2,4),] => X2
# data_example_r[6,] => X1
# data_example_r[8] => X0
s_output4._neg1 <- (agents = data_example_r,
states = (group1, group2,
group3),
min_max_time = (-1,))
testthat::expect_equivalent(s_output4._neg1 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 1, X1 = 1, X2 = 2, X3 = 8))
testthat::expect_equal(s_output4._neg1[s_output4._neg1$ > -1,],
s_output4)
})
test_that("agents_to_aggregate.data.frame - string, data_example_r example", {
data_example_r_cont <- (group1 = (-3.1, -3.1, , , -3.1, -3.1, , ),
group2 = (-2.1, -2.1,-2.1, -2.1, , , , ),
group3 = (-1.1, -.1, -1.1, -.1 , -1.1, -.1 , -1.1, -.1))
data_example_r_disc <- (group1 = (-3, , -3, ),
group2 = (-2, -2, , ),
group3 = (-1, -1, -1, -1))
data_example_r <- (data_example_r_cont, data_example_r_disc)
## three classes
s_output3 <- (agents = data_example_r,
states = ("group2", "group3"))
# if start time is 0, should start with all 12 X2,
testthat::expect_equivalent(s_output3 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 0, X1 = 0, X2 = 12))
testthat::expect_equivalent((s_output3),1)
# four classes
s_output4 <- (agents = data_example_r,
states = ("group1","group2","group3"),
min_max_time = (0,))
# if start time is 0, should start with 6 X2,
testthat::expect_equivalent(s_output4 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 0, X1 = 0, X2 = 0, X3 = 12))
# if start time is -1, start with 8 X3, 2 X2, 1 X1, 1 X0
# rest in X3
# data_example([c(1,3,5,7,9:12),]) => X3
# data_example_r[c(2,4),] => X2
# data_example_r[6,] => X1
# data_example_r[8] => X0
s_output4._neg1 <- (agents = data_example_r,
states = ("group1","group2",
"group3"),
min_max_time = (-1,))
testthat::expect_equivalent(s_output4._neg1 %>%
dplyr::select(dplyr::matches("X")) %>% .[1,],
(X0 = 1, X1 = 1, X2 = 2, X3 = 8))
testthat::expect_equal(s_output4._neg1[s_output4._neg1$ > -1,],
s_output4)
})
test_that("agents_to_aggregate.data.frame, births", {
data_example_s <- (group1 = (.1,0),
group2 = (2.1,2),
group3 = (3.1,3))
data_example_e <- (group1 = (-1.1, -.1,-1),
group2 = (2.1,2.1,2),
group3 = (3.1,3.1,3))
data_example_i <- (group1 = (, -2.1, , -2.1, , -2),
group2 = (-1.1,-1.1,-.1,-.1,-1,-1),
group3 = (3.1,3.1,3.1,3.1,3,3))
data_example_r_cont <- (group1 = (-3.1, -3.1, , , -3.1, -3.1, , ),
group2 = (-2.1, -2.1,-2.1, -2.1, , , , ),
group3 = (-1.1, -.1, -1.1, -.1 , -1.1, -.1 , -1.1, -.1))
data_example_r_disc <- (group1 = (-3, , -3, ),
group2 = (-2, -2, , ),
group3 = (-1, -1, -1, -1))
all_data <- (data_example_s,
data_example_e,
data_example_i,
data_example_r_cont,
data_example_r_disc) %>%
dplyr::mutate(birth = ((0,1,), = 23))
all_out <- (agents = all_data,
birth = birth,
states = (group1, group2, group3))
testthat::expect_equal(all_out %>%
dplyr::select(dplyr::matches("X")) %>% (1, ),
(23-8,(23,4)))
all_out_no_birth <- (agents = all_data,
states = (group1, group2,
group3))
# babies born at t == 0
# obs 2: g1
# obs 5: g1
# obs 8: g2
# obs 11:g2
# obs 14:g3
# obs 17:g3
# obs 20:g3
# obs 23:g3
testthat::expect_equal((all_out_no_birth - all_out)[1,],
( = 0, X0 = 0, X1 = 2, X2 = 2, X3 = 4))
})
test_that("agents_to_aggregate.data.frame - string, births", {
data_example_s <- (group1 = (.1,0),
group2 = (2.1,2),
group3 = (3.1,3))
data_example_e <- (group1 = (-1.1, -.1,-1),
group2 = (2.1,2.1,2),
group3 = (3.1,3.1,3))
data_example_i <- (group1 = (, -2.1, , -2.1, , -2),
group2 = (-1.1,-1.1,-.1,-.1,-1,-1),
group3 = (3.1,3.1,3.1,3.1,3,3))
data_example_r_cont <- (group1 = (-3.1, -3.1, , , -3.1, -3.1, , ),
group2 = (-2.1, -2.1,-2.1, -2.1, , , , ),
group3 = (-1.1, -.1, -1.1, -.1 , -1.1, -.1 , -1.1, -.1))
data_example_r_disc <- (group1 = (-3, , -3, ),
group2 = (-2, -2, , ),
group3 = (-1, -1, -1, -1))
all_data <- (data_example_s,
data_example_e,
data_example_i,
data_example_r_cont,
data_example_r_disc) %>%
dplyr::mutate(birth = ((0,1,), = 23))
all_out <- (agents = all_data,
birth = "birth",
states = ("group1","group2", "group3"))
testthat::expect_equal(all_out %>%
dplyr::select(dplyr::matches("X")) %>% (1, ),
(23-8,(23,4)))
all_out_no_birth <- (agents = all_data,
states = ("group1","group2",
"group3"))
# babies born at t == 0
# obs 2: g1
# obs 5: g1
# obs 8: g2
# obs 11:g2
# obs 14:g3
# obs 17:g3
# obs 20:g3
# obs 23:g3
testthat::expect_equal((all_out_no_birth - all_out)[1,],
( = 0, X0 = 0, X1 = 2, X2 = 2, X3 = 4))
})
test_that("agents_to_aggregate.group_df passes basic checks", {
(
(
(dplyr, quietly = )
))
# similar test as in the example string
max_time <- 100
new_raw <- %>%
dplyr::mutate(AGE2 = ((AGE,3)))
agents_g <- new_raw %>% dplyr::group_by(AGE2)
sir_group <- (agents_g, states = (tI, tR),
min_max_time = (0, max_time))
agents <- agents_g %>%
dplyr::(AGE2 == 1) %>% dplyr::ungroup()
sir_group1 <- (agents, states = (tI, tR),
min_max_time = (0, max_time))
sir_group_1 <- sir_group %>% dplyr::(AGE2 == 1)
testthat::expect_equal(sir_group1,
dplyr::select(dplyr::ungroup(sir_group_1),
, X0, X1, X2))
})
test_that("agents_to_aggregate.group_df -string passes basic checks", {
(
(
(dplyr, quietly = )
))
# similar test as in the example string
max_time <- 100
new_raw <- %>%
dplyr::mutate(AGE2 = ((AGE,3)))
agents_g <- new_raw %>% dplyr::group_by(AGE2)
sir_group <- (agents_g, states = ("tI", "tR"),
min_max_time = (0, max_time))
agents <- agents_g %>%
dplyr::(AGE2 == 1) %>% dplyr::ungroup()
sir_group1 <- (agents, states = ("tI", "tR"),
min_max_time = (0, max_time))
sir_group_1 <- sir_group %>% dplyr::(AGE2 == 1)
testthat::expect_equal(sir_group1,
dplyr::select(dplyr::ungroup(sir_group_1),
, X0, X1, X2))
})
test_that("agents_to_aggregate.group_df, max_t = NA basic checks", {
(
(
(dplyr, quietly = )
))
# similar test as in the example string
new_raw <- %>%
mutate(AGE2 = ((AGE,3)))
agents_g <- new_raw %>% dplyr::group_by(AGE2)
max_time_each <- agents_g %>%
dplyr::summarize(nmax = ((tR)))
max_time <- max_time_each %>% pull(nmax) %>% ()
sir_group <- (agents_g, states = (tI, tR),
min_max_time = (0, ))
# should all share max value if min_max_time[2] = NA
testthat::expect_equal(((sir_group %>%
dplyr::summarize(maxt = ()) %>%
dplyr::pull(maxt)) == max_time), 3)
for (age2_value 1:3){
agents <- agents_g %>%
dplyr::(AGE2 == age2_value) %>% dplyr::ungroup()
sir_group_sub_id <- (agents, states = (tI, tR),
min_max_time = (0, ))
sir_group_sub_g <- sir_group %>% (AGE2 == age2_value)
individual_max_t <- max_time_each$nmax[max_time_each$AGE2 == age2_value]
testthat::expect_equal(sir_group_sub_id %>% pull() %>% ,
individual_max_t)
testthat::expect_equal(sir_group_sub_id,
sir_group_sub_g %>% ungroup %>%
dplyr::select(, X0, X1, X2) %>%
( <= individual_max_t))
if (individual_max_t < max_time){
unique_rows_after_max <- sir_group_sub_g %>% ungroup %>%
( > individual_max_t) %>%
dplyr::select(X0, X1, X2) %>% distinct() %>% ()
testthat::expect_equal(unique_rows_after_max, 1)
}
}
})
test_that("agents_to_aggregate.group_df, max_t = NA basic checks, strings", {
(
(
(dplyr, quietly = )
))
# similar test as in the example string
new_raw <- %>%
mutate(AGE2 = ((AGE,3)))
agents_g <- new_raw %>% group_by(AGE2)
max_time_each <- agents_g %>% summarize(nmax = ((tR)))
max_time <- max_time_each %>% pull(nmax) %>% ()
sir_group <- (agents_g, states = ("tI", "tR"),
min_max_time = (0, ))
# should all share max value if min_max_time[2] = NA
testthat::expect_equal(((sir_group %>% summarize(maxt = ()) %>%
pull(maxt)) == max_time), 3)
for (age2_value 1:3){
agents <- agents_g %>%
(AGE2 == age2_value) %>% ungroup()
sir_group_sub_id <- (agents, states = ("tI", "tR"),
min_max_time = (0, ))
sir_group_sub_g <- sir_group %>% (AGE2 == age2_value)
individual_max_t <- max_time_each$nmax[max_time_each$AGE2 == age2_value]
testthat::expect_equal(sir_group_sub_id %>% pull() %>% ,
individual_max_t)
testthat::expect_equal(sir_group_sub_id,
sir_group_sub_g %>% ungroup %>%
dplyr::select(, X0, X1, X2) %>%
( <= individual_max_t))
if (individual_max_t < max_time){
unique_rows_after_max <- sir_group_sub_g %>% ungroup %>%
( > individual_max_t) %>%
dplyr::select(X0, X1, X2) %>% distinct() %>% ()
testthat::expect_equal(unique_rows_after_max, 1)
}
}
})
test_that("agents_to_aggregate + integer_time_expansion = FALSE -- more basic",{
data_example_s <- (group1 = (.1,0),
group2 = (2.1,2),
group3 = (3.1,3))
data_example_e <- (group1 = (-1.1, -.1,-1),
group2 = (2.1,2.1,2),
group3 = (3.1,3.1,3))
data_example_i <- (group1 = (, -2.1, , -2.1, , -2),
group2 = (-1.1,-1.1,-.1,-.1,-1,-1),
group3 = (3.1,3.1,3.1,3.1,3,3))
data_example_r_cont <- (group1 = (-3.1, -3.1, , , -3.1, -3.1, , ),
group2 = (-2.1, -2.1,-2.1, -2.1, , , , ),
group3 = (-1.1, -.1, -1.1, -.1 , -1.1, -.1 , -1.1, -.1))
data_example_r_disc <- (group1 = (-3, , -3, ),
group2 = (-2, -2, , ),
group3 = (-1, -1, -1, -1))
mult <- 3
all_data <- (data_example_s,
data_example_e,
data_example_i,
data_example_r_cont,
data_example_r_disc) %>%
dplyr::mutate(birth = ((0,1,), = 23)) * mult
all_out <- (agents = all_data,
birth = birth,
states = (group1, group2, group3))
all_out_filter <- (agents = all_data,
birth = birth,
states = (group1, group2, group3),
integer_time_expansion = )
testthat::expect_equal(all_out_filter, all_out!(all_out$ %in% (2,4,5,8)),])
})
testthat::test_that("check integer_time_expand works", {
test_df <- ("tI" = (-5,-2,-1,3,4,5,7),
"tR" = (-5,-2,-1,3,4,5,7)+4)
out <- (test_df, states = ("tI","tR"),
min_max_time = (-6, 12))
testthat::expect_equal(out$, (-6):12)
static_out <- (
= (-6):12,
X0 = (7,6,6,6,5,4,4,4,4,3,2,1,1,0,0,0,0,0,0),
X1 = (0,1,1,1,2,2,2,2,1,1,2,3,3,3,2,1,1,0,0),
X2 = (0,0,0,0,0,1,1,1,2,3,3,3,3,4,5,6,6,7,7)
) %>% tibble::tibble()
testthat::expect_equal(out, static_out)
})
