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dshemetovdshemetov
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refactor: locals data_targets
1 parent 17dc4ec commit be0cf77

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2 files changed

+224
-220
lines changed

2 files changed

+224
-220
lines changed

‎covid_hosp_explore/data_targets.R

Lines changed: 112 additions & 110 deletions
Original file line numberDiff line numberDiff line change
@@ -1,115 +1,117 @@
1-
geo_type <- "state"
2-
time_type <- "day"
3-
geo_values <- "*"
4-
time_values <- epidatr::epirange(from = "2020-01-01", to = "2024-01-01")
5-
fetch_args <- epidatr::fetch_args_list(return_empty = TRUE, timeout_seconds = 200)
6-
issues <- "*"
1+
data_targets <- local({
2+
geo_type <- "state"
3+
time_type <- "day"
4+
geo_values <- "*"
5+
time_values <- epidatr::epirange(from = "2020-01-01", to = "2024-01-01")
6+
fetch_args <- epidatr::fetch_args_list(return_empty = TRUE, timeout_seconds = 200)
7+
issues <- "*"
78

8-
data_targets <- list(
9-
tar_target(
10-
name = hhs_latest_data,
11-
command = {
12-
epidatr::pub_covidcast(
13-
source = "hhs",
14-
signals = "confirmed_admissions_covid_1d",
15-
geo_type = geo_type,
16-
time_type = time_type,
17-
geo_values = geo_values,
18-
time_values = time_values,
19-
fetch_args = fetch_args
20-
)
21-
}
22-
),
23-
tar_target(
24-
name = chng_latest_data,
25-
command = {
26-
epidatr::pub_covidcast(
27-
source = "chng",
28-
signals = "smoothed_adj_outpatient_covid",
29-
geo_type = geo_type,
30-
time_type = time_type,
31-
geo_values = geo_values,
32-
time_values = time_values,
33-
fetch_args = fetch_args
34-
)
35-
}
36-
),
37-
tar_target(
38-
name = hhs_evaluation_data,
39-
command = {
40-
hhs_latest_data %>%
41-
rename(
42-
actual = value,
43-
target_end_date = time_value
9+
list(
10+
tar_target(
11+
name = hhs_latest_data,
12+
command = {
13+
epidatr::pub_covidcast(
14+
source = "hhs",
15+
signals = "confirmed_admissions_covid_1d",
16+
geo_type = geo_type,
17+
time_type = time_type,
18+
geo_values = geo_values,
19+
time_values = time_values,
20+
fetch_args = fetch_args
4421
)
45-
}
46-
),
47-
tar_target(
48-
name = hhs_latest_data_2022,
49-
command = {
50-
hhs_latest_data %>%
51-
filter(time_value >= "2022-01-01")
52-
}
53-
),
54-
tar_target(
55-
name = chng_latest_data_2022,
56-
command = {
57-
chng_latest_data %>%
58-
filter(time_value >= "2022-01-01")
59-
}
60-
),
61-
tar_target(
62-
name = hhs_archive_data_2022,
63-
command = {
64-
epidatr::pub_covidcast(
65-
source = "hhs",
66-
signals = "confirmed_admissions_covid_1d",
67-
geo_type = geo_type,
68-
time_type = time_type,
69-
geo_values = geo_values,
70-
time_values = time_values,
71-
issues = "*",
72-
fetch_args = fetch_args
73-
)
74-
}
75-
),
76-
tar_target(
77-
name = chng_archive_data_2022,
78-
command = {
79-
epidatr::pub_covidcast(
80-
source = "chng",
81-
signals = "smoothed_adj_outpatient_covid",
82-
geo_type = geo_type,
83-
time_type = time_type,
84-
geo_values = geo_values,
85-
time_values = time_values,
86-
issues = "*",
87-
fetch_args = fetch_args
88-
)
89-
}
90-
),
91-
tar_target(
92-
name = joined_archive_data_2022,
93-
command = {
94-
hhs_archive_data_2022 %<>%
95-
select(geo_value, time_value, value, issue) %>%
96-
rename("hhs" := value) %>%
97-
rename(version = issue) %>%
98-
as_epi_archive(
99-
geo_type = "state",
100-
time_type = "day",
101-
compactify = TRUE
22+
}
23+
),
24+
tar_target(
25+
name = chng_latest_data,
26+
command = {
27+
epidatr::pub_covidcast(
28+
source = "chng",
29+
signals = "smoothed_adj_outpatient_covid",
30+
geo_type = geo_type,
31+
time_type = time_type,
32+
geo_values = geo_values,
33+
time_values = time_values,
34+
fetch_args = fetch_args
10235
)
103-
chng_archive_data_2022 %<>%
104-
select(geo_value, time_value, value, issue) %>%
105-
rename("chng" := value) %>%
106-
rename(version = issue) %>%
107-
as_epi_archive(
108-
geo_type = "state",
109-
time_type = "day",
110-
compactify = TRUE
36+
}
37+
),
38+
tar_target(
39+
name = hhs_evaluation_data,
40+
command = {
41+
hhs_latest_data %>%
42+
rename(
43+
actual = value,
44+
target_end_date = time_value
45+
)
46+
}
47+
),
48+
tar_target(
49+
name = hhs_latest_data_2022,
50+
command = {
51+
hhs_latest_data %>%
52+
filter(time_value >= "2022-01-01")
53+
}
54+
),
55+
tar_target(
56+
name = chng_latest_data_2022,
57+
command = {
58+
chng_latest_data %>%
59+
filter(time_value >= "2022-01-01")
60+
}
61+
),
62+
tar_target(
63+
name = hhs_archive_data_2022,
64+
command = {
65+
epidatr::pub_covidcast(
66+
source = "hhs",
67+
signals = "confirmed_admissions_covid_1d",
68+
geo_type = geo_type,
69+
time_type = time_type,
70+
geo_values = geo_values,
71+
time_values = time_values,
72+
issues = "*",
73+
fetch_args = fetch_args
11174
)
112-
epix_merge(hhs_archive_data_2022, chng_archive_data_2022, sync = "locf")
113-
}
75+
}
76+
),
77+
tar_target(
78+
name = chng_archive_data_2022,
79+
command = {
80+
epidatr::pub_covidcast(
81+
source = "chng",
82+
signals = "smoothed_adj_outpatient_covid",
83+
geo_type = geo_type,
84+
time_type = time_type,
85+
geo_values = geo_values,
86+
time_values = time_values,
87+
issues = "*",
88+
fetch_args = fetch_args
89+
)
90+
}
91+
),
92+
tar_target(
93+
name = joined_archive_data_2022,
94+
command = {
95+
hhs_archive_data_2022 %<>%
96+
select(geo_value, time_value, value, issue) %>%
97+
rename("hhs" := value) %>%
98+
rename(version = issue) %>%
99+
as_epi_archive(
100+
geo_type = "state",
101+
time_type = "day",
102+
compactify = TRUE
103+
)
104+
chng_archive_data_2022 %<>%
105+
select(geo_value, time_value, value, issue) %>%
106+
rename("chng" := value) %>%
107+
rename(version = issue) %>%
108+
as_epi_archive(
109+
geo_type = "state",
110+
time_type = "day",
111+
compactify = TRUE
112+
)
113+
epix_merge(hhs_archive_data_2022, chng_archive_data_2022, sync = "locf")
114+
}
115+
)
114116
)
115-
)
117+
})

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