Skip to content

Commit

Permalink
Merge branch 'test_r18' into val_test_3
Browse files Browse the repository at this point in the history
  • Loading branch information
@LucieContamin
LucieContamin committed Apr 22, 2024
2 parents b074c9a + ff08354 commit f64e48a
Show file tree
Hide file tree
Showing 2 changed files with 77 additions and 185 deletions.
154 changes: 77 additions & 77 deletions code/make_round.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,8 @@ source("code/utils.R")
config <- hubUtils::read_config(getwd(), config = "tasks")

# Validate hub config
a <- hubAdmin::validate_config()
hubAdmin::view_config_val_errors(a)
#a <- hubAdmin::validate_config()
#hubAdmin::view_config_val_errors(a)

## RSV ROUND 1 -------------
#rsv1 <- config$rounds[[4]]
Expand Down Expand Up @@ -40,81 +40,81 @@ hubAdmin::view_config_val_errors(a)
#
## EQUITY ROUNDS ------------
## Phase I
lapply(config$rounds[5], function(x) {
req_df <- make_df_sample(x$model_tasks,
max_sample = max_sample(x))
default_pairing <- def_grp(x)
max_sample <- max_sample(x)
lapply(unique(req_df$team_model), function(model_id) {
print(paste0("Generate example data for: ", model_id))
df <- dplyr::filter(req_df, team_model == model_id)
df <- dplyr::select(df, -team_model)
if (model_id %in% c("team1-modela", "team2-modelb")) {
df2 <- dplyr::filter(df, target == "inc death")
df2$target <- "inc case"
df <- rbind(df, df2)
rm(df2)
}
print("-- Generate value")
if (!model_id %in% c("team1-modela", "team2-modelb")) {
df <- update_df_val_sample(df)
} else {
df <- update_df_val_sample(df, quantile = TRUE,
quant_group = c("origin_date", "scenario_id",
"location", "target", "horizon",
"race_ethnicity"),
cumul_group = c("origin_date", "scenario_id",
"location", "target",
"output_type",
"output_type_id",
"race_ethnicity"))
df <- dplyr::filter(df, grepl("inc", target))
}
print("-- Generate sample ID")
df <- dplyr::mutate(df, value = round(value, 1),
run_grouping = ifelse(output_type == "sample", 1, NA),
stochastic_run = ifelse(output_type == "sample", 1, NA),
output_type_id = ifelse(output_type == "sample", NA,
output_type_id))
if (model_id %in% c("team1-modela")) {
df <- prep_sample_information(df, "stochastic_run", default_pairing,
rep = max_sample)
} else if (model_id %in% c("team2-modelb")) {
df <- prep_sample_information(df, "run_grouping", default_pairing,
rep = max_sample)
} else if (model_id %in% c("team3-modelc")) {
df <-
prep_sample_information(df, "run_grouping", default_pairing,
rep = max_sample) %>%
prep_sample_information("stochastic_run", default_pairing,
rep = max_sample)
} else if (model_id %in% c("team4-modeld")) {
df <-
prep_sample_information(df, "run_grouping", default_pairing,
rep = max_sample, same_rep = TRUE) %>%
prep_sample_information("stochastic_run", default_pairing,
rep = max_sample)
} else {
df <-
prep_sample_information(df, "run_grouping", c(default_pairing,
"scenario_id"),
rep = max_sample, same_rep = TRUE) %>%
prep_sample_information("stochastic_run", default_pairing,
rep = max_sample)
}
print("-- Write output")
file_name <- paste0("data-processed/", model_id, "/", x$round_id, "-",
model_id, ".gz.parquet")
if (model_id %in% c("team1-modela")) {
df$value <- as.integer(df$value)
} else {
df$value <- round(df$value, 1)
}
arrow::write_parquet(df, file_name, compression = "gzip",
compression_level = 9)
})
})

#lapply(config$rounds[5], function(x) {
# req_df <- make_df_sample(x$model_tasks,
# max_sample = max_sample(x))
# default_pairing <- def_grp(x)
# max_sample <- max_sample(x)
# lapply(unique(req_df$team_model), function(model_id) {
# print(paste0("Generate example data for: ", model_id))
# df <- dplyr::filter(req_df, team_model == model_id)
# df <- dplyr::select(df, -team_model)
# if (model_id %in% c("team1-modela", "team2-modelb")) {
# df2 <- dplyr::filter(df, target == "inc death")
# df2$target <- "inc case"
# df <- rbind(df, df2)
# rm(df2)
# }
# print("-- Generate value")
# if (!model_id %in% c("team1-modela", "team2-modelb")) {
# df <- update_df_val_sample(df)
# } else {
# df <- update_df_val_sample(df, quantile = TRUE,
# quant_group = c("origin_date", "scenario_id",
# "location", "target", "horizon",
# "race_ethnicity"),
# cumul_group = c("origin_date", "scenario_id",
# "location", "target",
# "output_type",
# "output_type_id",
# "race_ethnicity"))
# df <- dplyr::filter(df, grepl("inc", target))
# }
# print("-- Generate sample ID")
# df <- dplyr::mutate(df, value = round(value, 1),
# run_grouping = ifelse(output_type == "sample", 1, NA),
# stochastic_run = ifelse(output_type == "sample", 1, NA),
# output_type_id = ifelse(output_type == "sample", NA,
# output_type_id))
# if (model_id %in% c("team1-modela")) {
# df <- prep_sample_information(df, "stochastic_run", default_pairing,
# rep = max_sample)
# } else if (model_id %in% c("team2-modelb")) {
# df <- prep_sample_information(df, "run_grouping", default_pairing,
# rep = max_sample)
# } else if (model_id %in% c("team3-modelc")) {
# df <-
# prep_sample_information(df, "run_grouping", default_pairing,
# rep = max_sample) %>%
# prep_sample_information("stochastic_run", default_pairing,
# rep = max_sample)
# } else if (model_id %in% c("team4-modeld")) {
# df <-
# prep_sample_information(df, "run_grouping", default_pairing,
# rep = max_sample, same_rep = TRUE) %>%
# prep_sample_information("stochastic_run", default_pairing,
# rep = max_sample)
# } else {
# df <-
# prep_sample_information(df, "run_grouping", c(default_pairing,
# "scenario_id"),
# rep = max_sample, same_rep = TRUE) %>%
# prep_sample_information("stochastic_run", default_pairing,
# rep = max_sample)
# }
# print("-- Write output")
# file_name <- paste0("data-processed/", model_id, "/", x$round_id, "-",
# model_id, ".gz.parquet")
# if (model_id %in% c("team1-modela")) {
# df$value <- as.integer(df$value)
# } else {
# df$value <- round(df$value, 1)
# }
# arrow::write_parquet(df, file_name, compression = "gzip",
# compression_level = 9)
# })
#})
#

#
# COVID Round 18 ------
Expand Down
108 changes: 0 additions & 108 deletions hub-config/tasks.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1695,114 +1695,6 @@
"time_unit": "week"
}
]
},
{
"task_ids": {
"origin_date": {
"required": ["2024-04-28"],
"optional": null
},
"scenario_id": {
"required": ["A-2024-03-01", "B-2024-03-01", "C-2024-03-01", "D-2024-03-01", "E-2024-03-01", "F-2024-03-01"],
"optional": null
},
"location": {
"required": null,
"optional": ["US", "01", "02", "04", "05", "06", "08", "09", "10", "11", "12", "13", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "44", "45", "46", "47", "48", "49", "50", "51", "53", "54", "55", "56", "60", "66", "69", "72", "74", "78"]
},
"target": {
"required": null,
"optional": ["peak time hosp"]
},
"horizon": {
"required": null,
"optional": null
},
"age_group": {
"required": ["0-130"],
"optional": null
}
},
"output_type": {
"cdf":{
"output_type_id":{
"required":["EW202418", "EW202419", "EW202420", "EW202421", "EW202422", "EW202423", "EW202424", "EW202425", "EW202426", "EW202427", "EW202428", "EW202429", "EW202430", "EW202431", "EW202432", "EW202433", "EW202434", "EW202435", "EW202436", "EW202437", "EW202438", "EW202439", "EW202440", "EW202441", "EW202442", "EW202443", "EW202444", "EW202445", "EW202446", "EW202447", "EW202448", "EW202449", "EW202450", "EW202451", "EW202452", "EW202501", "EW202502", "EW202503", "EW202504", "EW202505", "EW202506", "EW202507", "EW202508", "EW202509", "EW202510", "EW202511", "EW202512", "EW202513", "EW202514", "EW202515", "EW202516", "EW202517"],
"optional":null
},
"value":{
"type":"double",
"minimum":0,
"maximum":1
}
}
},
"target_metadata": [
{
"target_id": "peak time hosp",
"target_name": "Peak timing of hospitalization",
"description":"Cumulative probability of the incident hospitalization peak",
"target_units":"population",
"target_keys":{
"target":["peak time hosp"]
},
"target_type": "discrete",
"is_step_ahead": true,
"time_unit": "week"
}
]
},
{
"task_ids": {
"origin_date": {
"required": ["2024-04-28"],
"optional": null
},
"scenario_id": {
"required": ["A-2024-03-01", "B-2024-03-01", "C-2024-03-01", "D-2024-03-01", "E-2024-03-01", "F-2024-03-01"],
"optional": null
},
"location": {
"required": null,
"optional": ["US", "01", "02", "04", "05", "06", "08", "09", "10", "11", "12", "13", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24", "25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", "41", "42", "44", "45", "46", "47", "48", "49", "50", "51", "53", "54", "55", "56", "60", "66", "69", "72", "74", "78"]
},
"target": {
"required": null,
"optional": ["peak size hosp"]
},
"horizon": {
"required": null,
"optional": null
},
"age_group": {
"required": ["0-130"],
"optional": null
}
},
"output_type": {
"quantile":{
"output_type_id":{
"required":[0.01,0.025,0.05,0.1,0.15,0.2,0.25,0.3,0.35,0.4,0.45,0.5,0.55,0.6,0.65,0.7,0.75,0.8,0.85,0.9,0.95,0.975,0.99],
"optional":[0,1]
},
"value":{
"type":"double",
"minimum":0
}
}
},
"target_metadata": [
{
"target_id": "peak size hosp",
"target_name": "Peak size of hospitalization",
"description":"Magnitude of the peak of weekly incident hospitalizations",
"target_units":"population",
"target_keys":{
"target":["peak size hosp"]
},
"target_type": "discrete",
"is_step_ahead": false
}
]
}
],
"submissions_due": {
Expand Down

0 comments on commit f64e48a

Please sign in to comment.