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Merged
merged 5 commits into from
Jan 18, 2024
Merged

Combine timetype wiki twitter #236

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d1db445
combine epiweek and date into time_type and time_value for pub_wiki
nmdefries Jan 5, 2024
83e7ce3
combine epiweek and date into time_type and time_value for pvt_twitter
nmdefries Jan 5, 2024
5311e0c
test wildcard and day/week support
nmdefries Jan 9, 2024
61e5742
changelog
nmdefries Jan 18, 2024
3ae82e2
Merge branch 'ndefries/endpt-defaults' into ndefries/combine-timetype…
nmdefries Jan 18, 2024
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1 change: 1 addition & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@
- `get_api_key` no longer reads from R options and only uses environment variables (#217).
- Fix documentation related to CRAN submission.
- Fix some errors from passing "" as a key.
- `pvt_twitter` and `pub_wiki` now use `time_type` and `time_values` args instead of mutually exclusive `dates` and `epiweeks` (#236). This matches the interface of the `pub_covidcast` endpoint.
- All endpoints now support the use of "\*" as a wildcard to fetch all dates or epiweeks (#234).

# epidatr 1.0.0
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69 changes: 49 additions & 20 deletions R/endpoints.R
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Expand Up @@ -209,8 +209,10 @@ pub_covid_hosp_facility <- function(
cli::cli_warn(coercion_msg, class = "epidatr__epirange_week_coercion")
collection_weeks <- reformat_epirange(collection_weeks, to_type = "day")
# Single week date.
} else if ((test_integerish(collection_weeks) || test_character(collection_weeks)) &&
nchar(collection_weeks) == 6) {
} else if (
(test_integerish(collection_weeks) || test_character(collection_weeks)) &&
nchar(collection_weeks) == 6
) {
cli::cli_warn(coercion_msg, class = "epidatr__single_week_coercion")
collection_weeks <- parse_api_week(collection_weeks)
}
Expand Down Expand Up @@ -2094,15 +2096,17 @@ pvt_sensors <- function(
#' pvt_twitter(
#' auth = Sys.getenv("SECRET_API_AUTH_TWITTER"),
#' locations = "CA",
#' epiweeks = epirange(201501, 202001)
#' time_type = "week",
#' time_values = epirange(201501, 202001)
#' )
#' }
#' @param auth string. Restricted access key (not the same as API key).
#' @param locations character. Locations to fetch.
#' @param ... not used for values, forces later arguments to bind by name
#' @param dates [`timeset`]. Dates to fetch. Mutually exclusive with `epiweeks`.
#' @param epiweeks [`timeset`]. Epiweeks to fetch. Mutually exclusive with
#' `dates`.
#' @param time_type string. The temporal resolution of the data (either "day" or
#' "week", depending on signal).
#' @param time_values [`timeset`]. Dates or epiweeks to fetch. Defaults to all
#' ("*") dates.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
#' @return [`tibble::tibble`]
#' @keywords endpoint
Expand All @@ -2111,21 +2115,31 @@ pvt_twitter <- function(
auth,
locations,
...,
dates = NULL,
epiweeks = NULL,
time_type = c("day", "week"),
time_values = "*",
fetch_args = fetch_args_list()) {
rlang::check_dots_empty()

time_type <- match.arg(time_type)
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@dsweber2 dsweber2 Jan 10, 2024 •
edited
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I'm not entirely sure this is necessary, or else pub_covidcast is missing something important, since it doesn't do this. I would maybe make a function for this bit of logic if it is necessary, since it (should?) be included 3 times.

(I mean this and if statements below)

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Here it's necessary because the default value is c("day", "week"), but you can only have one time_type. match.arg() takes the first if the default is not overridden. It's a common convention in R that if the argument can be one of several string values, you make the default list all of them, and match.arg() takes care of picking the first (if none is provided) or ensuring the provided value is valid otherwise.

pub_covidcast() doesn't set a default for this argument, so it's not strictly necessary. However, pub_covidcast() could do match.arg(time_type, c("day", "week")) to enforce that the type must be one or the other but not both.

if (time_type == "day") {
dates <- time_values
epiweeks <- NULL
dates <- get_wildcard_equivalent_dates(dates, "day")
} else {
dates <- NULL
epiweeks <- time_values
epiweeks <- get_wildcard_equivalent_dates(epiweeks, "week")
}

assert_character_param("auth", auth, len = 1)
assert_character_param("locations", locations)
assert_character_param("time_type", time_type, len = 1)
assert_timeset_param("time_values", time_values)
assert_timeset_param("dates", dates, required = FALSE)
assert_timeset_param("epiweeks", epiweeks, required = FALSE)
dates <- parse_timeset_input(dates)
epiweeks <- parse_timeset_input(epiweeks)

if (!xor(is.null(dates), is.null(epiweeks))) {
stop("exactly one of `dates` and `epiweeks` is required")
}
time_field <- if (!is.null(dates)) {
create_epidata_field_info("date", "date")
} else {
Expand Down Expand Up @@ -2163,13 +2177,18 @@ pvt_twitter <- function(
#'
#' @examples
#' \dontrun{
#' pub_wiki(articles = "avian_influenza", epiweeks = epirange(201501, 201601))
#' pub_wiki(
#' articles = "avian_influenza",
#' time_type = "week",
#' time_values = epirange(201501, 201601)
#' )
#' }
#' @param articles character. Articles to fetch.
#' @param ... not used for values, forces later arguments to bind by name
#' @param dates [`timeset`]. Dates to fetch. Mutually exclusive with `epiweeks`.
#' @param epiweeks [`timeset`]. Epiweeks to fetch. Mutually exclusive with
#' `dates`.
#' @param time_type string. The temporal resolution of the data (either "day" or
#' "week", depending on signal).
#' @param time_values [`timeset`]. Dates or epiweeks to fetch. Defaults to all
#' ("*") dates.
#' @param language string. Language to fetch.
#' @param hours integer. Optionally, the hours to fetch.
#' @param fetch_args [`fetch_args`]. Additional arguments to pass to `fetch()`.
Expand All @@ -2179,24 +2198,34 @@ pvt_twitter <- function(
pub_wiki <- function(
articles,
...,
dates = NULL,
epiweeks = NULL,
time_type = c("day", "week"),
time_values = "*",
hours = NULL,
language = "en",
fetch_args = fetch_args_list()) {
rlang::check_dots_empty()

time_type <- match.arg(time_type)
if (time_type == "day") {
dates <- time_values
epiweeks <- NULL
dates <- get_wildcard_equivalent_dates(dates, "day")
} else {
dates <- NULL
epiweeks <- time_values
epiweeks <- get_wildcard_equivalent_dates(epiweeks, "week")
}

assert_character_param("articles", articles)
assert_character_param("time_type", time_type, len = 1)
assert_timeset_param("time_values", time_values)
assert_timeset_param("dates", dates, required = FALSE)
assert_timeset_param("epiweeks", epiweeks, required = FALSE)
assert_integerish_param("hours", hours, required = FALSE)
assert_character_param("language", language, len = 1, required = FALSE)
dates <- parse_timeset_input(dates)
epiweeks <- parse_timeset_input(epiweeks)

if (!xor(is.null(dates), is.null(epiweeks))) {
stop("exactly one of `dates` and `epiweeks` is required")
}
time_field <- if (!is.null(dates)) {
create_epidata_field_info("date", "date")
} else {
Expand Down
17 changes: 11 additions & 6 deletions man/pub_wiki.Rd
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14 changes: 8 additions & 6 deletions man/pvt_twitter.Rd
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61 changes: 58 additions & 3 deletions tests/testthat/test-endpoints.R
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Original file line number Diff line number Diff line change
Expand Up @@ -137,12 +137,27 @@ test_that("basic_epidata_call", {
expect_no_error(pvt_twitter(
auth = "yourkey",
locations = "CA",
epiweeks = epirange(201501, 202001),
time_type = "week",
time_values = epirange(201501, 202001),
fetch_args = fetch_args_list(dry_run = TRUE)
) %>% request_url())
expect_no_error(pvt_twitter(
auth = "yourkey",
locations = "CA",
time_type = "day",
time_values = epirange(20150101, 20200101),
fetch_args = fetch_args_list(dry_run = TRUE)
) %>% request_url())
expect_no_error(pub_wiki(
articles = "avian_influenza",
epiweeks = epirange(201501, 202001),
time_type = "week",
time_values = epirange(201501, 202001),
fetch_args = fetch_args_list(dry_run = TRUE)
) %>% request_url())
expect_no_error(pub_wiki(
articles = "avian_influenza",
time_type = "day",
time_values = epirange(20150101, 20200101),
fetch_args = fetch_args_list(dry_run = TRUE)
) %>% request_url())
})
Expand Down Expand Up @@ -322,6 +337,44 @@ test_that("endoints accept wildcard for date parameter", {
))
expect_identical(call$params$epiweeks$from, 100001)
expect_identical(call$params$epiweeks$to, 300001)

expect_no_error(call <- pvt_twitter(
auth = "yourkey",
locations = "CA",
time_type = "week",
time_values = "*",
fetch_args = fetch_args_list(dry_run = TRUE)
))
expect_identical(call$params$epiweeks$from, 100001)
expect_identical(call$params$epiweeks$to, 300001)

expect_no_error(call <- pvt_twitter(
auth = "yourkey",
locations = "CA",
time_type = "day",
time_values = "*",
fetch_args = fetch_args_list(dry_run = TRUE)
))
expect_identical(call$params$dates$from, 10000101)
expect_identical(call$params$dates$to, 30000101)

expect_no_error(call <- pub_wiki(
articles = "avian_influenza",
time_type = "week",
time_values = "*",
fetch_args = fetch_args_list(dry_run = TRUE)
))
expect_identical(call$params$epiweeks$from, 100001)
expect_identical(call$params$epiweeks$to, 300001)

expect_no_error(call <- pub_wiki(
articles = "avian_influenza",
time_type = "day",
time_values = "*",
fetch_args = fetch_args_list(dry_run = TRUE)
))
expect_identical(call$params$dates$from, 10000101)
expect_identical(call$params$dates$to, 30000101)
})

test_that("endpoints fail when given args via dots", {
Expand Down Expand Up @@ -413,13 +466,15 @@ test_that("endpoints fail when given args via dots", {
pvt_twitter(
auth = "yourkey",
locations = "CA",
date_range = epirange(201501, 202001)
time_type = "week",
time_range = epirange(201501, 202001)
),
regexp = dots_error
)
expect_error(
pub_wiki(
articles = "avian_influenza",
time_type = "week",
date_range = epirange(201501, 202001)
),
regexp = dots_error
Expand Down
10 changes: 8 additions & 2 deletions vignettes/signal-discovery.Rmd
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Expand Up @@ -282,7 +282,12 @@ pub_paho_dengue(regions = "ca", epiweeks = epirange(200201, 202319))
API docs: <https://cmu-delphi.github.io/delphi-epidata/api/wiki.html>

```{r, eval = FALSE}
pub_wiki(language = "en", articles = "influenza", epiweeks = epirange(202001, 202319))
pub_wiki(
language = "en",
articles = "influenza",
time_type = "week",
time_values = epirange(202001, 202319)
)
```

### Private methods
Expand Down Expand Up @@ -373,7 +378,8 @@ API docs: <https://cmu-delphi.github.io/delphi-epidata/api/twitter.html>
pvt_twitter(
auth = Sys.getenv("SECRET_API_AUTH_TWITTER"),
locations = "nat",
epiweeks = epirange(200301, 202105)
time_type = "week",
time_values = epirange(200301, 202105)
)
```

Expand Down