Merge pull request #168 from cmu-delphi/ds/polish

docs+feat+lint: final polish

Author: dshemetov

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.0
+current_version = 1.0.0
 commit = False
 tag = False
 

.lintr

@@ -1,4 +1,5 @@
 linters: linters_with_defaults(
   line_length_linter(120),
-  cyclocomp_linter = NULL
+  cyclocomp_linter = NULL,
+  object_length_linter(length = 40L)
   )

DESCRIPTION

@@ -1,13 +1,13 @@
 Package: epidatr
 Type: Package
 Title: Client for Delphi's Epidata API
-Version: 0.9.0
+Version: 1.0.0
 Authors@R: 
   c(
-    person("Logan", "Brooks", email = "[email protected]", role = c("aut", "cre")),
+    person("Logan", "Brooks", email = "[email protected]", role = c("aut")),
     person("Dmitry", "Shemetov", email = "[email protected]", role = c("aut")),
     person("Samuel", "Gratzl", email = "[email protected]", role = c("aut")),
-    person("David", "Weber", email = "[email protected]", role = c("ctb")),
+    person("David", "Weber", email = "[email protected]", role = c("ctb", "cre")),
     person("Alex", "Reinhart", role = c("ctb")),
     person("Daniel", "McDonald", role = c("ctb")),
     person("Kean Ming", "Tan", role = c("ctb")),
@@ -35,7 +35,6 @@ Imports:
     purrr,
     openssl,
     readr,
-    rlang,
     tibble,
     xml2
 RoxygenNote: 7.2.3
@@ -44,6 +43,7 @@ Suggests:
     ggplot2,
     knitr,
     rmarkdown,
+    rlang,
     testthat (>= 3.1.5),
     withr
 VignetteBuilder: knitr

NAMESPACE

@@ -3,38 +3,40 @@
 S3method(as_tibble,covidcast_data_signal_list)
 S3method(as_tibble,covidcast_data_source_list)
 S3method(print,covidcast_data_signal)
+S3method(print,covidcast_data_signal_list)
 S3method(print,covidcast_data_source)
 S3method(print,covidcast_epidata)
 S3method(print,epidata_call)
 export("%>%")
 export(avail_endpoints)
 export(cache_info)
 export(clear_cache)
-export(covid_hosp_facility)
-export(covid_hosp_facility_lookup)
-export(covid_hosp_state_timeseries)
-export(covidcast)
 export(covidcast_epidata)
-export(covidcast_meta)
-export(delphi)
-export(dengue_nowcast)
 export(disable_cache)
-export(ecdc_ili)
 export(epirange)
 export(fetch)
 export(fetch_args_list)
-export(flusurv)
-export(fluview)
-export(fluview_clinical)
-export(fluview_meta)
 export(get_auth_key)
-export(gft)
-export(kcdc_ili)
-export(meta)
-export(nidss_dengue)
-export(nidss_flu)
-export(nowcast)
-export(paho_dengue)
+export(pub_covid_hosp_facility)
+export(pub_covid_hosp_facility_lookup)
+export(pub_covid_hosp_state_timeseries)
+export(pub_covidcast)
+export(pub_covidcast_meta)
+export(pub_delphi)
+export(pub_dengue_nowcast)
+export(pub_ecdc_ili)
+export(pub_flusurv)
+export(pub_fluview)
+export(pub_fluview_clinical)
+export(pub_fluview_meta)
+export(pub_gft)
+export(pub_kcdc_ili)
+export(pub_meta)
+export(pub_nidss_dengue)
+export(pub_nidss_flu)
+export(pub_nowcast)
+export(pub_paho_dengue)
+export(pub_wiki)
 export(pvt_cdc)
 export(pvt_dengue_sensors)
 export(pvt_ght)
@@ -44,10 +46,8 @@ export(pvt_quidel)
 export(pvt_sensors)
 export(pvt_twitter)
 export(set_cache)
-export(wiki)
 import(cachem)
 import(glue)
-import(openssl)
 importFrom(MMWRweek,MMWRweek2Date)
 importFrom(checkmate,assert)
 importFrom(checkmate,assert_character)
@@ -73,6 +73,7 @@ importFrom(httr,modify_url)
 importFrom(httr,stop_for_status)
 importFrom(jsonlite,fromJSON)
 importFrom(magrittr,"%>%")
+importFrom(openssl,md5)
 importFrom(purrr,map_chr)
 importFrom(purrr,map_lgl)
 importFrom(readr,read_csv)

NEWS.md

@@ -1,3 +1,11 @@
+# epidatr 1.0.0
+
+- Add `set_cache` and other caching functions.
+- Prefix all non-private endpoints with `pub_`.
+- Update printing of `avail_endpoints` to be more readable.
+- Update printing of `covidcast_epidata()` to be more readable.
+- Update landing docs to be more friendly, add plots.
+
 # epidatr 0.9.0
 
 - Major interface change: all endpoints now fetch by default.
@@ -29,13 +37,13 @@
 # epidatr 0.6.0
 
 - The `fetch_{tbl,classic,df,json,csv}` functions have been replaced by the
-`fetch()` function, which almost always returns a tibble, except when used with
-a limited number of older endpoints (such as `delphi()` and `meta()`), where it
-will output a nested list structure.
+  `fetch()` function, which almost always returns a tibble, except when used with
+  a limited number of older endpoints (such as `delphi()` and `meta()`), where it
+  will output a nested list structure.
 
 # epidatr 0.5.0
 
 - The package that this installs is being renamed from `delphi.epidata` to
-`epidatr`. To migrate, run the installation command above, followed by
-`remove.packages("delphi.epidata")`, and adjust all references to the package
-name accordingly.
+  `epidatr`. To migrate, run the installation command above, followed by
+  `remove.packages("delphi.epidata")`, and adjust all references to the package
+  name accordingly.

R/avail_endpoints.R

@@ -17,5 +17,5 @@ avail_endpoints <- function() {
     Endpoint = paste0(h$Name, "()"),
     Description = h$Title
   )
-  tib
+  tib %>% print(n = 50)
 }

R/cache.R

@@ -3,7 +3,8 @@
 cache_environ <- new.env(parent = emptyenv())
 cache_environ$use_cache <- NULL
 cache_environ$epidatr_cache <- NULL
-#' create or renew a cache for this session
+
+#' Create or renew a cache for this session
 #' @aliases set_cache
 #' @description
 #' By default, epidatr re-requests data from the API on every call of `fetch`.
@@ -72,8 +73,7 @@ cache_environ$epidatr_cache <- NULL
 #'   dir = "some/subdir",
 #'   days = 14,
 #'   max_size = 512,
-#'   logfile = "some/subdir/logs.txt",
-#'   prune_rate = 20L
+#'   logfile = "some/subdir/logs.txt"
 #' )
 #' }
 #'
@@ -90,15 +90,10 @@ cache_environ$epidatr_cache <- NULL
 #' @param logfile where cachem's log of transactions is stored, relative to the
 #'   cache directory. By default, it is `"logfile.txt"`. The environmental
 #'   variable is `EPIDATR_CACHE_LOGFILE`.
-#' @param prune_rate how many calls to go between checking if any cache elements
-#'   are too old or if the cache overall is too large. Defaults to `2000L`.
-#'   Since cachem fixes the max time between prune checks to 5 seconds, there's
-#'   little reason to actually change this parameter. Doesn't have a
-#'   corresponding environmental variable.
 #' @param confirm whether to confirm directory creation. default is `TRUE`;
 #'   should only be set in non-interactive scripts
-#' @seealso [clear_cache] to delete the old cache while making a new one,
-#'   [disable_cache] to disable without deleting, and [cache_info]
+#' @seealso [`clear_cache`] to delete the old cache while making a new one,
+#'   [`disable_cache`] to disable without deleting, and [`cache_info`]
 #' @export
 #' @import cachem
 #' @import glue
@@ -107,7 +102,6 @@ set_cache <- function(cache_dir = NULL,
                       days = NULL,
                       max_size = NULL,
                       logfile = NULL,
-                      prune_rate = 2000L,
                       confirm = TRUE) {
   if (is.null(cache_dir) && sessionInfo()$R.version$major >= 4) {
     cache_dir <- Sys.getenv("EPIDATR_CACHE_DIR", unset = tools::R_user_dir("epidatr"))
@@ -129,7 +123,7 @@ set_cache <- function(cache_dir = NULL,
     logfile <- Sys.getenv("EPIDATR_CACHE_LOGFILE", unset = "logfile.txt")
   }
   stopifnot(is.character(logfile))
-  stopifnot(is.numeric(days), is.numeric(max_size), is.integer(prune_rate))
+  stopifnot(is.numeric(days), is.numeric(max_size))
   #
   # make sure that that directory exists and drag the user into that process
   cache_exists <- file.exists(cache_dir)
@@ -171,15 +165,14 @@ set_cache <- function(cache_dir = NULL,
       dir = cache_dir,
       max_size = as.integer(max_size * 1024^2),
       max_age = days * 24 * 60 * 60,
-      logfile = file.path(cache_dir, logfile),
-      prune_rate = prune_rate
+      logfile = file.path(cache_dir, logfile)
     )
   }
 }
 
-#' manually reset the cache, deleting all currently saved data and starting afresh
+#' Manually reset the cache, deleting all currently saved data and starting afresh
 #' @description
-#' deletes the current cache and resets a new cache. Deletes local data! If you
+#' Deletes the current cache and resets a new cache. Deletes local data! If you
 #'   are using a session unique cache, you will have to pass the arguments you
 #'   used for `set_cache` earlier, otherwise the system-wide `.Renviron`-based
 #'   defaults will be used.
@@ -190,15 +183,13 @@ set_cache <- function(cache_dir = NULL,
 #'   days = 14,
 #'   max_size = 512,
 #'   logfile = "some/subdir/logs.txt",
-#'   prune_rate = 20L
 #' )
 #' }
 #' @param disable instead of setting a new cache, disable caching entirely;
-#' defaults to `FALSE`
-#' @param ... see the `set_cache` arguments below
-#' @inheritParams set_cache
-#' @seealso [set_cache] to start a new cache (and general caching info),
-#'   [disable_cache] to only disable without deleting, and [cache_info]
+#'   defaults to `FALSE`
+#' @param ... arguments passed to `set_cache`
+#' @seealso [`set_cache`] to start a new cache (and general caching info),
+#'   [`disable_cache`] to only disable without deleting, and [`cache_info`]
 #' @export
 #' @import cachem
 clear_cache <- function(disable = FALSE, ...) {
@@ -210,26 +201,26 @@ clear_cache <- function(disable = FALSE, ...) {
   }
 }
 
-#' turn off the caching for this session
+#' Turn off the caching for this session
 #' @description
 #' Disable caching until you call `set_cache` or restart R. The files defining
 #'   the cache are untouched. If you are looking to disable the caching more
 #'   permanently, set `EPIDATR_USE_CACHE=FALSE` as environmental variable in
 #'   your `.Renviron`.
 #' @export
-#' @seealso [set_cache] to start a new cache (and general caching info),
-#'   [clear_cache] to delete the cache and set a new one, and [cache_info]
+#' @seealso [`set_cache`] to start a new cache (and general caching info),
+#'   [`clear_cache`] to delete the cache and set a new one, and [`cache_info`]
 #' @import cachem
 disable_cache <- function() {
   cache_environ$epidatr_cache <- NULL
 }
 
-#' describe current cache
+#' Describe current cache
 #' @description
 #' Print out the information about the cache (as would be returned by cachem's
 #' `info()` method)
-#' @seealso [set_cache] to start a new cache (and general caching info),
-#'   [clear_cache] to delete the cache and set a new one, and [disable_cache] to
+#' @seealso [`set_cache`] to start a new cache (and general caching info),
+#'   [`clear_cache`] to delete the cache and set a new one, and [`disable_cache`] to
 #'   disable without deleting
 #' @export
 cache_info <- function() {
@@ -240,16 +231,16 @@ cache_info <- function() {
   }
 }
 
-#' dispatch caching
+#' Dispatch caching
 #'
 #' @description
 #' the guts of caching, its interposed between fetch and the specific fetch
 #' methods. Internal method only.
 #'
 #' @param call the `epidata_call` object
-#' @param fetch_args the args list for fetch as generated by [fetch_args_list()]
+#' @param fetch_args the args list for fetch as generated by [`fetch_args_list()`]
 #' @keywords internal
-#' @import cachem openssl
+#' @importFrom openssl md5
 cache_epidata_call <- function(epidata_call, fetch_args = fetch_args_list()) {
   is_cachable <- check_is_cachable(epidata_call, fetch_args)
   if (is_cachable) {

R/constants.R

@@ -1,3 +1,3 @@
-version <- "0.9.0"
+version <- "1.0.0"
 http_headers <- httr::add_headers("User-Agent" = paste0("epidatr/", version), "Accept-Encoding" = "gzip")
 global_base_url <- "https://api.delphi.cmu.edu/epidata/"

R/covidcast.R

@@ -24,7 +24,7 @@ parse_signal <- function(signal, base_url) {
                           fetch_args = fetch_args_list()) {
     stopifnot(is.character(geo_type) & length(geo_type) == 1)
 
-    covidcast(
+    pub_covidcast(
       source = signal$source,
       signals = signal$signal,
       geo_type = geo_type,
@@ -77,34 +77,15 @@ as_tibble.covidcast_data_signal_list <- function(x, ...) {
   tib$format <- unname(map_chr(x, "format"))
   tib$category <- unname(map_chr(x, "category"))
   tib$high_values_are <- unname(map_chr(x, "high_values_are"))
-  if ("is_smoothed" %in% names(x)) {
-    tib$is_smoothed <- unname(map_lgl(x, "is_smoothed"))
-  } else {
-    tib$is_smoothed <- NA
-  }
-  if ("is_weighted" %in% names(x)) {
-    tib$is_weighted <- unname(map_lgl(x, "is_weighted"))
-  } else {
-    tib$is_weighted <- NA
-  }
-  if ("is_cumulative" %in% names(x)) {
-    tib$is_cumulative <- unname(map_lgl(x, "is_cumulative"))
-  } else {
-    tib$is_cumulative <- NA
-  }
-  if ("has_stderr" %in% names(x)) {
-    tib$has_stderr <- unname(map_lgl(x, "has_stderr"))
-  } else {
-    tib$has_stderr <- NA
-  }
-  if ("has_sample_size" %in% names(x)) {
-    tib$has_sample_size <- unname(map_lgl(x, "has_sample_size"))
-  } else {
-    tib$has_sample_size <- NA
-  }
   as_tibble(tib)
 }
 
+#' @export
+print.covidcast_data_signal_list <- function(x, ...) {
+  tib <- as_tibble(x)
+  print(tib[, c("source", "signal", "short_description")], ...)
+}
+
 #' @export
 print.covidcast_data_source <- function(x, ...) {
   print(x$name, ...)