Merge pull request #122 from signaturescience/dev

v0.0.2 release

.gitignore

@@ -1,44 +1,32 @@
 # History files
 .Rhistory
 .Rapp.history
-
 # Session Data files
 .RData
-
 # User-specific files
 .Ruserdata
-
 # Example code in package build process
 *-Ex.R
-
 # Output files from R CMD build
 /*.tar.gz
-
 # Output files from R CMD check
 /*.Rcheck/
-
 # RStudio files
 .Rproj.user/
-
 # produced vignettes
 vignettes/*.html
 vignettes/*.pdf
-
 # OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
 .httr-oauth
-
 # knitr and R markdown default cache directories
 *_cache/
 /cache/
-
 # Temporary files created by R markdown
 *.utf8.md
 *.knit.md
-
 # R Environment Variables
 .Renviron
 .Rproj.user
-
 # OS files
 .DS_Store
 docs

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: rplanes
 Title: Plausibility Analysis of Epidemiological Signals in 'R'
-Version: 0.0.1
+Version: 0.0.2
 Authors@R: 
     c(person(given = "VP",
              family = "Nagraj",
@@ -13,32 +13,41 @@ Authors@R:
       person(given = "Amy",
              family = "Benefield",
              role = "aut"))
-Description: The 'rplanes' package provides functionality to prepare data and and analyze plausibility of both forecasted and reported epidemiological signals. The functions implement a set of plausbility algorithms that are agnostic to geographic and time resolutions and are calculated independently then presented as a combined score. 
+Description: The 'rplanes' package provides functionality to prepare data and and analyze plausibility of both forecasted and reported epidemiological signals. The functions implement a set of plausbility algorithms that are agnostic to geographic and time resolutions and are calculated independently then presented as a combined score.
 License: MIT + file LICENSE
-Encoding: UTF-8
-LazyData: true
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+URL: https://signaturescience.github.io/rplanes/
+Depends: 
+    R (>= 2.10)
 Imports: 
     dplyr,
+    dtw,
+    ecp,
+    lubridate,
     magrittr,
     purrr,
+    readr,
     rlang,
-    tidyr,
     stringr,
-    readr,
-    lubridate,
-    ecp,
     tibble,
+    tidyr,
     utils
 Suggests:
-    testthat (>= 3.0.0),
-    MMWRweek,
+    DT,
+    ggplot2,
+    markdown,
     knitr,
+    MMWRweek,
     rmarkdown,
-    ggplot2
-Depends: 
-    R (>= 2.10)
+    shiny,
+    shinyjs,
+    shinyWidgets,
+    shinycssloaders,
+    testthat (>= 3.0.0),
+    tools
+VignetteBuilder: 
+    knitr
 Config/testthat/edition: 3
-URL: https://signaturescience.github.io/rplanes/
-VignetteBuilder: knitr
+Encoding: UTF-8
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3

NAMESPACE

@@ -9,9 +9,12 @@ export(plane_diff)
 export(plane_repeat)
 export(plane_score)
 export(plane_seed)
+export(plane_shape)
 export(plane_taper)
 export(plane_trend)
+export(plane_zero)
 export(read_forecast)
+export(rplanes_explorer)
 export(to_signal)
 export(valid_dates)
 importFrom(lubridate,"%m-%")

NEWS.md

@@ -1,3 +1,45 @@
+# rplanes 0.0.2
+
+## New features
+
+### New plausibility components
+
+The `rplanes` package now features two new plausibility components: "shape" and "zero". Each of these components is delivered in a function (`plane_shape()` and `plane_zero()`, respectively) to be run by `plane_score()` alongside all other specified components. As with the previously developed components, these two operate as binary classifications of plausibility for the signal evaluated at the given location. 
+
+The "shape" component uses a series of distance calculations to characterize how "similar" the evaluated signal is to previous windows of observed data in the seed. If the distance between the evaluated shape exceeds the maximum distance observed between any of the shapes then the signal is flagged as implausible. The "shape" component can only be used with a forecast signal.
+
+The "zero" component assesses whether or not any zeros have been observed in the seed for the given location. If not, then the component will look for zeros in the evaluated signal. If it finds any, then the signal will be flagged as implausible. Note that the "zero" component will work for either a forecast or an observed signal.
+
+### `rplanes_explorer()` app
+
+This release introduces a new feature to deliver a point-and-click interface for PLANES scoring directly in the `rplanes` package. The interface is written as a Shiny app, which is maintained as part of the package and can be launched using the `rplanes_explorer()` function. When the user installs `rplanes`, the app (which is stored in the `inst/` directory) will be visible on the host machine. `rplanes_explorer()` wraps `shiny::runApp()` and points the "appDir" argument to the directory that holds the `rplanes` explorer app. Users can take advantage of any of the arguments inherited by `shiny::runApp()` (e.g., `launch.browser=TRUE` to open the app directly in a browser window).
+
+### Improved documentation
+
+We have added improvements to overall documentation for the package. In particular, this release introduces two new vignettes: one to describe how individual components operate and another to briefly introduce the explore app. In addition to the new vignettes, we have also implemented a handful of grammatical and wording changes to make existing documentation more clear and concise.
+
+### "Hubverse" forecast format
+
+With updates to the quantile format used by some forecast hubs, we have introduced an option for the `read_forecast()` helper to optionally read different formats. The function now supports the "Hubverse" format used by the 2023-24 FluSight initiative (https://hubdocs.readthedocs.io/en/latest/user-guide/model-output.html).
+
+### Optional weighting scheme
+
+In this release we introduce a new feature for users to optionally weight the importance of individual components in the overall plausibility score. The weights must be specified as a named vector and passed to the `plane_score()` function. This argument is optional and by default the function will use equal weights for each component.
+
+## Bug fixes
+
+### Default components with `plane_score()`
+
+Prior to this release, if an observed signal was evaluated then `plane_score()` would strictly require that the user manually specify the compatible components (as of v0.0.1 this was only "diff" and "repeat"). In this version, `plane_score()` can now detect the type of signal and if "all" components are selected the function will identify only those that are compatible. For example, with the addition of the new components (see above), specifying `plane_score(..., components = "all")` for an observed signal will automatically use the "diff", "repeat", and "zero" components.
+
+### Hyphens in location names
+
+The `plane_score()` wrapper uses `-` (hyphen) to combine location and component in the returned list object. Before this release, if locations had a hyphen in their names (e.g., "United-States") then one of the internal data manipulation steps would not function as expected. We have updated the internals of `plane_score()` to now allow for location names that may contain hyphens.
+
+### Data ordering in seed
+
+Previously, the `plane_seed()` function used dates as arranged in the incoming observed signal data. As such, the seeding could have unexpected behavior. For example, if dates were ordered descending then the "last value" would actually be the *first* value chronologically. As of this release, the `plane_seed()` function internally now arranges data in case input data is not ordered ascending by date.
+
 # rplanes 0.0.1
 
 Alpha release for the `rplanes` package!