Merge pull request #595 from cmu-delphi/no-genlasso

No genlasso

Author: brookslogan

DESCRIPTION

@@ -1,7 +1,7 @@
-Package: epiprocess
 Type: Package
+Package: epiprocess
 Title: Tools for basic signal processing in epidemiology
-Version: 0.10.3
+Version: 0.10.4
 Authors@R: c(
     person("Jacob", "Bien", role = "ctb"),
     person("Logan", "Brooks", , "[email protected]", role = c("aut", "cre")),
@@ -23,17 +23,17 @@ Authors@R: c(
     person("Posit", role = "cph",
            comment = "Copyright holder of included rlang fragments"),
     person("Johns Hopkins University Center for Systems Science and Engineering", role = "dtc",
-            comment = "Owner of COVID-19 cases and deaths data from the COVID-19 Data Repository"),
+           comment = "Owner of COVID-19 cases and deaths data from the COVID-19 Data Repository"),
     person("Johns Hopkins University", role = "cph",
-            comment = "Copyright holder of COVID-19 cases and deaths data from the COVID-19 Data Repository"),
+           comment = "Copyright holder of COVID-19 cases and deaths data from the COVID-19 Data Repository"),
     person("Carnegie Mellon University Delphi Group", role = "dtc",
-            comment = "Owner of claims-based CLI data from the Delphi Epidata API")
+           comment = "Owner of claims-based CLI data from the Delphi Epidata API")
   )
-Description: This package introduces common data structures for working with
-    epidemiological data reported by location and time and offers associated
-    utilities to perform basic signal processing tasks. The package is designed
-    to be used in conjunction with `epipredict` for building and evaluating
-    epidemiological models.
+Description: This package introduces common data structures for working
+    with epidemiological data reported by location and time and offers
+    associated utilities to perform basic signal processing tasks. The
+    package is designed to be used in conjunction with `epipredict` for
+    building and evaluating epidemiological models.
 License: MIT + file LICENSE
 URL: https://cmu-delphi.github.io/epiprocess/
 Depends:
@@ -44,7 +44,6 @@ Imports:
     cli,
     data.table,
     dplyr (>= 1.1.0),
-    genlasso,
     ggplot2,
     glue,
     lifecycle (>= 1.0.1),
@@ -63,6 +62,7 @@ Imports:
     waldo
 Suggests:
     devtools,
+    distributional,
     epidatr,
     epipredict,
     here,
@@ -71,6 +71,7 @@ Suggests:
     readr,
     rmarkdown,
     testthat (>= 3.1.5),
+    trendfilter,
     withr
 VignetteBuilder:
     knitr
@@ -79,7 +80,7 @@ Remotes:
     cmu-delphi/epidatasets,
     cmu-delphi/epidatr,
     cmu-delphi/epipredict,
-    glmgen/genlasso,
+    glmgen/trendfilter,
     reconverse/outbreaks
 Config/Needs/website: cmu-delphi/delphidocs
 Config/testthat/edition: 3

NAMESPACE

@@ -46,6 +46,7 @@ S3method(mean,epi_df)
 S3method(print,epi_archive)
 S3method(print,epi_df)
 S3method(print,grouped_epi_archive)
+S3method(print,growth_rate_params)
 S3method(summary,epi_df)
 S3method(ungroup,epi_df)
 S3method(ungroup,grouped_epi_archive)
@@ -80,6 +81,7 @@ export(group_by)
 export(group_epi_df)
 export(group_modify)
 export(growth_rate)
+export(growth_rate_params)
 export(guess_period)
 export(is_epi_df)
 export(is_grouped_epi_archive)
@@ -109,6 +111,7 @@ importFrom(checkmate,assert_function)
 importFrom(checkmate,assert_int)
 importFrom(checkmate,assert_list)
 importFrom(checkmate,assert_logical)
+importFrom(checkmate,assert_number)
 importFrom(checkmate,assert_numeric)
 importFrom(checkmate,assert_scalar)
 importFrom(checkmate,assert_string)

NEWS.md

@@ -5,6 +5,16 @@ Pre-1.0.0 numbering scheme: 0.x will indicate releases, while 0.x.y will indicat
 # epiprocess 0.11
 
 ## Breaking changes
+
+- `growth_rate()` argument order and names have changed. You will need to
+  rewrite `growth_rate(x, y)` as `growth_rate(y, x)`. The interface for passing
+  arguments to the `"smooth_spline"` and `"trend_filter"` methods has also
+  changed. Finally, `growth_rate()` with `method = "trendfilter"` now uses the
+  `{trendfilter}` package rather than `{genlasso}`; results for this method will
+  be different than before. In order to make `{epiprocess}` installation easier
+  for users without a compiler, we have placed `{trendfilter}` in Suggests:; if
+  you want to use `method = "trendfilter"` you will need to manually install
+  this dependency (e.g., with `remotes::install_github("glmgen/trendfilter")`).
 - In `revision_summary()`:
   - Output now uses the name `lag_near_latest` instead of `time_near_latest`. To
     migrate, update references to `time_near_latest` to `lag_near_latest`.