fix: updates from review

Author: dshemetov

DEVELOPMENT.md

@@ -21,21 +21,25 @@ devtools::check(vignettes = FALSE) # check package without vignettes
 
 ## Developing the documentation site
 
-Our CI builds two version of the documentation:
+Our CI builds two versions of the documentation:
 
 - https://cmu-delphi.github.io/epipredict/ from the `main` branch and
 - https://cmu-delphi.github.io/epipredict/dev from the `dev` branch.
 
-We include the script `pkgdown-watch.R` that will automatically rebuild the
-documentation locally and preview it. It can be used with:
+Commands for developing the documentation site:
 
 ```sh
-# Make sure you have servr installed
-R -e 'renv::install("servr")'
-# Will start a local server
-Rscript pkgdown-watch.R
-# You may need to first build the site with
+# Basic build and preview
+R -e 'pkgdown::clean_site()'
+R -e 'devtools::document()'
+R -e 'pkgdown::build_site()'
+
+# A smart rebuild workflow for non-RStudio users.
+# You may need to first build the site.
 R -e 'pkgdown::build_site(".", examples = FALSE, devel = TRUE, preview = FALSE)'
+R -e 'renv::install("servr")'
+# Will start a local docs server and monitor for changes.
+Rscript inst/pkgdown-watch.R
 ```
 
 ## Versioning

pkgdown-watch.r renamed to inst/pkgdown-watch.r

@@ -6,6 +6,9 @@
 #
 # Note that the `pattern` regex is case sensitive, so make sure your Rmd files
 # end in `.Rmd` and not `.rmd`.
+#
+# Also I had issues with `pkgdown::build_reference()` not working, so I just run
+# it manually when I need to.
 
 rlang::check_installed(c("pkgdown", "servr", "devtools", "here", "cli", "fs"))
 
@@ -32,7 +35,7 @@ servr::httw(
 
     refs <- grep("man.+R(m?d)?$", files, value = TRUE)
     if (length(refs)) {
-      # TODO: This does not work for me, so I just run it manually.
+      # Doesn't work for me, so I run it manually.
       # pkgdown::build_reference(pkg, preview = FALSE, examples = FALSE, lazy = FALSE)
     }
 

vignettes/arx-classifier.Rmd

@@ -7,15 +7,8 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
-```{r setup, include = FALSE}
-knitr::opts_chunk$set(
-  echo = TRUE,
-  collapse = FALSE,
-  comment = "#>",
-  warning = FALSE,
-  message = FALSE,
-  out.width = "100%"
-)
+```{r, include = FALSE}
+source("_common.R")
 ```
 
 ## Load required packages

vignettes/backtesting.Rmd

@@ -7,8 +7,8 @@ vignette: >
   %\VignetteEncoding{UTF-8}
 ---
 
-```{r setup, include = FALSE}
-source(here::here("vignettes", "_common.R"))
+```{r, include = FALSE}
+source("_common.R")
 ```
 
 ```{r pkgs, include=FALSE, echo=TRUE}
@@ -132,16 +132,20 @@ Let's use the `epix_as_of()` method to generate a snapshot of the archive at the
 last date, and then run the forecaster.
 
 ```{r}
+# Let's forecast 14 days prior to the last date in the archive, to compare.
+forecast_date <- archive_cases_dv_subset$versions_end - 14
 # The .versions argument selects only the last version in the archive and
 # produces a forecast only on that date.
 forecasts <- archive_cases_dv_subset %>%
   epix_slide(
     ~ arx_forecaster(
       .x,
       outcome = "percent_cli",
-      predictors = c("case_rate_7d_av", "percent_cli")
-    )$predictions,
-    .versions = archive_cases_dv_subset$versions_end
+      predictors = c("case_rate_7d_av", "percent_cli"),
+      args_list = arx_args_list()
+    )$predictions %>%
+      pivot_quantiles_wider(.pred_distn),
+    .versions = forecast_date
   )
 # Join the forecasts with with the latest data at the time of the forecast to
 # compare. Since `percent_cli` data has a few days of lag, we use `tidyr::fill` to
@@ -152,9 +156,9 @@ forecasts %>%
       epix_as_of(archive_cases_dv_subset$versions_end) %>%
       group_by(geo_value) %>%
       tidyr::fill(percent_cli),
-    by = c("geo_value", "forecast_date" = "time_value")
+    by = c("geo_value", "target_date" = "time_value")
   ) %>%
-  select(geo_value, forecast_date, .pred, .pred_distn, percent_cli)
+  select(geo_value, forecast_date, .pred, `0.05`, `0.95`, percent_cli)
 ```
 
 The resulting epi_df now contains two new columns: `.pred` and `.pred_distn`,

vignettes/epipredict.Rmd

@@ -8,12 +8,7 @@ vignette: >
 ---
 
 ```{r, include = FALSE}
-knitr::opts_chunk$set(
-  echo = TRUE,
-  collapse = TRUE,
-  comment = "#>",
-  out.width = "100%"
-)
+source("_common.R")
 ```
 
 ```{r setup, message=FALSE}