classifier

.devcontainer/Dockerfile

@@ -84,7 +84,7 @@ RUN echo "C.UTF-8 en_US.UTF-8 UTF-8" >> /etc/locale.gen \
   && locale-gen en_US.utf8 \
   && /usr/sbin/update-locale LANG=en_US.UTF-8
 
-ENV R_BASE_VERSION 4.2.1
+ENV R_BASE_VERSION 4.3.0
 ENV RENV_PATHS_ROOT "${HOME_WORK}/.cache/R/renv"
 ENV RENV_PATHS_LIBRARY_ROOT "${HOME_WORK}/.cache/R/renv/library"
 ENV TZ UTC

README.Rmd

@@ -73,9 +73,9 @@ alarms <- tribble(
   "Ventricular Flutter/Fibrillation", "Fibrillatory, flutter, or oscillatory waveform for at least 4 seconds"
 )
 
-kbl(alarms, booktabs = TRUE, caption = "Definition of the 5 alarm types used in CinC/Physionet Challenge 2015 challenge.", align = "ll") %>%
-  kable_styling(full_width = TRUE) %>%
-  column_spec(1, width = "5cm") %>%
+kbl(alarms, booktabs = TRUE, caption = "Definition of the 5 alarm types used in CinC/Physionet Challenge 2015 challenge.", align = "ll") |>
+  kable_styling(full_width = TRUE) |>
+  column_spec(1, width = "5cm") |>
   row_spec(0, bold = TRUE)
 ```
 

_contrast_profile_ex/.gitignore

@@ -0,0 +1,5 @@
+*
+!.gitignore
+!meta
+meta/*
+!meta/meta

_targets.yaml

@@ -12,6 +12,11 @@ classifier:
   script: scripts/_classifier.R
 
 contrast_profile:
+  inherits: main
+  store: _contrast_profile_ex
+  script: scripts/_contrast_profile_ex.R
+
+contrast_profile_not:
   inherits: main
   store: _contrast_profile
   script: scripts/_contrast_profile.R

analysis/index.Rmd

@@ -58,7 +58,7 @@ Last Targets Run network:
 ```{r network, echo=FALSE, fig.width=10}
 library(magrittr)
 network <- readRDS(here("output/network.rds"))
-network <- network %>%
+network <- network |>
   visNetwork::visPhysics(hierarchicalRepulsion = list(
     springLength = 1,
     avoidOverlap = 0.5,

analysis/regime_optimize.Rmd

@@ -71,12 +71,13 @@ my_graphics <- function(image_name, base_path = here::here("docs", "figure")) {
 }
 
 my_plot_html <- function(html, options) {
-  structure(paste0(
-    "<div class=\"figure\" style=\"text-align: ",
-    options$fig.align, "\">", html, "<p class=\"caption\">(#",
-    options$fig.lp, options$label, ")", options$fig.cap, "</p></div>"
-  ),
-  class = "knit_asis"
+  structure(
+    paste0(
+      "<div class=\"figure\" style=\"text-align: ",
+      options$fig.align, "\">", html, "<p class=\"caption\">(#",
+      options$fig.lp, options$label, ")", options$fig.cap, "</p></div>"
+    ),
+    class = "knit_asis"
   )
 }
 
@@ -1229,8 +1230,6 @@ my_plot_html(shap_html_test2, knitr::opts_current$get())
 
 
 ```{r tests, eval=FALSE, echo=FALSE, out.width="80%", fig.cap="FLOSS pipeline."}
-
-
 # all_scores2 <- all_scores %>% dplyr::mutate(test = score_regimes_precision(truth, pred, 0,
 #   window = 250,
 #   delta_prec = "flat",

analysis/report.Rmd

@@ -217,8 +217,8 @@ kbl(alarms,
   align = "ll",
   position = "ht",
   linesep = "\\addlinespace"
-) %>%
-  row_spec(0, bold = TRUE) %>%
+) |>
+  row_spec(0, bold = TRUE) |>
   kable_styling(full_width = TRUE)
 ```
 
@@ -231,7 +231,6 @@ For comparison, on Table \@ref(tab:challenge) we collected the score of the five
 of the challenge [@plesinger2015; @kalidas2015; @couto2015; @fallet2015; @hoogantink2015].
 
 ```{r challenge, echo=FALSE}
-
 challenge <- tribble(
   ~Score, ~Authors,
   "81.39", "Filip Plesinger, Petr Klimes, Josef Halamek, Pavel Jurak",
@@ -246,10 +245,10 @@ kbl(challenge,
   caption = "Challenge Results on real-time data. The scores were multiplied by 100.",
   align = "cl",
   position = "ht"
-) %>%
-  row_spec(0, bold = TRUE) %>%
-  # column_spec(1, width = "5em") %>%
-  # column_spec(2, width = "30em") %>%
+) |>
+  row_spec(0, bold = TRUE) |>
+  # column_spec(1, width = "5em") |>
+  # column_spec(2, width = "30em") |>
   kable_styling(full_width = TRUE)
 ```
 
@@ -317,8 +316,8 @@ kbl(criteria,
   align = "ll",
   position = "ht",
   linesep = "\\addlinespace"
-) %>%
-  row_spec(0, bold = TRUE) %>%
+) |>
+  row_spec(0, bold = TRUE) |>
   kable_styling(full_width = TRUE)
 ```
 
@@ -1034,7 +1033,6 @@ floss_data_1250 <- get_dist(0, 1250)
 ```
 
 ```{r distributions, echo=FALSE, fig.cap="1D-IAC distributions for earlier temporal constraint (on Matrix Profile).", message=FALSE, warning=FALSE}
-
 floss_dist <- ggplot(data_5000, aes(index, counts)) +
   geom_line(size = 0.1) +
   ggtitle("a) No constraint") +