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commit 5c1d4f9 Author: Dan Dediu <ddediu@gmail.com> Date: Fri Jun 24 17:39:41 2022 +0200 As submitted to CRAN commit fdeb7d8 Author: Dan Dediu <ddediu@gmail.com> Date: Sat Jun 18 20:33:35 2022 +0200 Fix CRAN check errors and warnings commit a6d8423 Author: Dan Dediu <ddediu@gmail.com> Date: Fri Jun 17 16:43:49 2022 +0200 Solve GitHub #190 by allowing the recovery of the mapping between events and episodes/sliding windows, and even plotting it commit 5a74ae9 Author: Dan Dediu <ddediu@gmail.com> Date: Fri Jun 17 12:42:44 2022 +0200 Implement return.mapping.events.sliding.window for CMA_sliding_window commit 7768564 Author: Dan Dediu <ddediu@gmail.com> Date: Fri Jun 17 11:33:07 2022 +0200 Fix GitHub #192: now align.first.event.at.zero is FALSE by default commit f0f3b5d Author: Dan Dediu <ddediu@gmail.com> Date: Thu Jun 16 23:39:57 2022 +0200 The simple CMAs return .EVENT.USED.IN.CMA in event.info commit 9b5975a Author: Dan Dediu <ddediu@gmail.com> Date: Wed Jun 15 16:28:13 2022 +0200 Fix GitHub #191 and bump version to 0.8 commit 3cac87b Author: Dan Dediu <ddediu@gmail.com> Date: Mon Jun 6 16:46:45 2022 +0200 Fix GitHub #184: Python 3 wrapper does not show anymore warnings about overriding some arguments commit 85475b1 Author: Dan Dediu <ddediu@gmail.com> Date: Mon Jun 6 16:15:44 2022 +0200 Python3 wrapper: handle plotting complex CMAs with event intervals commit 2880088 Author: Dan Dediu <ddediu@gmail.com> Date: Mon Jun 6 16:14:31 2022 +0200 Fix bug when plotting complex CMAs showing event intervals with custom column names commit 37c25c7 Author: Dan Dediu <ddediu@gmail.com> Date: Tue May 31 18:13:47 2022 +0200 Update the NEWS.md to reflect the Python 3 changes commit 58d2b7d Author: Dan Dediu <ddediu@gmail.com> Date: Tue May 31 18:11:18 2022 +0200 Rebuild the Python3 vignette (and remove the junyper checkpoint) commit 6c4a539 Author: Dan Dediu <ddediu@gmail.com> Date: Tue May 31 18:07:55 2022 +0200 AdhereR works from Python 3 Jupyter Notebooks (and with rpy2)! I also update the vignette and added two notebook examples commit bc77b21 Author: Dan Dediu <ddediu@gmail.com> Date: Tue May 31 15:06:44 2022 +0200 Fix GitHub #184 and a bug with Python3 and plotting complex CMAs commit 675d57a Author: Dan Dediu <ddediu@gmail.com> Date: Tue May 31 14:05:24 2022 +0200 Pyhton3 wrapper: handle medication groups (defined by a column in the data) commit 17d6b22 Author: Dan Dediu <ddediu@gmail.com> Date: Tue May 31 11:29:49 2022 +0200 Python 3 wrapper: finished updating plot() + small bug fixes commit 8d5d13e Author: Dan Dediu <ddediu@gmail.com> Date: Mon May 30 16:51:35 2022 +0200 Python3 wrapper: add plot.partial.CMAs* to plot() commit bac9449 Author: Dan Dediu <ddediu@gmail.com> Date: Mon May 30 13:43:37 2022 +0200 Python3 wrapper: add CMA.cex to plot() commit 9ed89d2 Author: Dan Dediu <ddediu@gmail.com> Date: Mon May 30 11:51:04 2022 +0200 Python3 wrapper: add dose* to plot() commit e641baa Author: Dan Dediu <ddediu@gmail.com> Date: Mon May 30 10:52:01 2022 +0200 Python3 wrapper: implemented medication.groups in plot() commit a135ce3 Author: Dan Dediu <ddediu@gmail.com> Date: Fri May 27 19:31:06 2022 +0200 Python3 wrapper: xlab, ylab & title added to plot() commit 69e6575 Author: Dan Dediu <ddediu@gmail.com> Date: Fri May 27 12:54:08 2022 +0200 Python3 wrapper: make col.cats in plot() work commit be1a454 Author: Dan Dediu <ddediu@gmail.com> Date: Fri May 27 11:32:19 2022 +0200 Fix bug: cex.title in plot() was not implemented commit e1b5b65 Author: Dan Dediu <ddediu@gmail.com> Date: Fri May 27 11:08:08 2022 +0200 Starting to update the Python3 wrapper to reflect the new parameters commit c2ddb1a Author: Dan Dediu <ddediu@gmail.com> Date: Wed May 25 17:05:02 2022 +0200 Fix GitHub #182: the vignette shows how to change an AdhereR plot commit b19e6bd Author: Dan Dediu <ddediu@gmail.com> Date: Mon May 23 22:10:25 2022 +0200 Fixes issue #181 (plotting with aligned patients) and shows how to use AdhereR with pipe commit 05d02b4 Author: Dan Dediu <ddediu@gmail.com> Date: Thu May 19 19:21:46 2022 +0200 Latest source packages AdhereR 0.7.1 and bump to AdhereRViz 0.2.1 commit 79a966f Author: Dan Dediu <ddediu@gmail.com> Date: Thu May 19 19:19:16 2022 +0200 Work-around for GitHub #156 by allowing the plotting of the legend only commit 9e5a311 Author: Dan Dediu <ddediu@gmail.com> Date: Thu May 19 12:35:57 2022 +0200 Fix #169 by forcing arguments.that.should.not.be.defined=NULL (smartly) in sliding windows and per episodes commit 42a3a82 Author: Dan Dediu <ddediu@gmail.com> Date: Thu May 19 11:59:10 2022 +0200 Shiny: make sure the event interval defaults are correctly reset on changing the CMA commit cf985f3 Author: Dan Dediu <ddediu@gmail.com> Date: Thu May 19 11:51:36 2022 +0200 Fix #179 (CMA class not correctly initialised/updated in Shiny) commit 9348b76 Author: Dan Dediu <ddediu@gmail.com> Date: Wed May 18 19:19:00 2022 +0200 Shiny UI allows plotting event intervals for sliding windows and per per episodes Controlled from Aesthetics -> Event intervals; default = FALSE commit 6e28af7 Author: Dan Dediu <ddediu@gmail.com> Date: Wed May 18 16:22:25 2022 +0200 AdhererViz: bump version and fix check warnings commit e4f5d36 Author: Dan Dediu <ddediu@gmail.com> Date: Wed May 18 13:09:18 2022 +0200 Fixes GitHub issue #172 commit af2443c Author: Dan Dediu <ddediu@gmail.com> Date: Wed May 18 13:05:10 2022 +0200 Per episodes can also show the event intervals and gaps commit ae58093 Author: Dan Dediu <ddediu@gmail.com> Date: Tue May 17 14:44:20 2022 +0200 Update documentation and fix check warnings commit 24eb65e Author: Dan Dediu <ddediu@gmail.com> Date: Tue May 17 14:27:27 2022 +0200 Plotting events and gaps seems to work for sliding windows commit a51e0b1 Author: Dan Dediu <ddediu@gmail.com> Date: Fri May 13 13:25:32 2022 +0200 Plotting intervals and gaps for sliding windows seems to work (but needs testing) commit 95facec Author: Dan Dediu <ddediu@gmail.com> Date: Fri May 13 11:14:48 2022 +0200 ... actually, it does make sense to compute the inner.event.info even for overlapping windows (it is the user's problem to use them or not) commit 9426ed5 Author: Dan Dediu <ddediu@gmail.com> Date: Fri May 13 11:06:24 2022 +0200 Don't compute the inner.event.info if the sliding windows are overlapping commit f3ac228 Author: Dan Dediu <ddediu@gmail.com> Date: Fri May 13 10:22:04 2022 +0200 Don't print inner.event.info if present for per_episode and sliding_window objects commit f0c6a68 Author: Dan Dediu <ddediu@gmail.com> Date: Tue Apr 5 19:57:25 2022 +0200 Now plot() respects the order of patients given through patients.to.plot commit f8cfb67 Author: Dan Dediu <ddediu@gmail.com> Date: Wed Nov 24 17:31:12 2021 +0100 GitHub #172 : initial plotting of inner event intervals commit 049760a Author: Dan Dediu <ddediu@gmail.com> Date: Wed Nov 24 16:56:02 2021 +0100 Fix GitHub #175 + some other preliminary work on plotting event intervals in sliding windows and per intervals (but nothing user-visible yet) commit ac22abe Author: Dan Dediu <ddediu@gmail.com> Date: Mon Nov 22 12:44:14 2021 +0100 Fix GitHub #174 (plus a small bug fix when plotting as a time series with 1 point) Now the placeholder for partial CMAs is plotted even if they don't have one... commit 6c9846e Author: Dan Dediu <ddediu@gmail.com> Date: Sun Nov 7 23:56:53 2021 +0100 GitHub #172 Proof-of-concept that I can return the full event.info from sliding windows -> it adds overheads so disabled by default, but can be enabled by forcing the new argument return.inner.event.info to TRUE
ddediu · Jun 24, 2022 · 6d4955e · 6d4955e
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diff --git a/AdhereR/DESCRIPTION b/AdhereR/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: AdhereR
 Type: Package
 Title: Adherence to Medications
-Version: 0.7.0
+Version: 0.8.0
 Authors@R: c(person("Dan", "Dediu", role = c("aut", "cre"),
                      email = "ddediu@gmail.com"),
              person("Alexandra", "Dima", role = "aut",
@@ -33,17 +33,18 @@ LazyData: TRUE
 Imports: lubridate (>= 1.5),
     parallel (>= 3.0),
     data.table (>= 1.9),
-	rsvg (>= 1.3),
-	jpeg (>= 0.1),
-	png (>= 0.1),
-	webp (>= 1.0),
-	methods
+	  rsvg (>= 1.3),
+	  jpeg (>= 0.1),
+	  png (>= 0.1),
+	  webp (>= 1.0),
+	  methods
 Depends: R (>= 3.0)
 Suggests: rmarkdown (>= 1.1),
     knitr (>= 1.20),
     R.rsp (>= 0.40),
-    base64(>= 2.0),
+    base64 (>= 2.0),
+    viridisLite (>= 0.4),
     AdhereRViz (>= 0.2)
 VignetteBuilder: knitr, R.rsp
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0
diff --git a/AdhereR/NAMESPACE b/AdhereR/NAMESPACE
@@ -7,6 +7,8 @@ S3method(getCMA,CMA_sliding_window)
 S3method(getEventInfo,CMA0)
 S3method(getEventInfo,CMA_per_episode)
 S3method(getEventInfo,CMA_sliding_window)
+S3method(getInnerEventInfo,CMA_per_episode)
+S3method(getInnerEventInfo,CMA_sliding_window)
 S3method(getMGs,CMA0)
 S3method(getMGs,CMA_per_episode)
 S3method(getMGs,CMA_sliding_window)
@@ -62,6 +64,9 @@ export(get.plotted.partial.cmas)
 export(getCMA)
 export(getCallerWrapperLocation)
 export(getEventInfo)
+export(getEventsToEpisodesMapping)
+export(getEventsToSlidingWindowsMapping)
+export(getInnerEventInfo)
 export(getMGs)
 export(last.plot.get.info)
 export(map.event.coords.to.plot)

diff --git a/AdhereR/NEWS.md b/AdhereR/NEWS.md
@@ -1,3 +1,40 @@
+# AdhereR 0.7.1
+
+## New features
+
+  - now `plot()` respects the order of patients given through the `patients.to.plot` argument.
+
+  - plotting sliding windows and per episodes can now show the events and gaps (as for simple plots, but things are a bit more complicated as different windows/events might result in different estimates).
+
+  - `plot()` has an "advanced" parameter `do.not.draw.plot` which, when `TRUE`, does not draw the plot but only the legend, allowing its display separate from (or next to) the plot.
+
+  - `AdhereR` is compatible with the pipe operator (`%>%` or `|>`), the overview vignette now shows several examples.
+
+  - the overview vignette now shows an example of modifying an `AdhereR` plot *a posteriori* by adding various elements (lines, symbols and text) to a CMA plot.
+
+  - the `Python 3` wrapper (bridge) was updated, as was the associated vignette; `AdhereR` can now be used transparently from Junyper Notebooks (and even through `rpy2`) and two example notebooks have been included. 
+
+  - the `event.info` table returned by the simple CMAs (`CMA1`..`CMA9`) now includes an extra column, `.EVENT.USED.IN.CMA`, which is `TRUE` if and only if the event on that row was actually used to estimate the CMA; this info can be used by itself, but is aimed at finding out which event is included in which episode or sliding window (see below).
+
+  - `CMA_per_episode` and `CMA_sliding_window` can now return the mapping between events and episodes or sliding windows, if the parameter `return.mapping.events.episodes` or `return.mapping.events.sliding.window` (respectively) is set to `TRUE`; in this case, there is an extra component of the constructed object, called `mapping.episodes.to.events` or `mapping.windows.to.events` respectively, which give, for each event or sliding window, the row number (in the data) of the event(s) that participate in it.
+
+  - plotting a `CMA_per_episode` or `CMA_sliding_window` object with a `mapping.episodes.to.events` or `mapping.windows.to.events` component, respectively, can how which events belong to which episode or sliding window visually, if the parameter `print.episode.or.sliding.window` is set to `TRUE`.
+
+## Bug fixes
+
+  - `plot()`'s `align.all.patients` and `align.first.event.at.zero` did not work as intended.
+
+  - the unneeded columns of the `data` argument to the CMA functions are now ignored, avoiding cases where "reserved" column names might be used (moreover, there is now an explicit check against using such reserved column names).
+
+  - various other enhancements and bugfixes.
+
+### `CMA_polypharmacy`
+
+  - remove option to supply medication class as list after `.check.medication.class` was suppressed from `AdhereR`.
+
+  - specify columns to merge by.
+
+
 # AdhereR 0.7
 
 ## New features

diff --git a/AdhereR/R/adherer.R b/AdhereR/R/adherer.R
diff --git a/AdhereR/R/call-adherer-external.R b/AdhereR/R/call-adherer-external.R
diff --git a/AdhereR/R/plotting.R b/AdhereR/R/plotting.R
diff --git a/AdhereR/inst/wrappers/python3/ReadMe.md b/AdhereR/inst/wrappers/python3/ReadMe.md
@@ -0,0 +1,4 @@
+# Python 3 wrapper and Junyper Notebook examples
+
+This folder contains the `Python 3` module `adherer.py` that implementes the `Python 3` wrapper for `AdhereR`, as well as two examples of using `AdhereR` from `Python 3 Junypper Notebooks`.
+While `jupyter_notebook_python3_wrapper.ipynb` shows the use of the Python 3 wrapper to compute and plot CMAs, `jupyter_notebook_python3_py2.ipynb` shows the same thing but using the more generic `rpy2` mechanism (which, however, results in a shlightly clunckier code).