interactive CMA option to not display histogram for sliding window or treatment episode

[alexadima]

bold blah

[alexadima]

for displaying CMA estimates using sliding window and treatment episode functions, there is the option of plot CMA, and as staked bars, as overlapping bars, as time series. when plot CMA is ON, the histogram of CMA values is shown on the left side, and the other 3 become optional. There is no possibility to take out the left side plot and leave one of the 3 optional on top.

DATA <- med.events;

get.data.for.patients.fnc <- function(patientid, d, idcol, cols=NA, maxrows=NA) d[ d[[idcol]] %in% patientid, ]

Try to extract the data only for the selected patient ID(s):

DATApat1 <- get.data.for.patients.fnc( c("1"), DATA, ### don't forget to put here your REAL DATA! ### "PATIENT_ID" );

Compute the appropriate CMA:

cma <- CMA_sliding_window(data=DATApat1, CMA="CMA7",

(please note that even if some parameters are

                      # not relevant for a particular CMA type, we
                      # nevertheless pass them as they will be ignored)
                      ID.colname="PATIENT_ID",
                      event.date.colname="DATE",
                      event.duration.colname="DURATION",
                      event.daily.dose.colname="PERDAY",
                      medication.class.colname="CATEGORY",
                      carry.only.for.same.medication=FALSE,
                      consider.dosage.change=FALSE,
                      followup.window.start=0,
                      followup.window.start.unit="days",
                      followup.window.duration=730,
                      followup.window.duration.unit="days",
                      observation.window.start=0,
                      observation.window.start.unit="days",
                      observation.window.duration=730,
                      observation.window.duration.unit="days",
                      sliding.window.start=0,
                      sliding.window.start.unit="days",
                      sliding.window.duration=90,
                      sliding.window.duration.unit="days",
                      sliding.window.step.duration=60,
                      sliding.window.step.unit="days",
                      sliding.window.no.steps=10,
                      date.format="%m/%d/%Y"

);

if( !is.null(cma) ) # if the CMA was computed ok {

Try to plot it:

plot(cma,

(same idea as for CMA: we send arguments even if

   # they aren't used in a particular case)
   align.all.patients=FALSE,
   align.first.event.at.zero=FALSE,
   show.legend=TRUE,
   legend.x="right",
   legend.y="bottom",
   legend.bkg.opacity=0.5,
   legend.cex=0.75,
   legend.cex.title=1,
   duration=NA,
   show.period="days",
   period.in.days=90,
   bw.plot=FALSE,
   col.na="#D3D3D3",
   unspecified.category.label="drug",
   col.cats=rainbow,
   lty.event="solid",
   lwd.event=2,
   pch.start.event=15,
   pch.end.event=16,
   col.continuation="#000000",
   lty.continuation="dotted",
   lwd.continuation=1,
   cex=1,
   cex.axis=0.75,
   cex.lab=1,
   highlight.followup.window=TRUE,
   followup.window.col="#00FF00",
   highlight.observation.window=TRUE,
   observation.window.col="#FFFF00",
   observation.window.opacity=0.3,
   show.real.obs.window.start=TRUE,
   print.CMA=TRUE,
   CMA.cex=0.5,
   plot.CMA=TRUE,
   CMA.plot.ratio=0.1,
   CMA.plot.col="#90EE90",
   CMA.plot.border="#006400",
   CMA.plot.bkg="#7FFFD4",
   CMA.plot.text="#006400",
   plot.CMA.as.histogram=FALSE,
   show.event.intervals=TRUE,
   print.dose=FALSE,
   cex.dose=0.01,
   print.dose.outline.col="#FFFFFF",
   print.dose.centered=FALSE,
   plot.dose=FALSE,
   lwd.event.max.dose=8,
   plot.dose.lwd.across.medication.classes=FALSE,
   min.plot.size.in.characters.horiz=0,
   min.plot.size.in.characters.vert=0

); }

[ddediu]

Fixed in the devel branch: now the summary of the CMAs on the left and the partial CMAs on top are independent; also the help entries should be clearer. Likewise, the Shiny interface controls them now independently.