Changes in version 1.4.2 (2018-03-08)
-------------------------------------
User Visible Changes:
* BUG FIX [backported from 1.5.6]: the G2 peak of the B sample was not
getting incorporated into model construction, which caused model
fitting to fail on samples with histograms skewed towards the left.
Changes in version 1.4.1 (2017-12-04)
-------------------------------------
[Note: this bugfix backported from 1.5.1 to 1.4.1, 2017-12-12]
Minor bug squashed:
* Changes made upstream to `car::deltaMethod()` introduced a bug. This
will be resolved as of `car` version 2.1-7. Until that version of
`car` makes it's way into CRAN, calling `deltaMethod()` on an `nls`
object will require the argument `vcov.` be explicitly set to `vcov`,
a function in the stats package. This has been done in `flowPloidy`,
and should be invisible to users. In addition, the bug is not present
in the current R release, so it should not need to be backported to
previous versions of flowPloidy.
Changes in version 1.1.9 (2017-04-19)
-------------------------------------
User Visible Changes
* Users may now specify one or more internal standard sizes in
functions FlowHist() and batchFlowHist(), via the argument
'standards'. These values will be presented to the user in the
browseFlowHist() viewer, and after being set by the user, the value
will be used to calculate the GC size in pg in the function
tabulateFlowHist.
* Users may now select which peak in the histogram to treat as the
internal standard when calculating GC values.
* New vignettes added: "Getting Started", and "Histogram Tour".
* Old vignette "overview" removed.
* Internal help pages greatly expanded, including many internal
functions. See ?flowPloidy for an overview
* Many minor bug fixes and GUI tweaks (for browseFlowHist).
Changes in version 1.1.3 (2016-11-25)
-------------------------------------
User Visible Changes
* Gating fully implemented in browseFlowHist! Major reorganization of
the browseFlowHist layout.
Changes in version 1.1.2 (2016-11-22)
-------------------------------------
User Visible Changes
* Added support for processing files with two standards present. A new
argument is available for functions that load FCS files
(batchFlowHist, FlowHist etc.): `samples`. By default this is set to
2, to account for a single unknown and an co-chopped standard. If you
are using two co-chopped standards (or really anytime you have three
distinct samples chopped together), set samples = 3. This can also be
changed interactively in the browseFlowHist GUI.
* The layout of the browseFlowHist GUI has been re-arranged somewhat to
accomodate the new features mentioned above.
* The linearity flag is over-ridden when no G2 peaks are present.
Without a G2 peak, linearity can't be properly fit. This leads to
linear gradients, because the linearity parameter is used in the
S-phase components.
Changes in version 1.1.1 (2016-10-26)
-------------------------------------
Internal Changes:
* Improved peak finding algorithm
* Reduced region searched for the starting bin for model fitting. Was
originally 20, now set to 10. Need more data to establish best
approach.
Changes in version 0.99.3 (2016-10-17)
--------------------------------------
Internal Changes
* Updated DESCRIPTION to include URL and BugReports fields, mostly as
an exercise to test SVN access and syncing SVN <-> git
Changes in version 0.99.2 (2016-10-12)
--------------------------------------
Internal Changes
* added a new slot to ModelComponents, `paramLimits`, which allows
lower and upper limits to be set for each model parameter. (corrects
bug where linearity wanders below 1, giving nonsense results).
* rationalized the bounds of the data fit in the NLS procedure. Model
fitting, and RCS calculation, are now all tied to the bin identified
by fhStart. This selects the highest intensity (peak) in the first 20
non-zero channels, and ignores all channels below this point. Prior
to this, the number of observations and associated degrees of freedom
was calculated in an ad-hoc manner, making the RCS values (even-more)
difficult to interpret; in addition, the single- and multi- cut
values started at one channel, but the RCS calculations started on
another channel, which didn't make sense.
Changes in version 0.99.1 (2016-10-11)
--------------------------------------
User Visible Changes
* Vignette updated to include installation instructions for
BioConductor
Internal Changes
* Added accessor functions for ModelComponent and FlowHist classes, so
direct access of slots via the `@` operator is no longer used outside
of the initialization functions.
* replaced some loops with vectorized calculations
* replaced call to `eval` with a normal function call to `nlsLM` in
flowAnalyze.R.
* formatted NEWS file
Changes in version 0.99.0 (2016-08-25)
--------------------------------------
* What's NEW? Everything so far!