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ChangeLog
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CHANGES IN OUTBREAKTOOLS 0.1-13
BUG FIXES
o Minor modifications to documentation to pass new CRAN checks.
CHANGES IN OUTBREAKTOOLS 0.1-12
NEW FEATURES
o Modified summary and .inlineSummary functions to handle NAs more effectively.
o Modified JSON2obkData function to filter out a wider range of missing values
under different notations (ie. NA, "", "NR") when importing data from JSON format
and converting to obkData objects.
o Added .importFromJSON function to allow for automatic retrieval (with
package RCurl), reformatting (into slots appropriate to obkData class)
, and conversion of JSON-formatted data from URL addresses to obkData
objects (with JSON2obkData function).
CHANGES IN OUTBREAKTOOLS 0.1-1
BUG FIXES
o examples involving plotting maps commented out to prevent check
to fail when no internet connection
CHANGES IN OUTBREAKTOOLS 0.1-0
NEW FEATURES
o epibase 0.1-2 becomes OutbreakTools 0.1-0 due to a trademark
infringement.
CHANGES IN EPIBASE 0.1-2
NEW FEATURES
o Changed the structure of obkData and obkSequences objects. The
@samples slot was too contraining and has been replaced with a
slot @records, storing any time-stamped information at an
individual level. The @clinical slot has been renamed to @context,
and is used to store any time-stamped information at a
populational level (e.g. climatic variables, school closures,
etc.). okbSequence objects are now storing meta-information on the
sequences as well.
o Improvement of various plotting methods; in particular,
plotIndividualTimeline now allows for visualizing any time-stamped
information.
o New accessors for dates and individuals in obkSequences, and for
dates in obkContacts
o New procedure as.data.frame for obkContacts
o New functions make.tip.attributes, make.sequence.attribute,
make.individual.attributes, returning a wide-format data.frame
where all information relating to these items is displayed.
CHANGES IN EPIBASE 0.1-0
FIXES
o changed the NAMESPACE so as to depend on less packages
o as the vignette uses knir, OutbreakTools now explicitely depends on R
>= 3.0.0
CHANGES IN EPIBASE 0.1-0
NEW FEATURES
o first release of the package!
o Data classes & accessors: obkData, obkSequences, obkContacts
o plotting methods: plotGeo, plotIndividualTimeline, plotggphy,
plotggMST
o subset for obkData
o read.annotated.tree and read.annotated.nexus
o simuEpi to simulate outbreak under a SIR model
o a 46-pages vignette (using knitr)