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Updated to use roxygen2 version 7.3.2 to build the documentation.
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Define 'R_NO_REMAP' and 'STRICT_R_HEADERS'.
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Register native routines.
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Updated to use roxygen2 version 7.2.3 to build the documentation.
- Fixed broken examples for InDegree, OutDegree and IngoingContactChain.
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NetworkStructure: add a method that works on a list of ContactTrace objects.
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NetworkSummary: add a method that works on a list of ContactTrace objects.
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Renamed the
NEWSfile toNEWS.mdand changed to use markdown format style. -
Removed the dependency to the plyr package for building pdf reports.
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Added orcid id:s in the DESCRIPTION file for the package authors.
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Changed the file extension for files in the R folder from '.r' to '.R'.
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Used roxygen2 ver 7.1.1 to build the documentation.
- Added the missing table for direct outgoing contacts in the html report.
- Set 'stringsAsFactors = FALSE' in the data.frame returned by 'NetworkSummary'.
- Fix format of authors in CITATION file.
- Added missing calls to 'R_forceSymbols' and 'R_useDynamicSymbols' in the C init function.
- Added the 'maxDistance' argument to the 'Trace' method to stop contact tracing at 'maxDistance' (inclusive) from the root node. Default is ‘NULL’ i.e. to not use the 'maxDistance' stop criteria.
- Fixed build failure on the Solaris platform.
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Removed Animate method to pass the CRAN checks. Install version 0.8.8 manually from the archive if that method is required. See section 6.3 in 'R Installation and Administration' on how to install packages from source.
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Removed dependencies to plyr, R2HTML and Rcpp.
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Removed usage of testthat when testing the package.
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Removed list methods for ContactTrace objects. When calculating measures for several roots, the purpose is to use methods that work directly on the data.frame with movements.
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Updated maintainer email
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Changed 'Title' field in DESCRIPTION to title case
- Improved performance when calculating ShortestPaths on a data.frame of movements.
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Fixed failing test case 'Duplicate movements'
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Fixed NOTE not importing 'methods' from R CMD check
- Changed argument representation to slots in setClass for the two S4 classes ContactTrace and Contacts. The package now requires R>=3.0.0
- Plots are not supported in version 0.8.6 since igraph0 has been archived. We intend to resolve the issue in a future version. Install version 0.8.5 and igraph0 manually from the archive if plots are required. See section 6.3 in 'R Installation and Administration' on how to install packages from source.
- Updated DESCRIPTION to use Imports instead of Depends for igraph0, plyr, R2HTML.
- Added method ReportObject to be called from a Sweave report template to get the current ContactTrace object.
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inDays and outDays now returned as integer from NetworkSummary of a ContactTrace object.
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Added 'all' to interval argument in Animate to view visualize all movements in one image. The default interval argument was changed to 'all'.
- Fixed a bug that was introduced in ver 0.7.6 when performing contact tracing.
- Fixed a bug that was introduced in ver 0.7.6 when calculating IngoingContactChain and OutgoingContactChain using NetworkSummary.
- Using the the animation and ggmap package, contacts can now be visualized and animated.
- Improved performance when calculating contact chain in C++ code by counting the number of visited nodes more efficient.
NEW FEATURES
- Report now uses match.arg to check output format.
- Added the parameters inBegin, inEnd, outBegin and outEnd to NetworkSummary to allow for different time windows for ingoing and outgoing contacts.
- Fixed bug in Report. InDegree were not defined for the S4 class Contacts.
- Improved performance in C++ code by using visited nodes more efficient
- Updated documentation
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Fixed bug in C++ code not checking tEnd constraint.
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Fixed bug in NetworkSummary when calculating degree.
- When the methods Trace, NetworkSummary, InDegree, OutDegree, IngoingContactChain, OutgoingContactChain are called with the arguments movements, root, tEnd and days; the measures are calculated for each combination of root, tEnd and days.
- Ongoing work to improve performance using Rcpp.
- Changed from igraph to igraph0 to handle the update of igraph to 0.6.
- Fixed bug with Report of a list of ContactTrace objects. Each ContactTrace object called Report with missing parameter clean.
- The html and pdf reports have been corrected. The table displaying individual outgoing contacts erronously switched source and destination.
- Removed unused parameters from Report method.
- Updated documentation.
- Updated documentation.
- Updated documentation.
- All documentation generated via roxygen.
- If movements contained duplicate contacts, they were all added. Now only unique contacts are included from the contact tracing.
- 'plot' now works as intended for the S4 ContactTrace object with only outgoing contacts
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Added the method ShortestPaths
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NetworkStructure gives the distance from root for each node during the depth first search.
- Added the example dataset transfers
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Can now generate an 'html' report for the contact tracing using 'Report'
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Can now generate a 'pdf' report for the contact tracing using 'Report'
- 'show' now works as intended for the S4 ContactTrace object