Package: SMITIDvisu 0.0.9

SMITIDvisu: Visualize Data for Host and Viral Population from 'SMITIDstruct' using 'HTMLwidgets'

Visualisation tools for 'SMITIDstruct' package. Allow to visualize host timeline, transmission tree, index diversities and variant graph using 'HTMLwidgets'. It mainly using 'D3JS' javascript framework.

Authors:Jean-Francois Rey [aut, cre], Julien Boge [ctb]

SMITIDvisu_0.0.9.tar.gz
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SMITIDvisu_0.0.9.tgz(r-4.4-x86_64)SMITIDvisu_0.0.9.tgz(r-4.4-arm64)SMITIDvisu_0.0.9.tgz(r-4.3-x86_64)SMITIDvisu_0.0.9.tgz(r-4.3-arm64)
SMITIDvisu_0.0.9.tar.gz(r-4.5-noble)SMITIDvisu_0.0.9.tar.gz(r-4.4-noble)
SMITIDvisu_0.0.9.tgz(r-4.4-emscripten)SMITIDvisu_0.0.9.tgz(r-4.3-emscripten)
SMITIDvisu.pdf |SMITIDvisu.html✨
SMITIDvisu/json (API)

# Install 'SMITIDvisu' in R:
install.packages('SMITIDvisu', repos = c('https://mechantrouquin.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • hostline - A host infomation over time
  • st.dist113_2 - Distance matrix of observed variants sequences of a host 113 at time 2 from simulation.
  • st.dist113_all - Distance matrix of observed variants sequences of a host 113 at time 2, 3 and 4 from simulation.
  • st.listTimeProp113 - List of variants ID with subvector for time and value.
  • st.prop113_2 - Variants proportions and count for host 113 at time 2 from simulation.
  • st.prop113_all - Variants proportions and count for an host 113 at time 2, 3 and 4 from simulation.
  • tt.edges - Pathogen link over the time
  • tt.events - Data.frame of hosts events information by time. Fake data.
  • tt.nodes - Host list with there status over the time.

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.63 score 43 scripts 176 downloads 22 exports 29 dependencies

Last updated 4 years agofrom:ded781b1b3. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-win-x86_64NOTEOct 30 2024
R-4.5-linux-x86_64NOTEOct 30 2024
R-4.4-win-x86_64NOTEOct 30 2024
R-4.4-mac-x86_64NOTEOct 30 2024
R-4.4-mac-aarch64NOTEOct 30 2024
R-4.3-win-x86_64NOTEOct 30 2024
R-4.3-mac-x86_64NOTEOct 30 2024
R-4.3-mac-aarch64NOTEOct 30 2024

Exports:demo.SMITIDvisu.rundf2geojsonmapttmapttOutputmapttProxymapttSelectHostmstVariantmstVariantOutputmstVariantProxyrenderMapttrendermstVariantrenderTimeLinerenderTransmissionTreetimeLinetimeLineOutputtimeLineProxytransmissionTreetransmissionTreeOutputtransmissionTreeProxyupdatemstVariantupdateTimeLineupdateTransmissionTree

Dependencies:base64encbslibcachemclidigestevaluatefastmapfontawesomefsgluehighrhtmltoolshtmlwidgetsjquerylibjsonliteknitrlifecyclemagrittrmemoisemimeR6rappdirsRcpprlangrmarkdownsasstinytexxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Visualize Data for Host and Viral Population from SMITIDstruct using HTMLwidgetsSMITIDvisu-package SMITIDvisu
createRainbowColors Create a list of colors for each value vcreateRainbowColors
demo.SMITIDvisu.rundemo.SMITIDvisu.run
df2geojsondf2geojson
A host infomation over timehostline
mapttmaptt
mapttProxymapttProxy
mapttSelectHostmapttSelectHost
compute the minimum spanning treemstCompute
mstVariantmstVariant
mstVariantProxymstVariantProxy
Shiny bindings for visualisation widgetsmapttOutput mstVariantOutput renderMaptt rendermstVariant renderTimeLine renderTransmissionTree SMITIDvisu-shiny timeLineOutput transmissionTreeOutput
A SMITIDstruct package variable.st
Distance matrix of observed variants sequences of a host 113 at time 2 from simulation.st.dist113_2
Distance matrix of observed variants sequences of a host 113 at time 2, 3 and 4 from simulation.st.dist113_all
List of variants ID with subvector for time and value.st.listTimeProp113
Variants proportions and count for host 113 at time 2 from simulation.st.prop113_2
Variants proportions and count for an host 113 at time 2, 3 and 4 from simulation.st.prop113_all
timeLinetimeLine
timeLineProxy get an instance of a timelinetimeLineProxy
transmissionTreetransmissionTree
transmissionTreeProxytransmissionTreeProxy
Pathogen link over the timett.edges
Data.frame of hosts events information by time. Fake data.tt.events
Host list with there status over the time.tt.nodes
updatemstVariantupdatemstVariant
updateTimeLineupdateTimeLine
updateTransmissionTreeupdateTransmissionTree