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

## Documentation for package ‘SMITIDvisu’ version 0.0.9

- DESCRIPTION file.

## Help Pages

SMITIDvisu-package | Visualize Data for Host and Viral Population from SMITIDstruct using HTMLwidgets
createRainbowColors | createRainbowColors Create a list of colors for each value v
demo.SMITIDvisu.run | demo.SMITIDvisu.run
df2geojson | df2geojson
hostline | A host infomation over time
maptt | maptt
mapttOutput | Shiny bindings for visualisation widgets
mapttProxy | mapttProxy
mapttSelectHost | mapttSelectHost
mstCompute | compute the minimum spanning tree
mstVariant | mstVariant
mstVariantOutput | Shiny bindings for visualisation widgets
mstVariantProxy | mstVariantProxy
renderMaptt | Shiny bindings for visualisation widgets
rendermstVariant | Shiny bindings for visualisation widgets
renderTimeLine | Shiny bindings for visualisation widgets
renderTransmissionTree | Shiny bindings for visualisation widgets
SMITIDvisu | Visualize Data for Host and Viral Population from SMITIDstruct using HTMLwidgets
SMITIDvisu-shiny | Shiny bindings for visualisation widgets
st | A SMITIDstruct package variable.
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.
timeLine | timeLine
timeLineOutput | Shiny bindings for visualisation widgets
timeLineProxy | timeLineProxy get an instance of a timeline
transmissionTree | transmissionTree
transmissionTreeOutput | Shiny bindings for visualisation widgets
transmissionTreeProxy | transmissionTreeProxy
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.
updatemstVariant | updatemstVariant
updateTimeLine | updateTimeLine
updateTransmissionTree | updateTransmissionTree