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| 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 |