VIsualisation and Monitoring of EpidemicS
The function vimes is used to identify clusters of related cases based
on multiple data.
vimes(x, method = c("basic"), cutoff = NULL, log_dens = NULL, graph_opt = vimes_graph_opt(), ...)
Arguments
- x
- a list of the class 'vimes_data' as returned by
vimes_data. - method
- a character string indicating the pruning method to be used; see details.
- cutoff
- a vector with the same length as 'x' indicating cutoff distances beyond which individuals will not be connected in the separate graphs; recycled if needed. If NULL, interactive mode will be triggered to ask the user for cutoff distances.
- log_dens
- a list of log-density functions to be used for ML estimation; one function is needed for each type of data.
- graph_opt
- a list of graphical options for the graphs, as
returned by
vimes_graph_opt. - ...
- further arguments to be passed to
hist.
Details
!!! This package is still under development. Do not use it without contacting the author. !!!
Different methods can be used for graph pruning:
- basic
- pre-defined cutoffs are used if provided as
cutoff; if missing, they are chosen interactively by the user by examining the distribution of distances
See also
vimes_data- to prepare the input data.
vimes_prune- for getting individual pruned graphs.
Examples
## generate data set.seed(2) dat1 <- rnorm(30, c(0,1,6)) dat2 <- rnorm(30, c(0,0,1)) dat3 <- rnorm(30, c(8,1,2)) x <- lapply(list(dat1, dat2, dat3), dist) x <- vimes_data(x) plot(x)## analyse data res <- vimes(x, cutoff=c(2,4,2)) res#> $graph #> IGRAPH UN-- 30 104 -- #> + attr: layout_1 (g/n), layout_2 (g/n), layout_3 (g/n), layout (g/n), #> | color_1 (v/c), color_2 (v/c), color_3 (v/c), size_1 (v/n), size_2 #> | (v/n), size_3 (v/n), label.family_1 (v/c), label.family_2 (v/c), #> | label.family_3 (v/c), label.color_1 (v/c), label.color_2 (v/c), #> | label.color_3 (v/c), name (v/c), color (v/c), size (v/n), #> | label.family (v/c), label.color (v/c), weight_1 (e/n), weight_2 #> | (e/n), weight_3 (e/n), label.color_1 (e/c), label.color_2 (e/c), #> | label.color_3 (e/c), label.color (e/c) #> + edges (vertex names): #> [1] 27--30 25--28 24--30 24--27 23--29 22--28 22--25 21--30 21--27 20--29 #> + ... omitted several edges #> #> $clusters #> $clusters$membership #> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 #> 1 2 3 1 2 3 1 2 3 1 2 3 1 2 3 1 2 3 1 2 3 1 2 3 1 2 #> 27 28 29 30 #> 3 1 2 3 #> #> $clusters$size #> [1] 10 10 10 #> #> $clusters$K #> [1] 3 #> #> $clusters$color #> 1 2 3 #> "#ccddff" "#79d2a6" "#ffb3b3" #> #> #> $cutoff #> [1] 2 4 2 #> #> $separate_graphs #> $separate_graphs[[1]] #> $separate_graphs[[1]]$graph #> IGRAPH UNW- 30 177 -- #> + attr: layout (g/n), name (v/c), color (v/c), size (v/n), label.family #> | (v/c), label.color (v/c), weight (e/n), label.color (e/c) #> + edges (vertex names): #> [1] 1--4 1--5 1--7 1--8 1--10 1--13 1--14 1--16 1--19 1--22 1--25 1--26 #> [13] 1--28 2--5 2--7 2--8 2--10 2--11 2--13 2--14 2--17 2--19 2--20 2--23 #> [25] 2--25 2--28 2--29 3--6 3--9 3--12 3--15 3--18 3--21 3--24 3--27 3--30 #> [37] 4--7 4--8 4--10 4--13 4--14 4--16 4--22 4--25 4--26 4--28 5--7 5--8 #> [49] 5--10 5--11 5--13 5--14 5--17 5--19 5--20 5--23 5--25 5--28 5--29 6--9 #> [61] 6--12 6--15 6--18 6--21 6--24 6--27 6--30 7--8 7--10 7--11 7--13 7--14 #> [73] 7--17 7--19 7--20 7--22 7--23 7--25 7--28 7--29 8--10 8--11 8--13 8--14 #> + ... omitted several edges #> #> $separate_graphs[[1]]$clusters #> $separate_graphs[[1]]$clusters$membership #> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 #> 1 1 2 1 1 2 1 1 2 1 1 2 1 1 2 1 1 2 1 1 2 1 1 2 1 1 #> 27 28 29 30 #> 2 1 1 2 #> #> $separate_graphs[[1]]$clusters$size #> [1] 20 10 #> #> $separate_graphs[[1]]$clusters$K #> [1] 2 #> #> $separate_graphs[[1]]$clusters$color #> 1 2 #> "#ccddff" "#79d2a6" #> #> #> $separate_graphs[[1]]$cutoff #> [1] 2 #> #> #> $separate_graphs[[2]] #> $separate_graphs[[2]]$graph #> IGRAPH UNW- 30 429 -- #> + attr: layout (g/n), name (v/c), color (v/c), size (v/n), label.family #> | (v/c), label.color (v/c), weight (e/n), label.color (e/c) #> + edges (vertex names): #> [1] 1--2 1--3 1--4 1--5 1--6 1--7 1--8 1--9 1--10 1--11 1--12 1--13 #> [13] 1--14 1--15 1--16 1--17 1--18 1--19 1--20 1--21 1--22 1--23 1--24 1--25 #> [25] 1--26 1--27 1--28 1--29 1--30 2--3 2--4 2--5 2--6 2--7 2--8 2--9 #> [37] 2--10 2--11 2--12 2--13 2--14 2--15 2--16 2--17 2--18 2--19 2--20 2--21 #> [49] 2--22 2--23 2--24 2--25 2--26 2--27 2--28 2--29 2--30 3--4 3--5 3--6 #> [61] 3--7 3--8 3--9 3--10 3--11 3--12 3--13 3--14 3--15 3--16 3--17 3--18 #> [73] 3--19 3--20 3--21 3--22 3--23 3--24 3--25 3--27 3--28 3--29 3--30 4--5 #> + ... omitted several edges #> #> $separate_graphs[[2]]$clusters #> $separate_graphs[[2]]$clusters$membership #> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 #> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> 27 28 29 30 #> 1 1 1 1 #> #> $separate_graphs[[2]]$clusters$size #> [1] 30 #> #> $separate_graphs[[2]]$clusters$K #> [1] 1 #> #> $separate_graphs[[2]]$clusters$color #> 1 #> "#ccddff" #> #> #> $separate_graphs[[2]]$cutoff #> [1] 4 #> #> #> $separate_graphs[[3]] #> $separate_graphs[[3]]$graph #> IGRAPH UNW- 30 195 -- #> + attr: layout (g/n), name (v/c), color (v/c), size (v/n), label.family #> | (v/c), label.color (v/c), weight (e/n), label.color (e/c) #> + edges (vertex names): #> [1] 1--4 1--7 1--10 1--13 1--16 1--22 1--25 1--28 2--3 2--5 2--6 2--9 #> [13] 2--12 2--14 2--15 2--17 2--18 2--21 2--26 2--27 2--30 3--5 3--6 3--8 #> [25] 3--9 3--11 3--12 3--14 3--15 3--17 3--18 3--20 3--21 3--23 3--24 3--26 #> [37] 3--27 3--29 3--30 4--10 4--13 4--16 4--19 4--22 4--28 5--6 5--8 5--9 #> [49] 5--11 5--12 5--14 5--15 5--17 5--18 5--20 5--21 5--23 5--24 5--26 5--27 #> [61] 5--29 5--30 6--8 6--9 6--11 6--12 6--14 6--15 6--17 6--18 6--20 6--21 #> [73] 6--23 6--24 6--26 6--27 6--29 6--30 7--10 7--13 7--16 7--22 7--25 7--28 #> + ... omitted several edges #> #> $separate_graphs[[3]]$clusters #> $separate_graphs[[3]]$clusters$membership #> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 #> 1 2 2 1 2 2 1 2 2 1 2 2 1 2 2 1 2 2 1 2 2 1 2 2 1 2 #> 27 28 29 30 #> 2 1 2 2 #> #> $separate_graphs[[3]]$clusters$size #> [1] 10 20 #> #> $separate_graphs[[3]]$clusters$K #> [1] 2 #> #> $separate_graphs[[3]]$clusters$color #> 1 2 #> "#ccddff" "#79d2a6" #> #> #> $separate_graphs[[3]]$cutoff #> [1] 2 #> #> #>plot(res$graph)
