Examples
# Creating a random diffnet object set.seed(84117) -mydiffnet <- rdiffnet(30, 5) +mydiffnet <- rdiffnet(30, 5) # Coercing it into an array as.array(mydiffnet)#> , , 1 diff --git a/docs/reference/bass-1.png b/docs/reference/bass-1.png index 2820f88..6d3b8e2 100644 Binary files a/docs/reference/bass-1.png and b/docs/reference/bass-1.png differ diff --git a/docs/reference/bass.html b/docs/reference/bass.html index 13426ae..9427199 100644 --- a/docs/reference/bass.html +++ b/docs/reference/bass.html @@ -267,11 +267,11 @@See a
+Other statistics:
classify_adopters,cumulative_adopt_count,dgr, -ego_variance,exposure, +ego_variance,exposure,hazard_rate,infection,moran,struct_equiv,threshold, -vertex_covariate_distvertex_covariate_distExamples
diff --git a/docs/reference/bootnet.html b/docs/reference/bootnet.html index 1628a19..e1dc58a 100644 --- a/docs/reference/bootnet.html +++ b/docs/reference/bootnet.html @@ -270,13 +270,13 @@R
See also
+Other Functions for inference:
moran, -struct_teststruct_testExamples
# set.seed(13) -g <- rgraph_ba(t=99) +g <- rgraph_ba(t=99) ans <- bootnet(g, function(w, ...) length(w@x), R=100) ans#> diff --git a/docs/reference/c.diffnet.html b/docs/reference/c.diffnet.html index 2db35e2..5995b6c 100644 --- a/docs/reference/c.diffnet.html +++ b/docs/reference/c.diffnet.html @@ -190,10 +190,10 @@Examp city4 <- medInnovationsDiffNet[medInnovationsDiffNet[["city"]] == 4] # Computing exposure in each one -city1[["expo_se"]] <- exposure(city1, alt.graph="se", valued=TRUE) -city2[["expo_se"]] <- exposure(city2, alt.graph="se", valued=TRUE) -city3[["expo_se"]] <- exposure(city3, alt.graph="se", valued=TRUE) -city4[["expo_se"]] <- exposure(city4, alt.graph="se", valued=TRUE) +city1[["expo_se"]] <- exposure(city1, alt.graph="se", valued=TRUE) +city2[["expo_se"]] <- exposure(city2, alt.graph="se", valued=TRUE) +city3[["expo_se"]] <- exposure(city3, alt.graph="se", valued=TRUE) +city4[["expo_se"]] <- exposure(city4, alt.graph="se", valued=TRUE) # Concatenating all diffnet <- c(city1, city2, city3, city4) diff --git a/docs/reference/classify_adopters-1.png b/docs/reference/classify_adopters-1.png index 6d15df7..2aa34e0 100644 Binary files a/docs/reference/classify_adopters-1.png and b/docs/reference/classify_adopters-1.png differ diff --git a/docs/reference/classify_adopters.html b/docs/reference/classify_adopters.html index 29f0506..9a26b45 100644 --- a/docs/reference/classify_adopters.html +++ b/docs/reference/classify_adopters.html @@ -264,11 +264,11 @@
See a
+Other statistics:
bass,cumulative_adopt_count,dgr, -ego_variance,exposure, +ego_variance,exposure,hazard_rate,infection,moran,struct_equiv,threshold, -vertex_covariate_distvertex_covariate_distExamples
diff --git a/docs/reference/cumulative_adopt_count.html b/docs/reference/cumulative_adopt_count.html index 632484f..5f50340 100644 --- a/docs/reference/cumulative_adopt_count.html +++ b/docs/reference/cumulative_adopt_count.html @@ -163,11 +163,11 @@See a
+Other statistics:
bass,classify_adopters,dgr, -ego_variance,exposure, +ego_variance,exposure,hazard_rate,infection,moran,struct_equiv,threshold, -vertex_covariate_distvertex_covariate_distdiff --git a/docs/reference/dgr-1.png b/docs/reference/dgr-1.png index c7d983c..7dfc094 100644 Binary files a/docs/reference/dgr-1.png and b/docs/reference/dgr-1.png differ diff --git a/docs/reference/dgr-2.png b/docs/reference/dgr-2.png index 3560b9b..521335d 100644 Binary files a/docs/reference/dgr-2.png and b/docs/reference/dgr-2.png differ diff --git a/docs/reference/dgr.html b/docs/reference/dgr.html index 78f3d0e..c6122b7 100644 --- a/docs/reference/dgr.html +++ b/docs/reference/dgr.html @@ -218,11 +218,11 @@See a
Other statistics:
+bass,classify_adopters,cumulative_adopt_count, -ego_variance,exposure, +ego_variance,exposure,hazard_rate,infection,moran,struct_equiv,threshold, -vertex_covariate_distvertex_covariate_distOther visualizations:
diffusionMap,drawColorKey,grid_distribution, @@ -237,7 +237,7 @@Examp
# Comparing degree measurements --------------------------------------------- # Creating an undirected graph -graph <- rgraph_ba() +graph <- rgraph_ba() graph#> 11 x 11 sparse Matrix of class "dgCMatrix"#>#> #> 1 1 . . . . . . . . . . #> 2 . 1 . . . . . . . . . @@ -274,7 +274,7 @@Examp any(d_valued!=d_unvalued)
#> [1] TRUE# Classic Scale-free plot --------------------------------------------------- set.seed(1122) -g <- rgraph_ba(t=1e3-1) +g <- rgraph_ba(t=1e3-1) hist(dgr(g))# Since by default uses logscale, here we suppress the warnings # on points been discarded for <=0. diff --git a/docs/reference/diffnet-arithmetic-1.png b/docs/reference/diffnet-arithmetic-1.png index 52726c1..b395073 100644 Binary files a/docs/reference/diffnet-arithmetic-1.png and b/docs/reference/diffnet-arithmetic-1.png differ diff --git a/docs/reference/diffnet-class-1.png b/docs/reference/diffnet-class-1.png index 12919d6..6b89f88 100644 Binary files a/docs/reference/diffnet-class-1.png and b/docs/reference/diffnet-class-1.png differ diff --git a/docs/reference/diffnet-class.html b/docs/reference/diffnet-class.html index aade60b..ddc9b57 100644 --- a/docs/reference/diffnet-class.html +++ b/docs/reference/diffnet-class.html @@ -388,7 +388,7 @@Examp
# Creating a random graph set.seed(123) -graph <- rgraph_ba(t=9) +graph <- rgraph_ba(t=9) graph <- lapply(1:5, function(x) graph) # Pretty TOA diff --git a/docs/reference/diffnet_index.html b/docs/reference/diffnet_index.html index 975ad9f..c589cca 100644 --- a/docs/reference/diffnet_index.html +++ b/docs/reference/diffnet_index.html @@ -248,7 +248,7 @@Examp
# Creating a random diffusion network --------------------------------------- set.seed(111) -graph <- rdiffnet(100,5) +graph <- rdiffnet(100,5) # Accessing to a static attribute graph[["real_threshold"]]#> [1] 0.62034522 0.54853665 0.84659582 0.03114472 0.07245070 0.41045318 @@ -721,10 +721,10 @@diff --git a/docs/reference/egonet_attrs.html b/docs/reference/egonet_attrs.html index 092e04f..a3823b8 100644 --- a/docs/reference/egonet_attrs.html +++ b/docs/reference/egonet_attrs.html @@ -252,7 +252,7 @@Examp # Adding attributes (dynamic) ----------------------------------------------- # Preparing the data set.seed(1122) -x <- rdiffnet(30, 5, seed.p.adopt=.15) +x <- rdiffnet(30, 5, seed.p.adopt=.15) # Calculating exposure, and storing it diffe -expoM <- exposure(x) +expoM <- exposure(x) expoL <- lapply(seq_len(x$meta$nper), function(x) expoM[,x,drop=FALSE]) expoD <- do.call(rbind, expoL) diff --git a/docs/reference/diffnetmatmult.html b/docs/reference/diffnetmatmult.html index 079e738..45c92e8 100644 --- a/docs/reference/diffnetmatmult.html +++ b/docs/reference/diffnetmatmult.html @@ -184,7 +184,7 @@
Examp # Random diffnet graph set.seed(773) -net <- rdiffnet(100, 4, seed.graph='small-world', rgraph.args=list(k=8)) +net <- rdiffnet(100, 4, seed.graph='small-world', rgraph.args=list(k=8)) netsim <- net # According to Dekker (2006), Simmelian ties can be computed as follows diff --git a/docs/reference/diffusionMap.html b/docs/reference/diffusionMap.html index 29fccba..b1beee7 100644 --- a/docs/reference/diffusionMap.html +++ b/docs/reference/diffusionMap.html @@ -264,7 +264,7 @@
Examp set.seed(1231) # Random scale-free diffusion network -x <- rdiffnet(1000, 4, seed.graph="scale-free", seed.p.adopt = .025, +x <- rdiffnet(1000, 4, seed.graph="scale-free", seed.p.adopt = .025, rewire = FALSE, seed.nodes = "central", rgraph.arg=list(self=FALSE, m=4), threshold.dist = function(id) runif(1,.2,.4)) diff --git a/docs/reference/drawColorKey-1.png b/docs/reference/drawColorKey-1.png index cf96666..4fe03db 100644 Binary files a/docs/reference/drawColorKey-1.png and b/docs/reference/drawColorKey-1.png differ diff --git a/docs/reference/edgelist_to_adjmat-1.png b/docs/reference/edgelist_to_adjmat-1.png index 6fa24d1..a38f155 100644 Binary files a/docs/reference/edgelist_to_adjmat-1.png and b/docs/reference/edgelist_to_adjmat-1.png differ diff --git a/docs/reference/edges_coords-2.png b/docs/reference/edges_coords-2.png index 051f13f..317f94a 100644 Binary files a/docs/reference/edges_coords-2.png and b/docs/reference/edges_coords-2.png differ diff --git a/docs/reference/ego_variance.html b/docs/reference/ego_variance.html index b5a0e88..353a31a 100644 --- a/docs/reference/ego_variance.html +++ b/docs/reference/ego_variance.html @@ -170,21 +170,21 @@
Details the function specified in
funname, and, ifall=FALSE\(f_i = \sum_j a_{ij}f(y_i,y_j)^2/\sum_ja_{ij}\), otherwise \(f_i = f_j = \frac{1}{n^2}\sum_{i,j}f(y_i,y_j)\) -This is an auxiliary function for
struct_test. The idea is +This is an auxiliary function for
struct_test. The idea is to compute an adjusted measure of disimilarity between vertices, so the closest in terms of \(f\) is \(i\) to its neighbors, the smaller the relative variance.See also
-++
struct_testOther statistics:
bass,classify_adopters,cumulative_adopt_count,dgr, -exposure,hazard_rate, +exposure,hazard_rate,infection,moran,struct_equiv,threshold, -vertex_covariate_distvertex_covariate_distSee a
Examples
# Simple example with diffnet ----------------------------------------------- set.seed(1001) -diffnet <- rdiffnet(150, 5, seed.graph="small-world") +diffnet <- rdiffnet(150, 5, seed.graph="small-world") # Adding attributes indeg <- dgr(diffnet, cmode="indegree") diff --git a/docs/reference/exposure.html b/docs/reference/exposure.html index aa8ca23..5ccee9b 100644 --- a/docs/reference/exposure.html +++ b/docs/reference/exposure.html @@ -250,7 +250,7 @@+Details
If
+found at the examples section of the functionnormalize=FALSEthen denominator, \(S_t \times x_t\), is not included. This can be useful when, for example, exposure needs to be computed as a count instead of a proportion. A good example of this can be -found at the examples section of the functionrdiffnet.rdiffnet.References
@@ -268,14 +268,14 @@See a
ego_variance,hazard_rate,infection,moran,struct_equiv,threshold, -vertex_covariate_distvertex_covariate_distExamples
# Calculating lagged exposure ----------------------------------------------- set.seed(8) -graph <- rdiffnet(20, 4) +graph <- rdiffnet(20, 4) expo0 <- exposure(graph) expo1 <- exposure(graph, lags = 1) @@ -286,7 +286,7 @@Examp # Calculating the exposure based on Structural Equivalence ------------------ set.seed(113132) -graph <- rdiffnet(100, 10) +graph <- rdiffnet(100, 10) SE <- lapply(struct_equiv(graph), "[[", "SE") SE <- lapply(SE, function(x) { diff --git a/docs/reference/hazard_rate-1.png b/docs/reference/hazard_rate-1.png index ca6e12b..78d7356 100644 Binary files a/docs/reference/hazard_rate-1.png and b/docs/reference/hazard_rate-1.png differ diff --git a/docs/reference/hazard_rate.html b/docs/reference/hazard_rate.html index 1f27129..d86f403 100644 --- a/docs/reference/hazard_rate.html +++ b/docs/reference/hazard_rate.html @@ -258,10 +258,10 @@
See a
+Other statistics:
+bass,classify_adopters,cumulative_adopt_count,dgr, -ego_variance,exposure, +ego_variance,exposure,infection,moran,struct_equiv,threshold, -vertex_covariate_distvertex_covariate_distOther visualizations:
dgr,diffusionMap,drawColorKey,grid_distribution, diff --git a/docs/reference/infection.html b/docs/reference/infection.html index 6ac6126..fbe9f05 100644 --- a/docs/reference/infection.html +++ b/docs/reference/infection.html @@ -247,10 +247,10 @@See a
Other statistics:
bass,classify_adopters,cumulative_adopt_count,dgr, -ego_variance,exposure, +ego_variance,exposure,hazard_rate,moran,struct_equiv,threshold, -vertex_covariate_distvertex_covariate_distExamples
diff --git a/docs/reference/matrix_compare.html b/docs/reference/matrix_compare.html index f6daf0f..c283009 100644 --- a/docs/reference/matrix_compare.html +++ b/docs/reference/matrix_compare.html @@ -188,7 +188,7 @@Details
See also
+Other dyadic-level comparison functions:
vertex_covariate_compare, -vertex_covariate_distvertex_covariate_distExamples
@@ -196,8 +196,8 @@Examp # Creating two random matrices set.seed(89) -A <- rgraph_ba(t = 9, m = 4) -B <- rgraph_ba(t = 9, m = 4) +A <- rgraph_ba(t = 9, m = 4) +B <- rgraph_ba(t = 9, m = 4) A;B
#> 10 x 10 sparse Matrix of class "dgCMatrix"#>#> #> 1 1 . . . . . . . . . #> 2 1 . . . . . . . . . @@ -232,8 +232,8 @@# NOT RUN { set.seed(123123123) -A <- rgraph_ba(t = 5e3, m = 2) -B <- rgraph_ba(t = 5e3, m = 2) +A <- rgraph_ba(t = 5e3, m = 2) +B <- rgraph_ba(t = 5e3, m = 2) Am <- as.matrix(A) Bm <- as.matrix(B) @@ -241,7 +241,7 @@Examp # More elaborated example (speed) -------------------------------------------
Examp compfun <- function(a,b) ifelse(a > b, a, b) -microbenchmark::microbenchmark( +microbenchmark::microbenchmark( diffnet = matrix_compare(A, B, compfun), R = matrix(ifelse(Am > Bm, Am, Bm), ncol=ncol(Am)), times = 10 diff --git a/docs/reference/mentor_matching-1.png b/docs/reference/mentor_matching-1.png index ad4184a..7183107 100644 Binary files a/docs/reference/mentor_matching-1.png and b/docs/reference/mentor_matching-1.png differ diff --git a/docs/reference/moran.html b/docs/reference/moran.html index 4fb2b92..581a028 100644 --- a/docs/reference/moran.html +++ b/docs/reference/moran.html @@ -190,12 +190,12 @@
See a
+Other statistics:
-bass,classify_adopters,cumulative_adopt_count,dgr, -ego_variance,exposure, +ego_variance,exposure,hazard_rate,infection,struct_equiv,threshold, -vertex_covariate_distOther Functions for inference:
bootnet, -struct_testvertex_covariate_dist+Other Functions for inference:
bootnet, +struct_testExamples
@@ -203,7 +203,7 @@Examp # NOT RUN { # Generating a small random graph set.seed(123) - graph <- rgraph_ba(t = 4) + graph <- rgraph_ba(t = 4) w <- approx_geodesic(graph) x <- rnorm(5) diff --git a/docs/reference/netmatch.html b/docs/reference/netmatch.html index 0d8bcbe..6c4441d 100644 --- a/docs/reference/netmatch.html +++ b/docs/reference/netmatch.html @@ -21,9 +21,11 @@ + + + - @@ -38,6 +40,7 @@ + @@ -62,7 +65,7 @@ diff --git a/docs/reference/network.html b/docs/reference/network.html index c9436fa..f00b1c7 100644 --- a/docs/reference/network.html +++ b/docs/reference/network.html @@ -21,9 +21,11 @@ + + + - @@ -34,6 +36,7 @@ + @@ -58,7 +61,7 @@ @@ -222,7 +225,7 @@
See a
Examples
# Cohersing a diffnet to a list of networks --------------------------------- set.seed(1) -ans <- diffnet_to_network(rdiffnet(20, 2)) +ans <- diffnet_to_network(rdiffnet(20, 2)) ans# A random diffusion network ------------------------------------------------ set.seed(87) -dn <- rdiffnet(50, 4) +dn <- rdiffnet(50, 4) ans <- diffnet_to_networkDynamic(dn)#> Argument base.net not specified, using first element of network.list instead #> Created net.obs.period to describe network #> Network observation period info: diff --git a/docs/reference/nvertices.html b/docs/reference/nvertices.html index 30145ad..bdc0a61 100644 --- a/docs/reference/nvertices.html +++ b/docs/reference/nvertices.html @@ -21,9 +21,11 @@ + + + - @@ -34,6 +36,7 @@ + @@ -58,7 +61,7 @@@@ -165,7 +168,7 @@Details
Examples
# Creating a dynamic graph (we will use this for all the classes) ----------- set.seed(13133) -diffnet <- rdiffnet(100, 4) +diffnet <- rdiffnet(100, 4) # Lets use the first time period as a static graph graph_mat <- diffnet$graph[[1]] diff --git a/docs/reference/permute_graph.html b/docs/reference/permute_graph.html index f0b8c5c..b583f6c 100644 --- a/docs/reference/permute_graph.html +++ b/docs/reference/permute_graph.html @@ -21,9 +21,11 @@ + + + - @@ -37,6 +39,7 @@ + @@ -61,7 +64,7 @@@@ -174,8 +177,8 @@R
See also
@@ -183,7 +186,7 @@This function can be used as null distribution in
-struct_testOther simulation functions:
rdiffnet, -rewire_graph,rgraph_ba, +Other simulation functions:
rdiffnet, +rewire_graph,rgraph_ba,rgraph_er,rgraph_ws,ring_latticeSee a
Examples
+ color.palette = viridis::viridis_pal(), include.grid = TRUE, + exclude.zeros = FALSE, valued = getOption("diffnet.valued", FALSE), ...)# Simple example ------------------------------------------------------------ set.seed(1231) -g <- rgraph_ba(t=9) +g <- rgraph_ba(t=9) g#> 10 x 10 sparse Matrix of class "dgCMatrix"#>#> #> 1 1 . . . . . . . . . #> 2 1 . . . . . . . . . diff --git a/docs/reference/plot.diffnet-1.png b/docs/reference/plot.diffnet-1.png index 3b838c5..911505a 100644 Binary files a/docs/reference/plot.diffnet-1.png and b/docs/reference/plot.diffnet-1.png differ diff --git a/docs/reference/plot.diffnet.html b/docs/reference/plot.diffnet.html index 22e78b2..4d791ba 100644 --- a/docs/reference/plot.diffnet.html +++ b/docs/reference/plot.diffnet.html @@ -21,9 +21,11 @@ + + + - @@ -34,6 +36,7 @@ + @@ -58,7 +61,7 @@diff --git a/docs/reference/plot_adopters-1.png b/docs/reference/plot_adopters-1.png index 8e33850..22c313c 100644 Binary files a/docs/reference/plot_adopters-1.png and b/docs/reference/plot_adopters-1.png differ diff --git a/docs/reference/plot_adopters-2.png b/docs/reference/plot_adopters-2.png index c52b9ad..c076d53 100644 Binary files a/docs/reference/plot_adopters-2.png and b/docs/reference/plot_adopters-2.png differ diff --git a/docs/reference/plot_adopters.html b/docs/reference/plot_adopters.html index 25c5c57..338ce31 100644 --- a/docs/reference/plot_adopters.html +++ b/docs/reference/plot_adopters.html @@ -21,9 +21,11 @@ + + + - @@ -34,6 +36,7 @@ + @@ -58,7 +61,7 @@ @@ -224,7 +227,7 @@See a
Examples
diff --git a/docs/reference/plot_infectsuscep-1.png b/docs/reference/plot_infectsuscep-1.png index 442dca7..bf7ec50 100644 Binary files a/docs/reference/plot_infectsuscep-1.png and b/docs/reference/plot_infectsuscep-1.png differ diff --git a/docs/reference/plot_infectsuscep.html b/docs/reference/plot_infectsuscep.html index f9cf34c..3a087b4 100644 --- a/docs/reference/plot_infectsuscep.html +++ b/docs/reference/plot_infectsuscep.html @@ -21,9 +21,11 @@ + + + - @@ -36,6 +38,7 @@ + @@ -60,7 +63,7 @@ @@ -139,9 +142,8 @@# Generating a random diffnet ----------------------------------------------- set.seed(821) -diffnet <- rdiffnet(100, 5, seed.graph="small-world", seed.nodes="central") +diffnet <- rdiffnet(100, 5, seed.graph="small-world", seed.nodes="central") plot_adopters(diffnet)# Alternatively, we can use a TOA Matrix diff --git a/docs/reference/plot_diffnet-1.png b/docs/reference/plot_diffnet-1.png index 25c52b6..2dc08db 100644 Binary files a/docs/reference/plot_diffnet-1.png and b/docs/reference/plot_diffnet-1.png differ diff --git a/docs/reference/plot_diffnet.html b/docs/reference/plot_diffnet.html index d5dcfc9..c764761 100644 --- a/docs/reference/plot_diffnet.html +++ b/docs/reference/plot_diffnet.html @@ -21,9 +21,11 @@ + + + - @@ -36,6 +38,7 @@ + @@ -60,7 +63,7 @@diff --git a/docs/reference/plot_diffnet2.html b/docs/reference/plot_diffnet2.html index 3b2c89f..42c32af 100644 --- a/docs/reference/plot_diffnet2.html +++ b/docs/reference/plot_diffnet2.html @@ -21,9 +21,11 @@ + + + - @@ -34,6 +36,7 @@ + @@ -58,7 +61,7 @@ @@ -137,11 +140,10 @@Another way of visualizing diffusion
# S3 method for default plot_diffnet2(graph, toa, pers = min(toa, na.rm = TRUE):max(toa, na.rm = TRUE), - color.ramp = grDevices::colorRamp(c("steelblue", "gray", "tomato")), - layout = NULL, key.width = 0.1, key.args = list(), - main = "Diffusion dynamics", add.map = NULL, - diffmap.args = list(kde2d.args = list(n = 100)), diffmap.alpha = 0.5, - include.white = "first", vertex.size = "degree", + color.ramp = grDevices::colorRamp(viridis::magma(20)), layout = NULL, + key.width = 0.1, key.args = list(), main = "Diffusion dynamics", + add.map = NULL, diffmap.args = list(kde2d.args = list(n = 100)), + diffmap.alpha = 0.5, include.white = "first", vertex.size = "degree", minmax.relative.size = getOption("diffnet.minmax.relative.size", c(0.01, 0.04)), no.graph = FALSE, ...)Plot distribution of infect/suscep
main = "Distribution of Infectiousness and\nSusceptibility", xlab = "Infectiousness of ego", ylab = "Susceptibility of ego", sub = ifelse(logscale, "(in log-scale)", NA), - color.palette = grDevices::colorRampPalette(c("skyblue", "tomato")), - include.grid = TRUE, exclude.zeros = FALSE, - valued = getOption("diffnet.valued", FALSE), ...)Arguments
