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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,168 @@ | ||
| --- | ||
| title: "Commonly-used graph examples" | ||
| output: rmarkdown::html_vignette | ||
| vignette: > | ||
| %\VignetteIndexEntry{Commonly-used graph examples} | ||
| %\VignetteEngine{knitr::rmarkdown} | ||
| %\VignetteEncoding{UTF-8} | ||
| --- | ||
|
|
||
| ```{r, include = FALSE} | ||
| knitr::opts_chunk$set( | ||
| fig.align = "center", | ||
| collapse = TRUE, | ||
| comment = "#>" | ||
| ) | ||
| ``` | ||
|
|
||
| ```{r setup} | ||
| library(graphicalMCP) | ||
| ``` | ||
|
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| # Introduction | ||
|
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| Any valid graph can be made with `graph_create()`, but some patterns have been established over time. We demonstrate how to run some of these patterns with graphicalMCP. | ||
|
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| # Bonferroni-Holm | ||
|
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| ```{r bonferroni-holm, fig.dim=c(6, 6)} | ||
| transitions <- matrix(1 / 4, 5, 5) | ||
| diag(transitions) <- 0 | ||
| bonferroni_holm_graph <- graph_create(rep(1 / 5, 5), transitions) | ||
| plot(bonferroni_holm_graph) | ||
| ``` | ||
|
|
||
| # Fixed sequence | ||
|
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| ```{r fixed-sequence, fig.dim=c(6, 2)} | ||
| fixed_sequence_graph <- graph_create( | ||
| c(1, 0, 0, 0), | ||
| rbind( | ||
| c(0, 1, 0, 0), | ||
| c(0, 0, 1, 0), | ||
| c(0, 0, 0, 1), | ||
| c(0, 0, 0, 0) | ||
| ) | ||
| ) | ||
| plot(fixed_sequence_graph, layout = "grid", nrow = 1, asp = .1) | ||
| ``` | ||
|
|
||
| # Simplel successive | ||
|
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| ```{r simple-successive, fig.dim=c(5, 5)} | ||
| simple_successive_graph <- graph_create( | ||
| c(.5, .5, 0, 0), | ||
| rbind( | ||
| c(0, 0, 1, 0), | ||
| c(0, 0, 0, 1), | ||
| c(0, 1, 0, 0), | ||
| c(1, 0, 0, 0) | ||
| ) | ||
| ) | ||
| plot(simple_successive_graph, layout = "grid", nrow = 2) | ||
| ``` | ||
|
|
||
| General successive graphs are a good example where multiple variations may be useful with slight differences in starting edge weights. Variable edge weights are not currently supported, but they can be done for a particular graph with a light wrapper. | ||
|
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| ```{r simple-successive-var-fun} | ||
| simple_successive_var <- function(gamma) { | ||
| graph_create( | ||
| c(.5, .5, 0, 0), | ||
| rbind( | ||
| c(0, gamma, 1 - gamma, 0), | ||
| c(gamma, 0, 0, 1 - gamma), | ||
| c(0, 1, 0, 0), | ||
| c(1, 0, 0, 0) | ||
| ) | ||
| ) | ||
| } | ||
| ``` | ||
|
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| Then multiple variations can be created and compared easily. | ||
|
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| ```{r simple-successive-var, fig.show="hold", fig.align='default', out.width="47%"} | ||
| plot( | ||
| simple_successive_var(.75), | ||
| layout = "grid", | ||
| nrow = 2, | ||
| vertex.label.cex = .7, | ||
| edge.label.cex = .7 | ||
| ) | ||
| plot( | ||
| simple_successive_var(.9), | ||
| layout = "grid", | ||
| nrow = 2, | ||
| vertex.label.cex = .7, | ||
| edge.label.cex = .7 | ||
| ) | ||
| ``` | ||
|
|
||
| # Huque-Alosh-Bhore (2011) | ||
|
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| ```{r huque-alosh-bhore, fig.dim=c(5, 5)} | ||
| hab_2011_graph <- graph_create( | ||
| c(1, 0, 0, 0), | ||
| rbind( | ||
| c(0, .5, .5, 0), | ||
| c(0, 0, 0, 1), | ||
| c(0, .5, 0, .5), | ||
| c(0, 1, 0, 0) | ||
| ) | ||
| ) | ||
| plot(hab_2011_graph, layout = "grid") | ||
| ``` | ||
|
|
||
| # Wiens-Dmitrienko (2005) | ||
|
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| ```{r wiens-dmitrienko, fig.dim=c(6, 2)} | ||
| wd_2005_graph <- graph_create( | ||
| c(1 / 3, 1 / 3, 1 / 3), | ||
| rbind( | ||
| c(0, 1, 0), | ||
| c(0, 0, 1), | ||
| c(.5, .5, 0) | ||
| ) | ||
| ) | ||
| plot(wd_2005_graph, layout = "grid", nrow = 1, asp = .1, edge_curves = c(pairs = -6, "H3|H1" = -6)) | ||
| ``` | ||
|
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||
| # Parallel gate-keeping | ||
|
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| ```{r parallel-gatekeeping, fig.dim=c(5, 5)} | ||
| par_gate_graph <- graph_create( | ||
| c(.5, .5, 0, 0), | ||
| rbind( | ||
| c(0, 0, .5, .5), | ||
| c(0, 0, .5, .5), | ||
| c(0, 0, 0, 1), | ||
| c(0, 0, 1, 0) | ||
| ) | ||
| ) | ||
| plot(par_gate_graph, layout = "grid", nrow = 2) | ||
| ``` | ||
|
|
||
| # Improved parallel gate-keeping | ||
|
|
||
| ```{r improved-parallel-gatekeeping, fig.dim=c(5, 5)} | ||
| imp_par_gate_graph <- graph_create( | ||
| c(.5, .5, 0, 0), | ||
| rbind( | ||
| c(0, 0, .5, .5), | ||
| c(0, 0, .5, .5), | ||
| c(.0001, 0, 0, .9999), | ||
| c(0, .0001, .9999, 0) | ||
| ) | ||
| ) | ||
| plot(imp_par_gate_graph, layout = "grid", nrow = 2) | ||
| ``` |