stCEG README
stCEG
The goal of stCEG is to facilitate the creation of Chain Event Graphs
over spatial areas. It allows users to fully customise both the
structure and underlying model of the Chain Event Graph, offering a high
degree of flexibility for tailored analyses.
Installation
You can install the stable version of stCEG from CRAN with:
install.packages("stCEG")Or the development version from GitHub with:
remotes::install_github("holliecalley/stCEG")## Using github PAT from envvar GITHUB_PAT. Use `gitcreds::gitcreds_set()` and unset GITHUB_PAT in .Renviron (or elsewhere) if you want to use the more secure git credential store instead.
## Skipping install of 'stCEG' from a github remote, the SHA1 (f79d14af) has not changed since last install.
## Use `force = TRUE` to force installationUsage
With the stCEG package, it is simple for a user to create an event
tree from a given dataset, colour it to turn it into a staged tree,
specify priors over this, and then convert this into a Chain Event Graph
(CEG). The package also allows for model comparison and the creation of
maps based on spatial CEGs, as well as a Shiny user-interface.
library(stCEG)
data <- homicides
event_tree <- create_event_tree(data, columns = c(1,2,4,5), "both")
event_tree$eventtree## file:////private/var/folders/8q/_ftph8z911d1mg099mv8rt6h0000gn/T/RtmpJkb7Tq/filef92d77fde3b2/widgetf92d3d6ff8a9.html screenshot completedcoloured_tree <- ahc_colouring(event_tree)
coloured_tree$stagedtree## file:////private/var/folders/8q/_ftph8z911d1mg099mv8rt6h0000gn/T/RtmpJkb7Tq/filef92d1b1c0f8e/widgetf92d4f414189.html screenshot completedtree_priors <- specify_priors(coloured_tree, prior_type = "Uniform", ask_edit = FALSE)##
## Stage Colour Key:
## #FFFFFF
## #A54BE3
## #CFB8D1
## #D2D9B9
## #84DF9D
## #9DE956
## #DA74C8
## #DCCD64
## #7CD1D3
## #8287D4
## Calculated priors:
## # A tibble: 10 × 6
## color level2 outgoing_edges2 number_nodes prior stage
## <chr> <int> <int> <dbl> <chr> <chr>
## 1 #FFFFFF 1 4 1 1,1,1,1 u1
## 2 #A54BE3 2 2 1 1,1 u2
## 3 #CFB8D1 2 2 1 1,1 u3
## 4 #D2D9B9 2 2 2 2,2 u4
## 5 #84DF9D 3 2 3 3,3 u5
## 6 #9DE956 3 2 1 1,1 u6
## 7 #DA74C8 3 2 2 2,2 u7
## 8 #DCCD64 3 2 2 2,2 u8
## 9 #7CD1D3 4 2 7 7,7 u9
## 10 #8287D4 4 2 9 9,9 u10
## # A tibble: 10 × 7
## Stage Colour Level `Outgoing Edges` Nodes Prior `Prior Mean`
## <chr> <chr> <int> <int> <dbl> <chr> <chr>
## 1 u1 #FFFFFF 1 4 1 1,1,1,1 0.25,0.25,0.25,0.25
## 2 u2 #A54BE3 2 2 1 1,1 0.5,0.5
## 3 u3 #CFB8D1 2 2 1 1,1 0.5,0.5
## 4 u4 #D2D9B9 2 2 2 2,2 0.5,0.5
## 5 u5 #84DF9D 3 2 3 3,3 0.5,0.5
## 6 u6 #9DE956 3 2 1 1,1 0.5,0.5
## 7 u7 #DA74C8 3 2 2 2,2 0.5,0.5
## 8 u8 #DCCD64 3 2 2 2,2 0.5,0.5
## 9 u9 #7CD1D3 4 2 7 7,7 0.5,0.5
## 10 u10 #8287D4 4 2 9 9,9 0.5,0.5staged_tree <- staged_tree_prior(coloured_tree, tree_priors)
staged_tree$stagedtree## file:////private/var/folders/8q/_ftph8z911d1mg099mv8rt6h0000gn/T/RtmpJkb7Tq/filef92d135a61e4/widgetf92d12d0c9a9.html screenshot completedceg <- create_ceg(staged_tree, view_table = FALSE)## # A tibble: 13 × 8
## contract_id ids label level color id font size
## <chr> <chr> <chr> <int> <chr> <chr> <chr> <dbl>
## 1 1-#FFFFFF s0 w0 1 #FFF… w0 80px 100
## 2 2-#CFB8D1-3-#84DF9D-4-#7CD1D3-5-#F… s1 w1 2 #CFB… w1 80px 100
## 3 2-#A54BE3-3-#9DE956-4-#7CD1D3-5-#F… s2 w2 2 #A54… w2 80px 100
## 4 2-#D2D9B9-3-#DA74C8-4-#7CD1D3-5-#F… s3 w3 2 #D2D… w3 80px 100
## 5 2-#D2D9B9-3-#84DF9D-4-#7CD1D3-5-#F… s4 w4 2 #D2D… w4 80px 100
## 6 3-#84DF9D-4-#7CD1D3-5-#FFFFFF-5-#F… s5 w5 3 #84D… w5 80px 100
## 7 3-#DCCD64-4-#8287D4-5-#FFFFFF-5-#F… s6, … w6 3 #DCC… w6 80px 100
## 8 3-#9DE956-4-#7CD1D3-5-#FFFFFF-5-#F… s7 w7 3 #9DE… w7 80px 100
## 9 3-#DA74C8-4-#7CD1D3-5-#FFFFFF-5-#F… s8, … w8 3 #DA7… w8 80px 100
## 10 3-#84DF9D-4-#7CD1D3-5-#FFFFFF-5-#F… s11,… w9 3 #84D… w9 80px 100
## 11 4-#7CD1D3-5-#FFFFFF-5-#FFFFFF s13,… w10 4 #7CD… w10 80px 100
## 12 4-#8287D4-5-#FFFFFF-5-#FFFFFF s15,… w11 4 #828… w11 80px 100
## 13 5-#FFFFFF s29,… w∞ 5 #FFF… w∞ 80px 100
## # A tibble: 26 × 21
## from to label1 colour_from sumlabel2 sumlabel3 total label_individuals
## <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <chr>
## 1 w0 w1 Adolesce… #FFFFFF 816 1 817 "Adolescent/Youn…
## 2 w0 w2 Adult #FFFFFF 1522 1 1523 "Adult \n 1523"
## 3 w0 w3 Child #FFFFFF 133 1 134 "Child \n 134"
## 4 w0 w4 Elderly #FFFFFF 199 1 200 "Elderly \n 200"
## 5 w1 w5 Female #CFB8D1 103 1 104 "Female \n 104"
## 6 w1 w6 Male #CFB8D1 713 1 714 "Male \n 714"
## 7 w10 w∞ Solved #7CD1D3 501 7 508 "Solved \n 508"
## 8 w10 w∞ Unsolved #7CD1D3 23 7 30 "Unsolved \n 30"
## 9 w11 w∞ Solved #8287D4 1861 9 1870 "Solved \n 1870"
## 10 w11 w∞ Unsolved #8287D4 285 9 294 "Unsolved \n 294"
## # ℹ 16 more rows
## # ℹ 13 more variables: font.size <dbl>, stage_total_posterior <dbl>,
## # posterior_total <dbl>, stage_total_prior <dbl>, prior_total <dbl>,
## # prior_mean <dbl>, posterior_mean <dbl>, label_posterior <chr>,
## # label_prior_mean <chr>, label_prior <chr>, color <chr>, smooth <list>,
## # level <int>
## # A tibble: 13 × 9
## contract_id ids label level color id font size fixed
## <chr> <chr> <chr> <int> <chr> <chr> <chr> <dbl> <list>
## 1 1-#FFFFFF s0 w0 1 #FFF… w0 80px 100 <named list>
## 2 2-#CFB8D1-3-#84DF9D-4… s1 w1 2 #CFB… w1 80px 100 <named list>
## 3 2-#A54BE3-3-#9DE956-4… s2 w2 2 #A54… w2 80px 100 <named list>
## 4 2-#D2D9B9-3-#DA74C8-4… s3 w3 2 #D2D… w3 80px 100 <named list>
## 5 2-#D2D9B9-3-#84DF9D-4… s4 w4 2 #D2D… w4 80px 100 <named list>
## 6 3-#84DF9D-4-#7CD1D3-5… s5 w5 3 #84D… w5 80px 100 <named list>
## 7 3-#DCCD64-4-#8287D4-5… s6, … w6 3 #DCC… w6 80px 100 <named list>
## 8 3-#9DE956-4-#7CD1D3-5… s7 w7 3 #9DE… w7 80px 100 <named list>
## 9 3-#DA74C8-4-#7CD1D3-5… s8, … w8 3 #DA7… w8 80px 100 <named list>
## 10 3-#84DF9D-4-#7CD1D3-5… s11,… w9 3 #84D… w9 80px 100 <named list>
## 11 4-#7CD1D3-5-#FFFFFF-5… s13,… w10 4 #7CD… w10 80px 100 <named list>
## 12 4-#8287D4-5-#FFFFFF-5… s15,… w11 4 #828… w11 80px 100 <named list>
## 13 5-#FFFFFF s29,… w∞ 5 #FFF… w∞ 80px 100 <named list>
## # A tibble: 26 × 22
## from to label1 colour_from sumlabel2 sumlabel3 total label_individuals
## <chr> <chr> <chr> <chr> <dbl> <dbl> <dbl> <chr>
## 1 w0 w1 Adolesce… #FFFFFF 816 1 817 "Adolescent/Youn…
## 2 w0 w2 Adult #FFFFFF 1522 1 1523 "Adult \n 1523"
## 3 w0 w3 Child #FFFFFF 133 1 134 "Child \n 134"
## 4 w0 w4 Elderly #FFFFFF 199 1 200 "Elderly \n 200"
## 5 w1 w5 Female #CFB8D1 103 1 104 "Female \n 104"
## 6 w1 w6 Male #CFB8D1 713 1 714 "Male \n 714"
## 7 w10 w∞ Solved #7CD1D3 501 7 508 "Solved \n 508"
## 8 w10 w∞ Unsolved #7CD1D3 23 7 30 "Unsolved \n 30"
## 9 w11 w∞ Solved #8287D4 1861 9 1870 "Solved \n 1870"
## 10 w11 w∞ Unsolved #8287D4 285 9 294 "Unsolved \n 294"
## # ℹ 16 more rows
## # ℹ 14 more variables: font.size <dbl>, stage_total_posterior <dbl>,
## # posterior_total <dbl>, stage_total_prior <dbl>, prior_total <dbl>,
## # prior_mean <dbl>, posterior_mean <dbl>, label_posterior <chr>,
## # label_prior_mean <chr>, label_prior <chr>, color <chr>, smooth <list>,
## # level <int>, label <chr>ceg$ceg## file:////private/var/folders/8q/_ftph8z911d1mg099mv8rt6h0000gn/T/RtmpJkb7Tq/filef92d558d70da/widgetf92d38ec2417.html screenshot completed