rm(list = ls()) # Clear env
gc() # Clear unused memory## used (Mb) gc trigger (Mb) max used (Mb)
## Ncells 508409 27.2 1130474 60.4 644245 34.5
## Vcells 898578 6.9 8388608 64.0 1635533 12.5cat("\f") # Clear consoleDefine Variables
A1<-.2 # P(Sporting Event)
A2<-.35 # P(Academic Event)
A3<-.45 # P(No Event)
BGivenA1<-.7 # P(Garage Full Sporting)
BGivenA2<-.25 # P(Garage Full Academic)
BGivenA3<-.05 # P(Garage Full None)Calculate Bayes P(A1|B)
A1GivenB<-(BGivenA1*A1)/((BGivenA1*A1)+(BGivenA2*A2)+(BGivenA3*A3))
A1GivenB## [1] 0.56There is a 56% chance that it is a sporting event
Calculate and Define Missing Variable
notBGivenA1<- 1-BGivenA1 # P(Garage Not Full Sporting)
notBGivenA2<- 1-BGivenA2 # P(Garage Not Full Academic)
notBGivenA3<- 1-BGivenA3 # P(Garage Not Full None)
A1ANDB<- A1*BGivenA1 # P(A1&B)
A2ANDB<- A2*BGivenA2 # P(A2&B)
A3ANDB<- A3*BGivenA3 # P(A3&B)
A1ANDnotB<- A1*notBGivenA1 # P(A1&B')
A2ANDnotB<- A2*notBGivenA2 # P(A2&B')
A3ANDnotB<- A3*notBGivenA3 # P(A3&B')Plot the Tree Diagram Define Nodes, Edges, Add Labels
library(BiocManager)
library("Rgraphviz")## Loading required package: graph## Loading required package: BiocGenerics##
## Attaching package: 'BiocGenerics'## The following objects are masked from 'package:stats':
##
## IQR, mad, sd, var, xtabs## The following objects are masked from 'package:base':
##
## anyDuplicated, aperm, append, as.data.frame, basename, cbind,
## colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
## get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
## table, tapply, union, unique, unsplit, which.max, which.min## Loading required package: grid# Create Nodes
node1 <- "P"
node2 <- "A1"
node3 <- "A2"
node4 <- "A3"
node5 <- "A1&B"
node6 <- "A1&B'"
node7 <- "A2&B"
node8 <- "A2&B'"
node9 <- "A3&B"
node10 <- "A3&B'"
nodeNames <- c(node1, node2, node3, node4, node5, node6, node7, node8, node9, node10)
rEG <- new("graphNEL",
nodes = nodeNames,
edgemode="directed"
)
# Erase any existing plots
dev.off()## null device
## 1### LINES
# Draw the "lines" or "branches" of the probability Tree
rEG <- addEdge (nodeNames[1], nodeNames[2], rEG, 1)
rEG <- addEdge (nodeNames[1], nodeNames[3], rEG, 1)
rEG <- addEdge (nodeNames[1], nodeNames[4], rEG, 1)
rEG <- addEdge (nodeNames[2], nodeNames[5], rEG, 1)
rEG <- addEdge (nodeNames[2], nodeNames[6], rEG, 1)
rEG <- addEdge (nodeNames[3], nodeNames[7], rEG, 1)
rEG <- addEdge (nodeNames[3], nodeNames[8], rEG, 1)
rEG <- addEdge (nodeNames[4], nodeNames[9], rEG, 1)
rEG <- addEdge (nodeNames[4], nodeNames[10], rEG, 10)
eAttrs <- list()
q <- edgeNames(rEG)
eAttrs$label <- c(toString(A1), toString(A2), toString(A3),
toString(BGivenA1), toString(notBGivenA1),
toString(BGivenA2), toString(notBGivenA2),
toString(BGivenA3), toString(notBGivenA3)
)
names(eAttrs$label) <- c( q[1], q[2], q[3], q[4], q[5], q[6], q[7], q[8], q[9])
edgeAttrs <- eAttrs
### COLOR
# Set the color, etc, of the tree
attributes <- list(node = list(label = "foo",
fillcolor = "lightgreen",
fontsize = "12"
),
edge = list(color = "red"),
graph = list(rankdir = "LR")
)
### PLOT
# Plot the probability tree using Rgraphvis
plot (rEG, edgeAttrs = eAttrs, attrs=attributes)
nodes(rEG)## [1] "P" "A1" "A2" "A3" "A1&B" "A1&B'" "A2&B" "A2&B'" "A3&B"
## [10] "A3&B'"edges(rEG)## $P
## [1] "A1" "A2" "A3"
##
## $A1
## [1] "A1&B" "A1&B'"
##
## $A2
## [1] "A2&B" "A2&B'"
##
## $A3
## [1] "A3&B" "A3&B'"
##
## $`A1&B`
## character(0)
##
## $`A1&B'`
## character(0)
##
## $`A2&B`
## character(0)
##
## $`A2&B'`
## character(0)
##
## $`A3&B`
## character(0)
##
## $`A3&B'`
## character(0)### PROBABILITY (labels)
#Add the probability values to the leaves of A&B, A&B', A'&B, A'&B'
text(625,390, A1ANDB, cex = .8)
text(625,320, A1ANDnotB, cex = .8)
text(630,245, A2ANDB, cex = .8)
text(630,175, A2ANDnotB, cex = .8)
text(630,100, A3ANDB, cex = .8)
text(630,30, A3ANDnotB, cex = .8)
#Probability that it's a sporting event if the garage is full - P(A1|B)
text(125,25, paste(" P(A1|B)=",A1ANDB,"/(",A1ANDB,"+",A2ANDB,"+",A3ANDB,")=",A1GivenB ),cex = .9, col = "blue")Image isn’t plotting so publishing that separately. If anyone knows why the markdown file won’t plot the tree diagram, let me know
sessionInfo() # Session Information## R version 4.2.2 (2022-10-31 ucrt)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19044)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=English_United States.utf8
## [2] LC_CTYPE=English_United States.utf8
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.utf8
##
## attached base packages:
## [1] grid stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] Rgraphviz_2.42.0 graph_1.76.0 BiocGenerics_0.44.0
## [4] BiocManager_1.30.19
##
## loaded via a namespace (and not attached):
## [1] digest_0.6.31 R6_2.5.1 jsonlite_1.8.4 stats4_4.2.2
## [5] evaluate_0.20 cachem_1.0.6 rlang_1.0.6 cli_3.6.0
## [9] rstudioapi_0.14 jquerylib_0.1.4 bslib_0.4.2 rmarkdown_2.20
## [13] tools_4.2.2 xfun_0.36 yaml_2.3.7 fastmap_1.1.0
## [17] compiler_4.2.2 htmltools_0.5.4 knitr_1.42 sass_0.4.5