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Forenote: this is a follow-up question to this one.
I've programmed a Boggle Game Solver in R (see this github page for source code), and find its performance disappointing.
Here's how it works...
# Say we have the following set of letters
bog.letters <- c("t", "e", "n", "s", "d", "a", "i", "o",
"l", "e", "r", "o", "c", "f", "i", "e")
# We get the list of paths (permutations) from a pre-existing list
paths <- paths.by.length[[6]] # 6th element corresponds to 8-element "paths"
dim(paths) # [1] 183472 8
# The following function is the key here,
# mapping the 183,472 combinations to the 16 letters
candidates <- apply(X = paths, MARGIN = 1, FUN = function(x) paste(bog.letters[x], collapse=""))
# The only remaining thing is to intersect the candidate words
# with the actual words from our dictionary
dict.words <- dict.fr$mot[dict.fr$taille == 8]
valid.words <- intersect(candidates, dict.words)
Reproducible example for 13-letter words candidates
bog.letters <- c("t", "e", "n", "s", "d", "a", "i", "o", "l", "e", "r", "o", "c", "f", "i", "e")
n.letters <- 13
paths <- structure(list(V1 = c(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, 1, 1, 1, 1), V2 = c(2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2), V3 = c(3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3),
V4 = c(4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4), V5 = c(7, 7, 7, 7,
7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7,
7, 7, 7, 7, 7, 7, 7), V6 = c(6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6,
6), V7 = c(5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,
5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5), V8 = c(9, 9, 9,
9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9,
9, 9, 9, 9, 9, 9, 9, 9), V9 = c(10, 10, 10, 10, 10, 10, 10,
10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10,
10, 10, 10, 10, 10, 10, 10, 10), V10 = c(11, 11, 11, 11,
11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 13, 13,
13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14), V11 = c(8, 8,
12, 12, 12, 14, 14, 15, 15, 15, 15, 16, 16, 16, 16, 14, 14,
14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 11, 11, 11), V12 = c(12,
12, 15, 15, 16, 15, 15, 12, 12, 14, 16, 12, 12, 15, 15, 11,
11, 11, 11, 15, 15, 15, 8, 12, 12, 12, 15, 15, 16, 16), V13 = c(15,
16, 14, 16, 15, 12, 16, 8, 16, 13, 12, 8, 15, 12, 14, 8,
12, 15, 16, 11, 12, 16, 12, 8, 15, 16, 12, 16, 12, 15)), .Names = c("V1",
"V2", "V3", "V4", "V5", "V6", "V7", "V8", "V9", "V10", "V11",
"V12", "V13"), row.names = c(NA, 30L), class = "data.frame")
candidates <- apply(X = paths, MARGIN = 1, FUN = function(x) paste(bog.letters[x], collapse=""))
For such a small path list, this is pretty fast. But the actual number of paths for 13-letter words is 2,644,520. So it can take a minute or even more to find all candidates. Using doSNOW, I am able to parrallelize the searches, reducing the total time by a significant amount, but there is a huge drawback to this: when using a normal loop, I can exit/break whenever I reach the point where no more words are found. This is not obvious (impossible?) to do with parrallel processes.
So my question is: can you think of a better function/algorithm for this task? Some websites provide solutions to Boggle game in a matter of seconds... Either they generated all possible letter combinations and stored the results in a database (!), else they clearly use a better algorithm (and probably a compiled language) to achieve those results.
Any ideas?
Using cpp_str_split function from the Rcpp Gallery, running time is now reduced to 3secs for 2644520 paths.
library(stringi)
paths <- data.frame(matrix(sample(1:16, 13*2644520, TRUE), ncol=13))
a1 <- stri_c(bog.letters[t(as.matrix(paths))], collapse="")
candidates <- cpp_str_split(a1, 13)[[1]]
For 2644520 paths, apply approach takes about 80secs on my notebook.
Related
I have the following vector:
v<-c(1, 1, 8, 3, 1, 9, 4, 21, 13, 13, 1, 1, 3, 10, 1, 13, 22, 1,
1, 4, 2, 1, 13, 1, 5, 1, 2, 1, 1, 2, 12, 10, 26, 15, 2, 9, 6,
5, 1, 3, 18, 2, 10, 2, 8, 9, 4, 1, 11, 4, 2, 12, 3, 14, 2, 1,
27, 3, 6, 2, 1, 1, 3, 16, 3, 36, 13, 9, 11, 10, 24, 2, 27, 4,
4, 2, 9, 1, 3, 13, 3, 1, 8, 5, 5, 15, 1, 1, 3, 1, 4, 14, 8, 1,
1, 2, 20, 1, 9, 3, 1, 2, 5, 14, 5, 11, 1, 3, 2, 9, 10, 21, 9,
1, 20, 5, 11, 23, 2, 1, 1, 2, 1, 7, 2, 9, 1, 19, 9, 9, 2, 15,
17, 8, 11, 17, 2, 14, 2, 8, 13, 1, 2, 9, 15, 25, 3, 8, 32, 4,
11, 1, 1, 2)
I would like to estimate its density in R through the command density. With few lines of code:
d<-density(v)
df<-data.frame(x=d$x,y=d$y,stringsAsFactors = FALSE)
plot(df)
I obtained the following picture:
But the resulting plot doesn't add up, because max(v) is 36 and min(v) is 1 while the graph shows tails before and after 0 and 40.
I would like to pass the information I have to a normal list of axes with nodes but I don't know how to do it. The raw data with "deput" would look like this. If someone knows how to convert this list into something easier to use I would appreciate it.I can visualise the graph with "plot" but to edit it I need to have more precise information.
library(igraph)
dput (net2$graph_pajek)
structure(list(30, FALSE, c(1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2,
3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 6, 7, 13, 13,
14, 15, 16, 18, 20, 20, 21, 27, 27, 27, 27, 29, 2, 2, 2, 2, 2,
2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5,
6, 6, 7, 8, 8, 9, 9, 9, 10, 10, 10, 10, 10, 11, 11, 12, 12, 12,
13, 13, 13, 14, 14, 14, 15, 15, 15, 16, 18, 18, 18, 19, 20, 20,
21, 21, 23, 24, 25, 26, 27, 27, 27, 29, 3, 3, 3, 3, 3, 3, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5,
5, 5, 5, 5, 6, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 10,
10, 10, 10, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12,
12, 12, 12, 12, 12, 12, 13, 13, 14, 14, 15, 15, 15, 15, 15), list(c(1, 0, 1), structure(list(), .Names = character(0)),
list(name = c("A", "B", "C",
"D", "E", "F", "G", "H",
"I", "J", "K",
"L", "M", "N",
"O", "P", "Q", "R",
"S", "T", "U",
"V", "W", "X", "Y", "Z",
"AB", "AC", "AD", "AE"
), deg = c(248, 532, 855, 574, 1761, 261, 229, 216, 554,
628, 774, 223, 502, 295, 266, 910, 227, 312, 364, 260, 294,
741, 227, 471, 392, 376, 292, 295, 212, 287), size = c(2.,
6, 9, 6, 20,
2, 2, 2, 6,
7, 8, 2, 7,
3, 3, 10, 2,
3, 4, 2, 3.,
8, 2, 5, 4,
4, 3, 3, 2,
3), label.cex = c(0.7, 0.7, 0.7, 0.7, 0.7, 0.7,
0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7,
0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7, 0.7
), id = c("A", "B", "C",
"D", "E", "F", "G", "H",
"I", "J", "K",
"L", "M", "N",
"O", "P", "Q", "R",
"S", "T", "U",
"V", "W", "X", "Y", "Z",
"AB", "AC", "AD", "AE"
)), list(num = c(4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3,
10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 1, 1, 2,
2, 1, 1, 1, 1, 2, 2, 1, 4, 4, 4, 4, 1, 7, 7, 7, 7, 7, 7,
7, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 12,
12, 12, 12, 1, 2, 2, 1, 2, 2, 3, 3, 3, 5, 5, 5, 5, 5, 2,
2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 3, 1, 2,
2, 2, 2, 1, 1, 1, 1, 3, 3, 3, 1, 6, 6, 6, 6, 6, 6, 40, 40,
40, 40, 40, 40, 40, 40, 40), weight = c(4, 4, 4, 4,
7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10,
10, 10, 10, 3, 3, 3, 1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 1, 4,
4, 4, 4, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 12, 12,
12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 2, 2, 1, 2, 2,
3, 3, 3, 5, 5, 5, 5, 5, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 1, 3, 3, 3, 1, 2, 2, 2, 2, 1, 1, 1, 1, 3, 3, 3,
1, 6, 6, 6, 6, 6, 6, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 7, 7, 7, 7, 7, 7, 7, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7,
4, 4, 4, 4, 4, 4, 4, 4, 1, 18, 18))), <environment>), class = "igraph")
Are you looking for something like get.data.frame
> get.data.frame(net)
from to weight
1 A B 0.63502922
2 B C 0.79410173
3 C D 0.90802625
4 D E 0.09408188
5 E F 0.16450634
6 F G 0.75931882
7 G H 0.30409658
8 H I 0.23990324
9 I J 0.84762277
10 A J 0.88657718
data
Since I cannot reproduce the example in your post, I created a dummy example net like below
net <- make_ring(10) %>%
set_vertex_attr(name = "name", value = LETTERS[1:vcount(.)]) %>%
set_edge_attr(name = "weight", value = runif(ecount(.)))
To clarify a couple things:
The igraph file is not a plot per se, but a graph structure (as in, nodes and edges).
igraph has functions for plotting graphs, but there is no single and standard way of plotting a graph - instead, different algorithms can be used to determine visually-ideal ways of displaying them, and these algorithms oftentimes rely on random initializations.
The outputs from the plotting functions of igraph are only relevant in terms of R base plot drawing logic, AFAIK they don't use an intermediate format with coordinates handled in a user-comprehensible structure. You can nevertheless manage lots of aspects of how they are drawn - see ?igraph::igraph.plotting.
I want to generate a Sankey plot to visualize movements to different areas using sankeyNetwork() from the package networkd3 in r. I tried to mimic some examples as perfectly as possible. But when I run the function sankeyNetwork, no output is generated. On top of that, R doesn't show any warnings, erros et cetera. Therefore, I can't really check whether I made mistakes (obviously, because no plot is generated) and how to fix them. I provided a sample df and the code below.
library(networkD3)
nodes <- data.frame(area = c("a", "b", "c", "d", "e", "f", "g",
"h", "i", "j", "k", "l", "m", "n"))
links2 <- data.frame(source = c(1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4,
5, 5, 5, 5, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 8, 8, 8, 9, 9, 9, 9, 10, 10, 11, 11, 11, 12, 13, 13),
target = c(2, 8, 10, 11, 13, 0, 4, 5, 6, 7, 10, 11, 13, 0, 4, 9, 10, 12, 13, 0, 5, 6, 7, 10, 11, 13, 7, 10, 12,
0, 10, 11, 12, 13, 8, 9, 10, 11, 12, 13, 9, 10, 13, 10, 12, 13, 0, 11, 12, 13, 0, 14, 0, 0),
value = c(14, 4, 6, 23, 3, 6, 36, 3, 4, 4, 3, 12, 3, 24, 3, 6, 19, 3, 9, 3, 6, 3, 11, 9, 3, 22, 3, 3, 10, 3, 4,
3, 3, 9, 12, 5, 16, 13, 3, 10, 3, 4, 9, 7, 4, 4, 77, 4, 6, 6, 27, 3, 3, 3))
sankeyNetwork(Links = links2, Nodes = nodes,
Source = "source", Target = "target",
Value = "value", NodeID = "area",
fontSize= 12, nodeWidth = 30)
You refer to 15 unique nodes in your links2 data frame, but you only have 14 unique nodes in your nodes data frame.
length(unique(c(links2$source, links2$target)))
# [1] 15
length(nodes$area)
# [1] 14
If you add another node, it will work...
library(networkD3)
nodes <- data.frame(area = c("a", "b", "c", "d", "e", "f", "g",
"h", "i", "j", "k", "l", "m", "n", "o"))
links2 <- data.frame(source = c(1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4,
5, 5, 5, 5, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 8, 8, 8, 9, 9, 9, 9, 10, 10, 11, 11, 11, 12, 13, 13),
target = c(2, 8, 10, 11, 13, 0, 4, 5, 6, 7, 10, 11, 13, 0, 4, 9, 10, 12, 13, 0, 5, 6, 7, 10, 11, 13, 7, 10, 12,
0, 10, 11, 12, 13, 8, 9, 10, 11, 12, 13, 9, 10, 13, 10, 12, 13, 0, 11, 12, 13, 0, 14, 0, 0),
value = c(14, 4, 6, 23, 3, 6, 36, 3, 4, 4, 3, 12, 3, 24, 3, 6, 19, 3, 9, 3, 6, 3, 11, 9, 3, 22, 3, 3, 10, 3, 4,
3, 3, 9, 12, 5, 16, 13, 3, 10, 3, 4, 9, 7, 4, 4, 77, 4, 6, 6, 27, 3, 3, 3))
sankeyNetwork(Links = links2, Nodes = nodes,
Source = "source", Target = "target",
Value = "value", NodeID = "area",
fontSize= 12, nodeWidth = 30)
This question already has answers here:
Remove rows with all or some NAs (missing values) in data.frame
(18 answers)
Closed 4 years ago.
Let's start with some data to make the example reproducible:
x <- structure(list(DC1 = c(5, 5, NA, 5, 4, 6, 5, NA, 4, 6, 6, 6,
5, NA, 5, 5, 7), DC2 = c(4, 7, 4, 5, NA, 4, 6, 4, 4, 5, 5, 5,
5, NA, 6, 5, 5), DC3 = c(4, 7, 4, 4, NA, 4, 5, 4, 5, 4, 5, 5,
6, 4, 6, 6, 5), DC4 = c(4, 7, 5, NA, NA, 4, 6, 5, 5, 4, 3, 4,
6, 5, 5, 6, 3), DC5 = c(7, 8, 5, NA, NA, 10, 7, 6, 8, 6, 6, 7,
11, 10, 5, 7, 6), DC6 = c(8, 8, NA, NA, NA, 11, 9, 8, 9, 9, 10,
10, 12, 16, 6, 8, 9), DC7 = c(10, 10, 10, NA, NA, 8, 9, 8, 13,
8, 11, 9, 14, 13, 8, 8, 11), DC8 = c(17, 10, 10, NA, NA, 10,
10, 10, 15, 10, 14, 11, 23, 15, 14, 13, 14), DC9 = c(16, 9, 9,
NA, NA, 12, 13, 11, 13, 15, 15, 13, 17, 15, 25, 17, 12)), .Names = c("DC1",
"DC2", "DC3", "DC4", "DC5", "DC6", "DC7", "DC8", "DC9"), class = "data.frame", row.names = c(NA,
-17L))
How can I filter the data frame, keeping rows that contain data from column DC3 to DC10?
Here's a dplyr option:
library(dplyr)
x %>%
filter_at(vars(DC3:DC9), all_vars(!is.na(.)))
or:
x %>%
filter_at(vars(DC3:DC9), all_vars(complete.cases(.)))
and here's a tidyr option:
x %>% tidyr::drop_na(DC3:DC9)
We can subset the data and apply complete.cases
x[complete.cases(x[3:9]),]
or using column names
x[complete.cases(x[paste0("DC", 3:9)]),]
You could use function str_extract from package stringr, which can extract the number from the column name in the data frame.
# get number from column name
col_num <- as.numeric(stringr::str_extract(names(x), "\\d"))
# rows that contain data from column DC3 to DC10
x[(col_num >= 3) & (col_num < 10)]
Edited note:
To Install stringr please use install.packages("stringr")
I've got the following data which I can visualize like this
A = matrix(c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 2, 1, 5, 6, 3, 4, 9, 10, 7, 8, 12, 11, 3, 5, 1, 7, 2, 9, 4, 11, 6, 12, 8, 10, 4, 6, 7, 8, 9, 10, 11, 1, 12, 2, 3, 5, 5, 3, 2, 9, 1, 7, 6, 12, 4, 11, 10, 8, 6, 4, 9, 10, 7, 8, 12, 2, 11, 1, 5, 3, 7, 9, 4, 11, 6, 12, 8, 3, 10, 5, 1, 2, 8, 10, 11, 1, 12, 2, 3, 4, 5, 6, 7, 9, 9, 7, 6, 12, 4, 11, 10, 5, 8, 3, 2, 1, 10, 8, 12, 2, 11, 1, 5, 6, 3, 4, 9, 7, 11, 12, 8, 3, 10, 5, 1, 7, 2, 9, 4, 6, 12, 11, 10, 5, 8, 3, 2, 9, 1, 7, 6, 4),nrow=12,ncol=12,byrow=TRUE)
require(plotrix)
color2D.matplot(A)
(A could be any square matrix of whole numbers)
I need to make it display with random colors which aren't too similar. Here's an example of what I am trying to achieve:
I've been unable to get randomized colors to work. Is matplot the function for this? Can anyone show me how to randomize the colors?
Per #DWin's comment, try:
plot(NULL, type= "n", xlim = c(1,ncol(A)), ylim = c(1, nrow(A)), xlab = "column", ylab = "row",
main = "HCL colors, pseudo-random hue, scaled chroma and luminance")
rect(col(A)-.5,row(A)-.5,col(A)+.5,row(A)+.5,
col = hcl(h = round(runif(length(A))*360), c = 60*A/max(A)+20, l = 60*A/max(A)+20)
)
I guessed that you still wanted the values in your matrix to still determine the 'darkness' of the colors, as was the case in the grayscale image. The only thing random here is the hue- i.e. a randomly picked angle from a color wheel.