matching and recording in R - r

I have a data frame like this, called df:
a b c d e f
b c f a a a
d f a b c c
f e d f f d
The first row is actually the column name. Let's take an example to explain the meaning here: df[1,1] is b, which means there is relation from a to b, so the values in the column means there is relation from the 'column name' to that entry.
I want create a matrix(df1) with 6*6 dimension, column and row names are both column names of df. The (i,j) entry is 1, if there is relation from 'i' to 'j', otherwise, 0.
The output I want is:
a b c d e f
a 0 1 0 1 0 1
b 0 0 1 0 1 1
c 1 0 0 1 0 1
d 1 1 0 0 0 1
e 1 0 1 0 0 1
f 1 0 1 1 0 0
How to do this with a loop in R?
How to do this without a loop, and only use basic R?
How to do this using some fancy packages in R?

Using the reshape2 package, this is one way to go. My sample data has all columns as character. You use melt() to reshape your data in a long format. Then, you use dcast() from the same package.
library(magrittr)
library(reshape2)
melt(mydf, measure.vars = names(mydf)) %>%
dcast(variable ~ value, length)
variable a b c d e f
1 a 0 1 0 1 0 1
2 b 0 0 1 0 1 1
3 c 1 0 0 1 0 1
4 d 1 1 0 0 0 1
5 e 1 0 1 0 0 1
6 f 1 0 1 1 0 0
EDIT
As mentioned below by akrun, you can do all work using recast() in the reshape2 package.
recast(mydf, measure.var= names(mydf),variable~value, length)
DATA
mydf <- structure(list(a = c("b", "d", "f"), b = c("c", "f", "e"), c = c("f",
"a", "d"), d = c("a", "b", "f"), e = c("a", "c", "f"), f = c("a",
"c", "d")), .Names = c("a", "b", "c", "d", "e", "f"), class = "data.frame", row.names = c(NA,
-3L))

Just use table:
table(colnames(mydf)[col(mydf)], unlist(mydf) )
# a b c d e f
# a 0 1 0 1 0 1
# b 0 0 1 0 1 1
# c 1 0 0 1 0 1
# d 1 1 0 0 0 1
# e 1 0 1 0 0 1
# f 1 0 1 1 0 0
If you have multiple matches, then:
pmin(table(colnames(mydf)[col(mydf)], unlist(mydf) ), 1)

You can do this with reshaping.
library(dplyr)
library(tidyr)
data %>%
gather(from, to) %>%
distinct %>%
mutate(value = 1) %>%
spread(to, value, fill = 0)

The other solution using dplyr is really neat and smart. I recommend using that solution.
Here is an alternative solution to your problem using most basic functions in R.
Say your data frame has n columns and m rows i.e. n <- ncol(df) and m <- nrow(df).
output_matrix <- matrix(rep(0, n*n), ncol = n)
for(i in 1:n){
for(j in 1:m){
# UTF to integer conversion
# utf8ToInt("a") = 97
rowWithRelation <- utf8ToInt(df[j, i]) - 96
output_matrix[rowWithRelation, i] <- 1
}
}
rownames(output_matrix) <- letters[seq(from = 1, to = n)]
colnames(output_matrix) <- letters[seq(from = 1, to = n)]

Related

create weighted adjacency matrix from data frame R

I have a data frame of the following way
dat <- data.frame(A=c("D", "A", "D", "B"), B=c("B", "B", "D", "R"), C=c("A", "D", "C", ""), D=c("D", "C", "A", "A"))
My idea is to create a matrix with this information, based on the number of occasions that each column variable refers to the other columns (and ignore when referring to other things that are not in one of the columns (e.g. "R")). So I want to fill the following matrix:
n <- ncol(dat)
names_d <- colnames(dat)
mat <- matrix(0, nrow=n, ncol=n)
rownames(mat) <- names_d
colnames(mat) <- names_d
So in the end, I would have something like this:
A B C D
A 1 1 0 2
B 0 2 0 1
C 1 0 1 1
D 2 0 1 1
Which would be the most efficient way of doing this in R?
You can try the code below
> t(sapply(dat, function(x) table(factor(x, levels = names(dat)))))
A B C D
A 1 1 0 2
B 0 2 0 1
C 1 0 1 1
D 2 0 1 1
or
> t(xtabs(~., subset(stack(dat), values != "")))
values
ind A B C D
A 1 1 0 2
B 0 2 0 1
C 1 0 1 1
D 2 0 1 1
Another option is stack with table
table(subset(stack(dat), nzchar(values) & values != 'R'))

What code should be written to create a new variable from observations containing the same content in the R column?

My variable is as follows
variable
D
D
B
C
B
D
C
C
D
I want to make the column in the above figure below
variable
B
C
D
D
0
0
1
D
0
0
1
B
1
0
0
C
0
1
0
B
1
0
0
D
0
0
1
C
0
1
0
C
0
1
0
D
0
0
1
But I don't want a code like the one below. Because the number of factors in the variable column is too many
data = data %>% mutate(B=ifelse(variable=="B", 1,0),
C=ifelse(variable=="C", 1,0),
D=ifelse(variable=="D", 1,0))
Here is a base R approach. We can first find all unique variable values from the data frame. Then, sapply over that vector and generate a new column for each value. Finally, we can rbind this new data frame of 0/1 valued columns to the original data frame.
cols <- sort(unique(df$variable))
df2 <- sapply(cols, function(x) ifelse(df$variable == x, 1, 0))
df <- cbind(df, df2)
df
variable B C D
1 D 0 0 1
2 D 0 0 1
3 B 1 0 0
4 C 0 1 0
5 B 1 0 0
6 D 0 0 1
7 C 0 1 0
8 C 0 1 0
9 D 0 0 1
Data:
df <- data.frame(variable=c("D", "D", "B", "C", "B",
"D", "C", "C", "D"),
stringsAsFactors=FALSE)
Try this with reshaping and duplicating the original variable in order to have a reference for values. Then, you can reshape to obtain the expected output:
library(dplyr)
library(tidyr)
#Code
new <- df %>% mutate(Var=variable,Val=1,id=row_number()) %>%
pivot_wider(names_from = Var,values_from=Val,values_fill = 0) %>%
select(-id)
Output:
# A tibble: 9 x 4
variable D B C
<chr> <dbl> <dbl> <dbl>
1 D 1 0 0
2 D 1 0 0
3 B 0 1 0
4 C 0 0 1
5 B 0 1 0
6 D 1 0 0
7 C 0 0 1
8 C 0 0 1
9 D 1 0 0
Some data used:
#Data
df <- structure(list(variable = c("D", "D", "B", "C", "B", "D", "C",
"C", "D")), class = "data.frame", row.names = c(NA, -9L))
1) model.matrix
model.matrix will generate column names like variableB so the last line removes the variable part to ensure that the column names are exactly the same as in the question. Omit the last line if it is not important that the column names be exactly as shown there.
dat2 <- cbind(dat, model.matrix(~ variable - 1, dat))
names(dat2) <- sub("variable(.)", "\\1", names(dat2))
giving:
> dat2
variable B C D
1 D 0 0 1
2 D 0 0 1
3 B 1 0 0
4 C 0 1 0
5 B 1 0 0
6 D 0 0 1
7 C 0 1 0
8 C 0 1 0
9 D 0 0 1
2) outer
This can also be done using outer as shown. Each component of variable is compared to each level. We name the levels so that outer uses them as column names. The output is the same.
levs <- sort(unique(dat$variable))
names(levs) <- levs
cbind(dat, +outer(dat$variable, levs, `==`))
Note
The input in reproducible form:
Lines <- "
variable
D
D
B
C
B
D
C
C
D"
dat <- read.table(text = Lines, header = TRUE)

R - construct adjacency matrix based on other adjacency matrix

I have data that looks similar to these two adjacency matrices:
data1999 <- data.frame(node1=c("A", "A", "B", "D", "B", "C", "D"),
node2=c("A", "A", "D", "B", "B", "C", "D"),
link=c(1, 1, 1, 1, 1, 1, 1),
stringsAsFactors = FALSE)
adj.m1999 <- reshape2::acast(data1999, node1 ~ node2)
> adj.m1999
A B C D
A 2 0 0 0
B 0 1 0 1
C 0 0 1 0
D 0 1 0 1
data2000 <- data.frame(node1=c("A", "A", "B", "C", "D", "C", "D"),
node2=c("A", "A", "B", "C", "D", "D", "C"),
link=c(1, 1, 1, 1, 1, 1, 1),
stringsAsFactors = FALSE)
adj.m2000 <- reshape2::acast(data2000, node1 ~ node2)
> adj.m2000
A B C D
A 2 0 0 0
B 0 1 0 0
C 0 0 1 1
D 0 0 1 1
Note that in 1999, node D and B have a link.
Note that in 2000, node D and C have a link.
Based on this information, I want to construct a new adjacency matrix (with all the nodes of my 2000 data) in which B-D and D-B have a value of 1 while the rest has a zero:
> result
A B C D
A 0 0 0 0
B 0 0 1 0
C 0 1 0 0
D 0 0 0 0
In my real-life data, data 1999 can have additional nodes that don't return in 2000 and vice versa.
Any ideas?
In graph theory, the product of two adjacency matices m1 and m2 gives in position (i,j) the number of ways to go from i to j, going first through m1 then through m2. This is related to what you want but not exactly the same as, if we do adj.m1999 %*% adj.m2000, we get:
A B C D
A 4 0 0 0
B 0 1 1 1
C 0 0 1 1
D 0 1 1 1
So for example, you can go from C to D in one way, and that would be C -> C, followed by C -> D.
In your example, you don't take into account links (or edges) that are on the diagonal, and also your graph is not directed, so, if I understand correctly what you want, you could do:
## First make sure that you have in adj.m1999 only nodes that appear in adj.m2000:
adj.m1999 = adj.m1999[row.names(adj.m1999) %in% row.names(adj.m2000),colnames(adj.m1999) %in% colnames(adj.m2000)]
## Then turn both diagonals into zeros:
diag(adj.m1999) = 0
diag(adj.m2000) = 0
## Finally, get the sum of the two products
res = adj.m1999 %*% adj.m2000 + adj.m2000 %*% adj.m1999
A B C D
A 0 0 0 0
B 0 0 1 0
C 0 1 0 0
D 0 0 0 0

ordering columns in dataframe based on incomplete vector

I have a vector based on col names which looks like
x <- c("C", "A", "T")
my dataframe looks like with rownames and colnames defined.
names A B C D T
Dan 1 0 1 0 1
Joe 0 1 0 1 0
I want to order the dataframe so the columns in the vector appear first followed by columns not in the vector
names C A T B D
Dan 1 1 1 0 0
Joe 0 0 0 1 1
Thanks
The following will rearrange your data to set the columns specified in the vector x at the beginning, and the remaining columns in their original order afterwards.
x <- c("C", "A", "T")
mydata <- mydata[, c(x, setdiff(names(mydata), x))]
If the names column should stay at the first position and is not specified within x, use (Thanks #StevenBeaupré for pointing it out and providing the code):
mydata <- mydata[, c(names(mydata)[1], x, setdiff(names(mydata)[-1], x))]
Small data example:
mydata <- data.frame(names = c("Dan", "Joe"), A = c(1, 0), B = c(0,1),
C = c(1, 0), D = c(0,1), T = c(1, 0))
> mydata
names A B C D T
1 Dan 1 0 1 0 1
2 Joe 0 1 0 1 0
mydata <- mydata[, c(names(mydata)[1], x, setdiff(names(mydata)[-1], x))]
> mydata
names C A T B D
1 Dan 1 1 1 0 0
2 Joe 0 0 0 1 1

List to dataframe

I have the result of a select_multiple question stored in a list. That comes from a dataset collected with OpenDataKit
example <- list("a", c("b", "c"), c("d", "e", "f"), c(""))
In the example below for the record #4, there were no answers (meaning NA for all options).
I need to create a data frame from this list where each options from the select multiple would become a new variable. Each element of the list is de facto not of the same length.
The result should look like this:
variable | a b c d e f
row1 | 1 0 0 0 0 0
row2 | 0 1 1 0 0 0
row3 | 0 0 0 1 1 1
row4 | <NA> <NA><NA> <NA><NA> <NA>
I have found options with stri_list2matrix but that does not provide the expected results.
I tried as well
df <-data.frame( lNames <- rep(names(example), lapply(example, length)),
lVal <- unlist(example))
and got the same
arguments imply differing number of rows
Please help!
Thanks
You could use setNames, stack and dcast for that:
example <- list("a", c("b", "c"), c("d", "e", "f"), c(""))
example <- setNames(example, seq_along(example))
ex2 <- stack(example)
ex2[ex2$values=='','values'] <- NA
library(reshape2)
dcast(ex2, ind ~ values, fun.aggregate = length)
This will result in:
ind a b c d e f NA
1 1 1 0 0 0 0 0 0
2 2 0 1 1 0 0 0 0
3 3 0 0 0 1 1 1 0
4 4 0 0 0 0 0 0 1

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