R - count occurrences in long vectors - r

I have a dataframe that is 6249 rows long, filled with character-type data and will likely get a lot bigger.
I want to count the number of occurrences of each string. Normally I'd use table(df)
or
count(df)
but they both seem to stop after 250 rows.
Is there a different function or a way to force count() or table() to continue for 6000+ results?

A simple way to do this with any sized data frame is to add a count field to the data frame and then summarize the string field by count with the doBy package - like so:
require(doBy)
df$count <- 1
result <- summaryBy(count ~ string, data = df, FUN = sum, keep.names = TRUE)

As #Gregor noticed it seems like you interpreted the table output wrongly whereas it is actually doing the right counting. Anyway here goes a solution using Reduce, you should replace df where indicated by your dataframe and string column name by the column name of your actual dataframe in which you are counting.
# let's create some dataframe with three strings randomly distributed of length 1000
df <- data.frame(string = unlist(lapply(round(runif(1000, 1, 3)), function(i) c('hi', 'ok', 'my cat')[i])))
my.count <- function(word, df) {
# now let's count how many 'b' we found
Reduce(function(acc, r) {
# replace 'string' by the name of the column of your dataframe over which you want to count
if(r$string == word)
acc + 1
else
acc
}, apply(df, 1, as.list), init = 0)
}
# count how many 'my cat' strings are in the df dataframe at column 'string', replace with yours
my.count('my cat', df)
# now let's try to find the frequency of all of them
uniq <- unique(df$string)
freq <- unlist(lapply(uniq, my.count, df))
names(freq) <- uniq
freq
# output
# ok my cat hi
# 490 261 249
# we can check indeed that the sum is 1000
sum(freq)
# [1] 1000

Well, this won't be popular, but in the end I achieved the desired result with a for loop and and taking the number of rows in a subset.
y <- as.numeric(vector())
x <- as.numeric(vector())
for (i in test$token){
x <- as.numeric(nrow(df[(df$token == i),]))
y <- c(y, x)
}
Y then becomes a vector with the number of occurences of each string.

Related

Count number of entries in each column with result in dataframe

I have a dataframe with many columns. I want to count the number of times something is entered into each column.
#Example data
Gender<-c("","Male","Male","","Female","Female")
location<-c("UK","France","USA","","","")
dataset<-data.frame(Gender,location, stringsAsFactors = FALSE)
There are 4 entries in the gender column and 3 entries in the location column.
I want the results to be in a dataframe such as:
result<-data.frame(Results=c("Gender","location"), Totals=c(4,3))
Can anyone suggest an approach to do this?
You can use the namesof datasetas one column for resultand calculate the Totals by counting how often grep matches anything that is a character (as opposed to nothing in an empty cell):
result <- data.frame(
Results = names(dataset),
Totals = sapply(dataset, function(x) length(grep(".", x)))
)
rownames(result) <- NULL
Result:
result
Results Totals
1 Gender 4
2 location 3
A base R option using stack + colSums
setNames(
rev(stack(colSums(dataset != ""))),
c("Results", "Total")
)
gives
Results Total
1 Gender 4
2 location 3
This should work for you:
ngen <- sum(dataset$Gender != "") #sum number entries in column that are not empty
nloc <- sum(dataset$location != "") #sam thing
Totals <- c(ngen,nloc)
result<-data.frame(Results=c("Gender","location"), Totals)
You can simplify some of the steps if you want, but that would be the detailed way.

Create a function that replace values where n <5 with a random number between 1 and 4 (integer)

I am quite new to R and have run into a problem I apparently can't solve by myself. It should be fairly easy thou.
I aim to write a generic function that manipulates column n in dataframe df. I want it to peform a simple task, for each row, when n < 5 it should replace that value with a random number between 1 and 4.
df <- data.frame(n= 1:10, y = letters[1:10],
stringsAsFactors = FALSE)
What is the most elegant solution?
One way to do is create a logical index based on the column, subset the column based on the index and assign the sampled values
f1 <- function(dat, col) {
i1 <- dat[[col]] < 5
dat[[col]][i1] <- sample(1:4, sum(i1), replace = TRUE)
dat
}
f1(df, "n")

Using apply in R to extract rows from a dataframe

Using R, I have to extract specific rows from a data frame depending on certain conditions. The data frame is large (5.5 million rows to 251 columns) but I have given the code below to create a sample data frame.
df <- data.frame("Name" = c("Name1", "Name1", "Name1", "Name1","Name1" ), "Value"=c("X", "X", "Y", "Y", "X"))
I need to skip through the entire data frame row by row starting at the top, and while skipping, when the value of the 'Value' column changes from X to Y or Y to X, I need to extract that row and next row and append them to another data frame. For example, in the data frame above, the Value column of row 2 is X and that of row 3 is Y, and since the value has changed from X to Y, I need to extract the entire row 2 and row 3 and add them to another data frame.
The result of the operations can be seen by running the code below
dfextract <- data.frame("Name" = c("Name1", "Name1"), "Value"=c("X", "Y"))
Currently I have used a 'for' loop to skip row to row and extract the rows when the values don't match. But it very slow and inefficient. The code snippet is below
for (i in 1:count) {
if (df[[i+1, 2]] != df[i,2]) {
dfextract <- rbind(dfextract, df[i,])
dfextract <- rbind(dfextract, df[i+1,])
}
}
I am looking for a better and faster solution to the above situation. Perhaps using the functions belonging to the family of 'apply()' or using 'by()'. Any help would be greatly appreciated.
Thanks in advance.
Maybe the following does it. Note that there are two lapply based loop, in order to predict for changes in the values of column Name.
diffstr <- function(x) x[-1] == x[-length(x)]
res <- lapply(split(df, df$Name), function(x) {
inx <- which(c(FALSE, !diffstr(x$Value)))
do.call(rbind, lapply(inx, function(i) x[(i - 1):i, ]))
})
res <- do.call(rbind, res)
row.names(res) <- NULL
res
How it works.
First, I define a helper function diffstr. It compares all values of x but the first with all values of x but the last. Note that x[-1] is the vector x[2], x[3], ..., x[length(x)], negative indices remove that element from the vector. And the same for x[-length(x), the negative index removes the last x.
split(df, df$Name) splits the data frame into subsets each one of its own Name.
I then lapply an unnamed function to these subsets. This function's argument x will be each of the sub-data frames mentioned above.
That function start by determining where in df$Valueare the changes. This is done with the call to the helper function diffstr. I have to append a FALSE to the return value because at first there are no changes.
The next line is a tricky one. Use lapply on the index of change points inx and for each one get a two rows segment of the data frame x. Then use do.call to call rbind those two rows df's and reassemble them together.
Now res is a list, with one sub-data frame for each Name (done with the split). So it needs to be put back together with another call to do.call(rbind(...)).
Final tidy up. The whole process messed up with the data frame's row names. To set them to NULL is just a well known trick that forces R to renumber the rows.
That's it. If you need more explanations, just say so.
We can use dplyr. lag can shift the row by 1, so we can use Value != lag(Value) to compare if the value is different than the previous one. which(Value != lag(Value)) converts the result to row number. After that, sort(unique(unlist(lapply(which(Value != lag(Value)), function(x) c(x, x - 1))))) makes sure we also got the row number of those previous rows. Finally, slice can subset the data frame based on the row number provided.
library(dplyr)
df2 <- df %>%
slice(sort(unique(unlist(lapply(which(Value != lag(Value)), function(x) c(x, x - 1))))))
df2
# A tibble: 4 x 2
Name Value
<fctr> <fctr>
1 Name1 X
2 Name1 Y
3 Name1 Y
4 Name1 X
If the code is too long to read, you can also calculate the index before using the slice function as follows.
library(dplyr)
ind <- which(df$Value != lag(df$Value))
ind2 <- sort(unique(c(ind, ind - 1)))
df2 <- df %>% slice(ind2)
df2
# A tibble: 4 x 2
Name Value
<fctr> <fctr>
1 Name1 X
2 Name1 Y
3 Name1 Y
4 Name1 X
Using base R, I would probably use an id for the rows and with diff:
df <- data.frame(colA=c(1, 1, 1, 2, 1, 1, 1, 3, 3, 3, 1, 1),
colB=1:12)
keep <- which(diff(df$colA) != 0)
df[unique(c(keep, keep+1)), ]
colA colB
3 1 3
4 2 4
7 1 7
10 3 10
5 1 5
8 3 8
11 1 11
There is probably a faster option though.
When you have a large dataset, speed might be the bottleneck. In this case data.table might be the best option for you.
Using the data.table-library, I would solve it like so:
library(data.table)
dt <- data.table(Name = c("Name1", "Name1", "Name1", "Name1","Name1" ),
Value = c("X", "X", "Y", "Y", "X"))
# look if Value changes to the next instance
dt[, idx := Value != shift(Value, 1, fill = dt$Value[1])]
# filter the rows where the index changes and the next value
# and deselect the variable idx
dt[idx | shift(idx, 1)][, .(Name, Value)]
#> Name Value
#> 1: Name1 Y
#> 2: Name1 Y
#> 3: Name1 X
Why does it give an odd-number and not an even-number?
Well, that is because in your data example, the last row should be selected as it changes, but there is no next row to select as well.

extract highest and lowest values for columns in R, as well as row identifiers

Say I have some data of the following kind:
df<-as.data.frame(matrix(rnorm(10*10000, 1, .5), ncol=10))
I want a new dataframe that keeps the 10 original columns, but for every column retains only the highest 10 and lowest 10 values. Importantly, the rows have names corresponding to id values that need to be kept in the new data frame.
Thus, the end result data.frame is gonna be of dimensions m by 10, where m is very likely to be more than 20. But for every column, I want only 20 valid values.
The only way I can think of doing this is doing it manually per column, using dplyr and arrange, grabbing the top and bottom rows, and then creating a matrix from all the individual vectors. Clearly this is inefficient. Help?
Assuming you want to keep all the rows from the original dataset, where there is at least one value satisfying your condition (value among ten largest or ten smallest in the given column), you could do it like this:
# create a data frame
df<-as.data.frame(matrix(rnorm(10*10000, 1, .5), ncol=10))
# function to find lowes 10 and highest 10 values
lowHigh <- function(x)
{
test <- x
test[!(order(x) <= 10 | order(x) >= (length(x)- 10))] <- NA
test
}
# apply the function defined above
test2 <- apply(df, 2, lowHigh)
# use the original rownames
rownames(test2) <- rownames(df)
# keep only rows where there is value of interest
finalData <- test2[apply(apply(test2, 2, is.na), 1, sum) < 10, ]
Please note that there is definitely some smarter way of doing it...
Here is the data matrix with 10 highest and 10 lowest in each column,
x<-apply(df,2,function(k) k[order(k,decreasing=T)[c(1:10,(length(k)-9):length(k))]])
x is your 20 by 10 matrix.
Your requirement of rownames is conflicting column by column, altogether you only have 20 rownames in this matrix and it can not be same for all 10 columns. Instead, here is your order matrix,
x_roworder<-apply(df,2,function(k) order(k,decreasing=T)[c(1:10,(length(k)-9):length(k))])
This will give you corresponding rows in original data matrix within each column.
I offer a couple of answers to this.
A base R implementation ( I have used %>% to make it easier to read)
ix = lapply(df, function(x) order(x)[-(1:(length(x)-20)+10)]) %>%
unlist %>% unique %>% sort
df[ix,]
This abuses the fact that data frames are lists, finds the row id satisfying the condition for each column, then takes the unique ones in order as the row indices you want to keep. This should retain any row names attached to df
An alternative using dplyr (since you mentioned it) which if I remember correctly doesn't particular like row names
# add id as a variable
df$id = 1:nrow(df) # or row names
df %>%
gather("col",value,-id) %>%
group_by(col) %>%
filter(min_rank(value) <= 10 | min_rank(desc(value)) <= 10) %>%
ungroup %>%
select(id) %>%
left_join(df)
Edited: To fix code alignment and make a neater filter
I'm not entirely sure what you're expecting for your return / output. But this will get you the appropriate indices
# example data
set.seed(41234L)
N <- 1000
df<-data.frame(id= 1:N, matrix(rnorm(10*N, 1, .5), ncol=10))
# for each column, extract ID's for top 10 and bottom 10 values
l1 <- lapply(df[,2:11], function(x,y, n) {
xy <- data.frame(x,y)
xy <- xy[order(xy[,1]),]
return(xy[c(1:10, (n-9):n),2])
}, y= df[,1], n = N)
# check:
xx <- sort(df[,2])
all.equal(sort(df[l1[[1]], 2]), xx[c(1:10, 991:1000)])
[1] TRUE
If you want an m * 10 matrix with these unique values, where m is the number of unique indices, you could do:
l2 <- do.call("c", l1)
l2 <- unique(l2)
df2 <- df[l2,] # in this case, m == 189
This doesn't 0 / NA the columns which you're not searching on for each row. But it's unclear what your question is trying to do.
Note
This isn't as efficient as using data.table since you're going to get a copy of the data in xy <- data.frame(x,y)
Benchmark
library(microbenchmark)
microbenchmark(ira= {
test2 <- apply(df[,2:11], 2, lowHigh);
rownames(test2) <- rownames(df);
finalData <- test2[apply(apply(test2, 2, is.na), 1, sum) < 10, ]
},
alex= {
l1 <- lapply(df[,2:11], function(x,y, n) {
xy <- data.frame(x,y)
xy <- xy[order(xy[,1]),]
return(xy[c(1:10, (n-9):n),2])
}, y= df[,1], n = N);
l2 <- unique(do.call("c", l1));
df2 <- df[l2,]
}, times= 50L)
Unit: milliseconds
expr min lq mean median uq max neval cld
ira 4.360452 4.522082 5.328403 5.140874 5.560295 8.369525 50 b
alex 3.771111 3.854477 4.054388 3.936716 4.158801 5.654280 50 a

Passing vector with multiple values into R function to generate data frame

I have a table, called table_wo_nas, with multiple columns, one of which is titled ID. For each value of ID there are many rows. I want to write a function that for input x will output a data frame containing the number of rows for each ID, with column headers ID and nobs respectively as below for x <- c(2,4,8).
## id nobs
## 1 2 1041
## 2 4 474
## 3 8 192
This is what I have. It works when x is a single value (ex. 3), but not when it contains multiple values, for example 1:10 or c(2,5,7). I receive the warning "In ID[counter] <- x : number of items to replace is not a multiple of replacement length". I've just started learning R and have been struggling with this for a week and have searched manuals, this site, Google, everything. Can someone help please?
counter <- 1
ID <- vector("numeric") ## contain x
nobs <- vector("numeric") ## contain nrow
for (i in x) {
r <- subset(table_wo_nas, ID %in% x) ## create subset for rows of ID=x
ID[counter] <- x ## add x to ID
nobs[counter] <- nrow(r) ## add nrow to nobs
counter <- counter + 1 } ## loop
result <- data.frame(ID, nobs) ## create data frame
In base R,
# To make a named vector, either:
tmp <- sapply(split(table_wo_nas, table_wo_nas$ID), nrow)
# OR just:
tmp <- table(table_wo_nas$ID)
# AND
# arrange into data.frame
nobs_df <- data.frame(ID = names(tmp), nobs = tmp)
Alternately, coerce the table into a data.frame directly, and rename:
nobs_df <- data.frame(table(table_wo_nas$ID))
names(nobs_df) <- c('ID', 'nobs')
If you only want certain rows, subset:
nobs_df[c(2, 4, 8), ]
There are many, many more options; these are just a few.
With dplyr,
library(dplyr)
table_wo_nas %>% group_by(ID) %>% summarise(nobs = n())
If you only want certain IDs, add on a filter:
table_wo_nas %>% group_by(ID) %>% summarise(nobs = n()) %>% filter(ID %in% c(2, 4, 8))
Seems pretty straightforward if you just use table again:
tbl <- table( table_wo_nas[ , 'ID'] )
data.frame( IDs = names(tbl), nobs= tbl)
Could also get a quick answer although with different column names using:
as.data.frame(table( table_wo_nas[ , 'ID'] ))
Try this.
x=c(2,4,8)
count_of_id=0
#df is your data frame table_wo_nas
count_of<-function(x)
{for(i in 1 : length(x))
{count_of_id[i]<-length(which(df$id==x[i])) #find out the n of rows for each unique value of x
}
df_1<-cbind(id,count_of_id)
return(df_1)
}

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