Find string in data.frame - r

How do I search for a string in a data.frame? As a minimal example, how do I find the locations (columns and rows) of 'horse' in this data.frame?
> df = data.frame(animal=c('goat','horse','horse','two', 'five'), level=c('five','one','three',30,'horse'), length=c(10, 20, 30, 'horse', 'eight'))
> df
animal level length
1 goat five 10
2 horse one 20
3 horse three 30
4 two 30 horse
5 five horse eight
... so row 4 and 5 have the wrong order. Any output that would allow me to identify that 'horse' has shifted to the level column in row 5 and to the length column in row 4 is good. Maybe:
> magic_function(df, 'horse')
col row
'animal', 2
'animal', 3
'length', 4
'level', 5
Here's what I want to use this for: I have a very large data frame (around 60 columns, 20.000 rows) in which some columns are messed up for some rows. It's too large to eyeball in order to identify the different ways that order can be wrong, so searching would be nice. I will use this info to move data to the correct columns for these rows.

What about:
which(df == "horse", arr.ind = TRUE)
# row col
# [1,] 2 1
# [2,] 3 1
# [3,] 5 2
# [4,] 4 3

Another way around:
l <- sapply(colnames(df), function(x) grep("horse", df[,x]))
$animal
[1] 2 3
$level
[1] 5
$length
[1] 4
If you want the output to be matrix:
sapply(l,'[',1:max(lengths(l)))
animal level length
[1,] 2 5 4
[2,] 3 NA NA

We can get the indices where the value is equal to horse. Divide it by number of rows (nrow) to get the column indices and by columns (ncol) to get the row indices.
We use colnames to get column names instead of indices.
data.frame(col = colnames(df)[floor(which(df == "horse") / (nrow(df) + 1)) + 1],
row = floor(which(df == "horse") / ncol(df)) + 1)
# col row
#1 animal 1
#2 animal 2
#3 level 4
#4 length 5

Another way to do it is the following:
library(data.table)
library(zoo)
library(dplyr)
library(timeDate)
library(reshape2)
data frame name = tbl_account
first,Transpose it :
temp = t(tbl_Account)
Then, put it in to a list :
temp = list(temp)
This essentially puts every single observation in a data frame in to one massive string, allowing you to search the whole data frame in one go.
then do the searching :
temp[[1]][grep("Horse",temp[[1]])] #brings back the actual value occurrences
grep("Horse", temp[[1]]) # brings back the position of the element in a list it occurs in
hope this helps :)

Related

Function to recode multiple variables conditional on other variables

I have a dataset with multiple variables. Each question has the actual survey answer and three other characteristics. So there are four variables for each question. I want to specify if Q135_L ==1 , leave Q135_RT as it is, otherwise code it as NA. I can do that with an ifelse statement.
df$Q135_RT <- ifelse(df$Q135_L == 1, df$Q22_RT, NA)
However, I have hundreds of variables and the names are not related. For example, in the picture we can see Q135, SG1_1 and so on. How can I specify for the whole dataset if a variable ends at _L, then for the same variable ending at _RT should remain as it is, otherwise the variable ending at _RT should be coded as NA.
I tried this but it only returns NAs
ifelse(grepl("//b_L" ==1, df), "//b_RT" , NA)
If I understand your problem correctly, you have a data frame of which the columns represent survey question variables. Each column contains two identifiers, namely: a survey question number (134, 135, etc) and a variable letter (L, R, etc). Because you provide no reproducible example, I tried to make a simplified example of your data frame:
set.seed(5)
DF <- data.frame(array(sample(1:4, 24, replace = TRUE), c(4,6)))
colnames(DF) <- c("Q134_L","Q135_L", "Q134_R", "Q135_R", "Q_L1", "Q134_S")
DF
# Q134_L Q135_L Q134_R Q135_R Q_L1 Q134_S
# 1 2 3 2 3 1 1
# 2 3 1 3 2 4 4
# 3 1 1 3 2 4 3
# 4 3 1 3 3 2 1
What you want is that if Q135_L == 1, leave Q135_RT as it is, otherwise code it as NA. Here is a function that implements this recoding logic:
recode <- function(yourdf, questnums) {
for (k in 1:length(questnums)) {
charnum <- as.character(questnums)
col_end_L_k <- yourdf[grepl("_L\\b", colnames(yourdf)) &
grepl(charnum[k], colnames(yourdf))]
col_end_R_k <- yourdf[grepl("_RT\\b", colnames(yourdf)) &
grepl(charnum[k], colnames(yourdf))]
row_is_1 <- which(col_end_L_k == 1)
col_end_R_k[-row_is_1, ] <- NA
yourdf[, colnames(col_end_R_k)] <- col_end_R_k
}
return(yourdf)
}
This function takes a data frame and a vector of question numbers, and then returns the data frame that has been recoded.
What this function does:
Selecting each question number using for.
Using grepl to identify any column that contains the selected number and contains _L at the end of the column name.
Similar with above but for _RT at the end of the column name.
Using which to identify the location of rows in the _L column that contain 1.
Keeping the values of the _RT column, which has the same question number with the corresponding _L column, in those rows, and change values on other rows to NA.
The result:
recode(DF, 134:135)
# Q134_L Q135_L Q134_RT Q135_RT Q_L1 Q134_S
# 1 2 3 NA NA 1 1
# 2 3 1 NA 2 4 4
# 3 1 1 3 2 4 3
# 4 3 1 NA 3 2 1
Note that the Q_L1 column is not affected because _L in this column is not located on the end of the column name.
As for how to define questnums, the question numbers, you just need to create a numeric vector. Examples:
Your questnums are 1 to 200. Then use 1:200 or seq(200), so recode(DF, 1:200).
Your questnums are 1, 3, 134, 135. Then, use recode(DF, c(1, 3, 134, 135)).
You can also assign the question numbers to an object first, such as n = c(25, 135, 145) and the use it : recode(DF, n)

How can I create a vector of row numbers from a matrix in R (order of acquisition)?

I have two files. The first file is a data frame that is simply times in one column and individuals in a second
# [Time] [Individual]
# [1] 1528142 C5A1790
# [2] 1528142 C5A1059
# [3] 1528142 C5A1084
# [4] 1528142 C5A1564
# [5] 1528142 C5A1239
# [6] 1528142 C5A1180
the second is an N X N matrix in which both rows and columns are individuals, including those in the first matrix.
# [C5A1084] [C5A1059] [C5A1790] [C5A1180]
# 1 [C5A1084] 0 0.5 1 0
# 2 [C5A1059] 0.5 0 0 1
# 3 [C5A1790] 1 1 0 0.5
# 4 [C5A1180] 0 1 0.5 0
I need to create a vector containing the row numbers in the matrix at which I can find the individuals from the data frame, and in the order that they are listed in the data frame. For these example data it would be (3,2,1,4).
I tried to use the which() function as
RingIndex <- which(Matrix$IDcolumn == FrameIDs)
and received the "longer object length is not a multiple of shorter object length" message, presumably because the matrix includes more individuals than the data frame. %in% and match() are also returning errors stating that replacement has fewer rows than data.
Following the advice in the comments, I tried
RingIndex <- which(Matrix$IDcolumn %in% FrameIDs)
which successfully returned the correct row numbers, but in ascending order rather than the order of the original data. The match() function continues to complain of different replacement and original lengths.
What approach could I use to get my vector?
Many thanks!
df <- data.frame(Time = runif(6,1528142,1528150),
Individuals = c("C5A1790","C5A1791","C5A1792","C5A1793","C5A1794","C5A1795"))
> df
Time Individuals
1 1528144 C5A1790
2 1528143 C5A1791
3 1528144 C5A1792
4 1528148 C5A1793
5 1528145 C5A1794
6 1528143 C5A1795
nnMatrix <- matrix(runif(36,0,1),6,6)
colnames(nnMatrix) <- df$Individuals
rownames(nnMatrix) <- df$Individuals
> nnMatrix
C5A1790 C5A1791 C5A1792 C5A1793 C5A1794 C5A1795
C5A1790 0.08096946 0.8716328 0.6895134 0.05692825 0.4555460 0.53224424
C5A1791 0.42568532 0.5920239 0.4523232 0.11516185 0.8053652 0.72299411
C5A1792 0.42439187 0.6101881 0.8534429 0.86010851 0.1269521 0.41066857
C5A1793 0.26043345 0.8011337 0.8032234 0.30930988 0.2298927 0.93320166
C5A1794 0.43065533 0.2161525 0.6702832 0.89304071 0.6765714 0.09769635
C5A1795 0.70594252 0.1048099 0.7478553 0.87839534 0.5173364 0.69957502
> sapply(df$Individuals, function(t) which(colnames(nnMatrix) == t))
[1] 1 2 3 4 5 6
If you change the order
colnames(nnMatrix) <- rev(colnames(nnMatrix))
[1] 6 5 4 3 2 1
You may want to check for repetition and missing values, but the main approach is the same.
As suggested in the comments (#GKi) also match will work
> match(df$Individuals,colnames(nnMatrix))
[1] NA 1 3 4 5 6

R: Subset data frame based on multiple values for multiple variables

I need to pull records from a first data set (called df1 here) based on a combination of specific dates, ID#s, event start time, and event end time that match with a second data set (df2). Everything works fine when there is just 1 date, ID, and event start and end time, but some of the matching records between the data sets contain multiple IDs, dates, or times, and I can't get the records from df1 to subset properly in those cases. I ultimately want to put this in a FOR loop or independent function since I have a rather large dataset. Here's what I've got so far:
I started just by matching the dates between the two data sets as follows:
match_dates <- as.character(intersect(df1$Date, df2$Date))
Then I selected the records in df2 based on the first matching date, also keeping the other columns so I have the other ID and time information I need:
records <- df2[which(df2$Date == match_dates[1]), ]
The date, ID, start, and end time from records are then:
[1] "01-04-2009" "599091" "12:00" "17:21"
Finally I subset df1 for before and after the event based on the date, ID, and times in records and combined them into a new data frame called final to get at the data contained in df1 that I ultimately need.
before <- subset(df1, NUM==records$ID & Date==records$Date & Time<records$Start)
after <- subset(df1, NUM==records$ID & Date==records$Date & Time>records$End)
final <- rbind(before, after)
Here's the real problem - some of the matching dates have more than 1 corresponding row in df2, and return multiple IDs or times. Here is what an example of multiple records looks like:
records <- df2[which(df2$Date == match_dates[25]), ]
> records$ID
[1] 507646 680845 680845
> records$Date
[1] "04-02-2009" "04-02-2009" "04-02-2009"
> records$Start
[1] "09:43" "05:37" "11:59"
> records$End
[1] "05:19" "11:29" "16:47"
When I try to subset df1 based on this I get an error:
before <- subset(df1, NUM==records$ID & Date==records$Date & Time<records$Start)
Warning messages:
1: In NUM == records$ID :
longer object length is not a multiple of shorter object length
2: In Date == records$Date :
longer object length is not a multiple of shorter object length
3: In Time < records$Start :
longer object length is not a multiple of shorter object length
Trying to do it manually for each ID-date-time combination would be way to tedious. I have 9 years worth of data, all with multiple matching dates for a given year between the data sets, so ideally I would like to set this up as a FOR loop, or a function with a FOR loop in it, but I can't get past this. Thanks in advance for any tips!
If you're asking what I think you are the filter() function from the dplyr package combined with the match function does what you're looking for.
> df1 <- data.frame(A = c(rep(1,4),rep(2,4),rep(3,4)), B = c(rep(1:4,3)))
> df1
A B
1 1 1
2 1 2
3 1 3
4 1 4
5 2 1
6 2 2
7 2 3
8 2 4
9 3 1
10 3 2
11 3 3
12 3 4
> df2 <- data.frame(A = c(1,2), B = c(3,4))
> df2
A B
1 1 3
2 2 4
> filter(df1, A %in% df2$A, B %in% df2$B)
A B
1 1 3
2 1 4
3 2 3
4 2 4

Add index numbers when converting sorted table to dataframe

I have a vector of strings that I'm trying to convert into a data frame with a frequency column. So far so good, but when I dim my data frame, I get only one column instead of two. I guess R is using the words as the index values.
Anyway here is how it starts. My list:
a<-c("welcoming", "whatsyourexcuse", "whiteway", "zero", "yay", "whatsyourexcuse", "yay")
Then, I tried to sort the frequency values in decreasing order and store as data frame using:
df <- as.data.frame(sort(table(a), decreasing=TRUE))
Problem is when I dim(df) I get [1] 5 1 instead of [1] 5 2. Here is what df looks like:
sort(table(a), decreasing = TRUE)
whatsyourexcuse 2
yay 2
welcoming 1
whiteway 1
zero 1
instead of:
a Freq
[1] whatsyourexcuse 2
[2] yay 2
[3] welcoming 1
[4] whiteway 1
[5] zero 1
Any pointers please? Thanks.
Try:
library(plyr)
a1 <- count(a)
a1[order(-a1$freq),]
# x freq
# 2 whatsyourexcuse 2
# 4 yay 2
# 1 welcoming 1
# 3 whiteway 1
# 5 zero 1
dim(a1)
#[1] 5 2
Or
a2 <- stack(sort(table(a),decreasing=TRUE))[,2:1]
dim(a2)
#[1] 5 2
When you are converting to data.frame using as.data.frame(sort(table(a), decreasing=TRUE)), the names of the elements become the rownames of the dataframe, so you are creating only one column instead of two. When you do sort, it no longer is the table object. For comparison check str(table(a)) and str(sort(table(a), decreasing=TRUE)))
You can also create the data.frame by
tbl <- sort(table(a), decreasing=TRUE)
data.frame(col1= names(tbl), Values= as.vector(tbl))

Subset based on granularity and average values

I have large data-frame consists of two columns. I want to calculate the average of the second column values for each subset of the first column. The subset of the first column is based on a specified granularity. For example, for the following data-frame, df, I want to calculate the average of df$B values for each subset of df$A with an increment(granularity) of 1 for each subset. The results should be in two new columns.
A B expected results newA newB
0.22096 1 0 1.142857
0.33489 1 1 2
0.33655 1 2 4
0.43953 1
0.64933 2
0.86668 1
0.96932 1
1.09342 2
1.58314 2
1.88481 2
2.07654 4
2.34652 3
2.79777 5
This is a simple example, I'm not sure how to loop over the whole data-frame and perform the calculation i.e. the average of the df$B.
tried below to subset, but couldn't figure how to append the results and create final results:
Tried something like :
increment<-1
mx<-max(df$A)
i<-0
newDF<-data.frame()
while(i < mx){
tmp<-subset(df, (A >i & A< (i+increment)))
i<-i+granualrity
}
Not sure about the logic. But I'm sure there is a short way to do the required calculation. Any thoughts?
I would use findInterval for the subset selection (In your example a simple ceiling for each A value should be sufficient, too. But if your increment is different from 1 you need findInterval.) and tapply to calculate the mean:
df <- read.table(textConnection("
A B
0.22096 1
0.33489 1
0.33655 1
0.43953 1
0.64933 2
0.86668 1
0.96932 1
1.09342 2
1.58314 2
1.88481 2
2.07654 4
2.34652 3
2.79777 5"), header=TRUE)
## sort data.frame by column A (needed for findInterval)
df <- df[order(df$A), ]
## define granuality
subsets <- seq(1, max(ceiling(df$A)), by=1) # change the "by" argument for different increments
df$subset <- findInterval(df$A, subsets)
tapply(df$B, df$subset, mean)
# 0 1 2
#1.142857 2.000000 4.000000

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