James White James White - 1 year ago 79
R Question

Problems subsetting columns based on values from two separate dataframes

I am using data obtained from a spatially gridded system, for example a city divided up into equally spaced squares (e.g. 250m2 cells). Each cell possesses a unique column and row number with corresponding numerical information about the area contained within this 250m2 square (say temperature for each cell across an entire city). Within the entire gridded section (or the example city), I have various study sites and I know where they are located (i.e. which cell row and column each site is located within). I have a dataframe containing information on all cells within the city, but I want to subset this to only contain information from the cells where my study sites are located. I previously asked a question on this 'Matching information from different dataframes and filtering out redundant columns'. Here is some example code again:

###Dataframe showing cell values for my own study sites
Site <- as.data.frame(c("Site.A","Site.B","Site.C"))
Row <- as.data.frame(c(1,2,3))
Column <- as.data.frame(c(5,4,3))
df1 <- cbind(Site,Row, Column)
colnames(df1) <- c("Site","Row","Column")

###Dataframe showing information from ALL cells
eg1 <- rbind(c(1,2,3,4,5),c(5,4,3,2,1)) ##Cell rows and columns
eg2 <- as.data.frame(matrix(sample(0:50, 15*10, replace=TRUE), ncol=5)) ##Numerical information
df2 <- rbind(eg1,eg2)
rownames(df2)[1:2] <- c("Row","Column")

From this, I used the answer from the previous questions which worked perfectly for the example data.

output <- df2[, (df2['Row', ] %in% df1$Row) & (df2['Column', ] %in% df1$Column)]
names(output) <- df1$Site[mapply(function(r, c){which(r == df1$Row & c == df1$Column)}, output[1,], output[2,])]

However, I cannot apply this to my own data and cannot figure out why.

EDIT: Initially, I thought there was a problem with naming the columns (i.e. the 'names' function). But it would appear there may be an issue with the 'output' line of code, whereby columns are being included from df2 that shouldn't be (i.e. the output contained columns from df2 which possessed column and row numbers not specified within df1).

I have also tried:

output <- df2[, (df2['Row', ] == df1$Row) & (df2['Column', ] == df1$Column)]

But when using my own (seemingly comparable) data, I don't get information from all cells specified in the 'df1' equivalent (although again works fine in the example data above). I can get my own data to work if I do each study site individually.

SiteA <- df2[, which(df2['Row', ] == 1) & (df2['Column', ] == 5)]
SiteB <- df2[, which(df2['Row', ] == 2) & (df2['Column', ] == 4)]
SiteC <- df2[, which(df2['Row', ] == 3) & (df2['Column', ] == 3)]

But I have 1000s of sites and was hoping for a more succinct way. I am sure that I have maintained the same structure, double checked spellings and variable names. Would anyone be able to shed any light on potential things which I could be doing wrong? Or failing this an alternative method?

Apologies for not providing an example code for the actual problem (I wish I could pinpoint what the specific problem is, but until then the original example is the best I can do)! Thank you.

Answer Source

The only apparent issue I can see is that mapply is not wrapped around unlist. mapply returns a list, which is not what you're after for subsetting purposes. So, try:

output <- df2[, (df2['Row', ] %in% df1$Row) & (df2['Column', ] %in% df1$Column)]
names(output) <- df1$Site[unlist(mapply(function(r, c){which(r == df1$Row & c == df1$Column)}, output[1,], output[2,]))]


If the goal is to grab columns whose first 2 rows match the 2nd and 3rd elements of a given row in df1, you can try the following:

output_df <- Filter(function(x) !all(is.na(x)), data.frame(do.call(cbind,apply(df2, 2, function(x) {
  ##Create a condition vector for an if-statement or for subsetting
  condition <- paste0(x[1:2], collapse = "") == apply(df1[,c('Row','Column')], 1, function(y) {
    paste0(y,collapse = "")
  ##Return a column if it meets the condition (first 2 rows are matched in df1)
  if(sum(condition) != 0) {
    tempdf <- data.frame(x)
    names(tempdf) <- df1[condition,]$Site[1]
  } else {
    ##If they are not matched, then return an empty column

It is quite a condensed piece of code, so I hope the following explanation will help clarify some things:

This basically goes through every column in df2 (with apply(df2, 2, FUN)) and checks if its first 2 rows can be found in the 2nd and 3rd elements of every row in df1. If the condition is met, then it returns that column in a data.frame format with its column name being the value of Site in the matching row in df1; otherwise an empty column (with NA's) is returned. These columns are then bound together with do.call and cbind, and then coerced into a data.frame. Finally, we use the Filter function to remove columns whose values are NA's.

All that should give the following:

Site.A Site.B Site.C
  1      2      3    
  5      4      3    
 40     42     33    
 13     47     25    
 23      0     34    
  2     41     17    
 10     29     38    
 43     27      8    
 31      1     25    
 31     40     31    
 34     12     43    
 43     30     46    
 46     49     25    
 45      7     17    
  2     13     38    
 28     12     12    
 16     19     15    
 39     28     30    
 41     24     30    
 10     20     42    
 11      4      8    
 33     40     41    
 34     26     48    
  2     29     13    
 38      0     27    
 38     34     13    
 30     29     28    
 47      2     49    
 22     10     49    
 45     37     30    
 29     31      4    
 25     24     31

I hope this helps.

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