CODEWITHSUNDEEP
rsubset
bashful
bashful

Reputation: 13

Exclude data in R based on minimum sample size

I have a data frame that looks kind of like this: 

#1  sampleid     replication    measurement
#2  1            1              0.5
#3  1            2              0.4
#4  1            3              0.3
#5  1            4              0.2
#6  1            5              0.3
#7  2            1              0.5
#8  3            1              0.5
#9  4            1              0.5
#10 4            2              0.3
#11 4            3              0.2
#12 5            1              0.1

This is my second day with R so I'm sorry if this is a rather simple task.

What I would like to do is exclude "measurement" and "sampleid" if the corresponding "replication" is <2. Based on the sample I gave, I'd like to see exclusions in lines #7, #8, and #12.

I tried using a combination of subset and length, but it didn't achieve what I needed. Is there a simple way that I'm missing?

Thanks a lot.

Upvotes: 1

Views: 247

Answers (3)

akrun
akrun

Reputation: 887048

An option using dplyr is

library(dplyr)
dat %>% 
   group_by(sampleid) %>% 
   filter(n() > 1)
#   sampleid replication measurement
#     <int>       <int>       <dbl>
#1        1           1         0.5
#2        1           2         0.4
#3        1           3         0.3
#4        1           4         0.2
#5        1           5         0.3
#6        4           1         0.5
#7        4           2         0.3
#8        4           3         0.2

Upvotes: 0

Zheyuan Li
Zheyuan Li

Reputation: 73265

We can use ave:

subset(dat, ave(replication, sampleid, FUN = length) >= 2)

#   sampleid replication measurement
#1         1           1         0.5
#2         1           2         0.4
#3         1           3         0.3
#4         1           4         0.2
#5         1           5         0.3
#8         4           1         0.5
#9         4           2         0.3
#10        4           3         0.2

Data:

dat <- structure(list(sampleid = c(1L, 1L, 1L, 1L, 1L, 2L, 3L, 4L, 4L, 
4L, 5L), replication = c(1L, 2L, 3L, 4L, 5L, 1L, 1L, 1L, 2L, 
3L, 1L), measurement = c(0.5, 0.4, 0.3, 0.2, 0.3, 0.5, 0.5, 0.5, 
0.3, 0.2, 0.1)), .Names = c("sampleid", "replication", "measurement"
), class = "data.frame", row.names = c(NA, -11L))

Upvotes: 2

parksw3
parksw3

Reputation: 659

subset(data, sampleid %in% unique(data$sampleid[duplicated(data$sampleid)]))

Upvotes: 0

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