How to replace an NA with an equivalent value from elsewhere in a dataset?

Question

I tried looking for a similar question but couldn't find one. If you do please let me know!

I've been working on a project looking at grain staples

Here is a subset of my dataset:

                nutrient.component.      grain nutrients
1                Beta-carotene (μg) White Rice      0.00
2                Beta-carotene (μg) Brown Rice        NA
3                      Calcium (mg) White Rice     28.00
4                      Calcium (mg) Brown Rice     23.00
5                 Carbohydrates (g) White Rice     80.00
6                 Carbohydrates (g) Brown Rice     77.00
7                       Copper (mg) White Rice      0.22
8                       Copper (mg) Brown Rice        NA
9                       Energy (kJ) White Rice   1528.00
10                      Energy (kJ) Brown Rice   1549.00
11                          Fat (g) White Rice      0.66
12                          Fat (g) Brown Rice      2.92
13                        Fiber (g) White Rice      1.30
14                        Fiber (g) Brown Rice      3.50
15           Folate Total (B9) (μg) White Rice      8.00
16           Folate Total (B9) (μg) Brown Rice     20.00
17                        Iron (mg) White Rice      0.80
18                        Iron (mg) Brown Rice      1.47
19           Lutein+zeaxanthin (μg) White Rice      0.00
20           Lutein+zeaxanthin (μg) Brown Rice        NA
21                   Magnesium (mg) White Rice     25.00
22                   Magnesium (mg) Brown Rice    143.00
23                   Manganese (mg) White Rice      1.09
24                   Manganese (mg) Brown Rice      3.74
25  Monounsaturated fatty acids (g) White Rice      0.21
26  Monounsaturated fatty acids (g) Brown Rice      1.05
27                 Niacin (B3) (mg) White Rice      1.60
28                 Niacin (B3) (mg) Brown Rice      5.09
29       Pantothenic acid (B5) (mg) White Rice      1.01
30       Pantothenic acid (B5) (mg) Brown Rice      1.49
31                  Phosphorus (mg) White Rice    115.00
32                  Phosphorus (mg) Brown Rice    333.00
33  Polyunsaturated fatty acids (g) White Rice      0.18
34  Polyunsaturated fatty acids (g) Brown Rice      1.04
35                   Potassium (mg) White Rice    115.00
36                   Potassium (mg) Brown Rice    223.00
37                      Protein (g) White Rice      7.10
38                      Protein (g) Brown Rice      7.90
39              Riboflavin (B2)(mg) White Rice      0.05
40              Riboflavin (B2)(mg) Brown Rice      0.09
41        Saturated fatty acids (g) White Rice      0.18
42        Saturated fatty acids (g) Brown Rice      0.58
43                    Selenium (μg) White Rice     15.10
44                    Selenium (μg) Brown Rice        NA
45                      Sodium (mg) White Rice      5.00
46                      Sodium (mg) Brown Rice      7.00
47                        Sugar (g) White Rice      0.12
48                        Sugar (g) Brown Rice      0.85
49                 Thiamin (B1)(mg) White Rice      0.07
50                 Thiamin (B1)(mg) Brown Rice      0.40
51                   Vitamin A (IU) White Rice      0.00
52                   Vitamin A (IU) Brown Rice      0.00
53                  Vitamin B6 (mg) White Rice      0.16
54                  Vitamin B6 (mg) Brown Rice      0.51
55                   Vitamin C (mg) White Rice      0.00
56                   Vitamin C (mg) Brown Rice      0.00
57 Vitamin E, alpha-tocopherol (mg) White Rice      0.11
58 Vitamin E, alpha-tocopherol (mg) Brown Rice      0.59
59                  Vitamin K1 (μg) White Rice      0.10
60                  Vitamin K1 (μg) Brown Rice      1.90
61                        Water (g) White Rice     12.00
62                        Water (g) Brown Rice     10.00
63                        Zinc (mg) White Rice      1.09
64                        Zinc (mg) Brown Rice      2.02

Brown Rice has four NA values.
Based on this graphic, I think it would be fair to assume that the NA values for Brown Rice will be very close to the equivalent value for White Rice. And that it would be more accurate to mirror the white rice values rather than convert the values to zero.

My question is, besides manually looking up and inputting the white rice equivalent nutrient for brown rice, how would the code look to replace NA with the equivalent value for white rice? I would expect the result to convert the NA value for Copper; Brown Rice to be the same value as Copper; White Rice (which is 0.22). Would it be better to first replace NA with zero? But if I do that then I have six nutrients with a value of zero rather than four values with NA. I am trying to figure out the right mindset to solve this through code. Any insight into this would be greatly appreciated.

Thank you

Answer 1

Assuming that the data frame of your input data is called dt, we can use the fill function from the tidyr package to achieve this task. dt2 is the final output.

library(tidyr)

dt2 <- dt %>% fill(nutrients)

dt2
  nutrient.component.                         grain nutrients
1                   1 Beta-carotene (µg) White Rice      0.00
2                   2 Beta-carotene (µg) Brown Rice      0.00
3                   3       Calcium (mg) White Rice     28.00
4                   4       Calcium (mg) Brown Rice     23.00
5                   5  Carbohydrates (g) White Rice     80.00
6                   6  Carbohydrates (g) Brown Rice     77.00
7                   7        Copper (mg) White Rice      0.22
8                   8        Copper (mg) Brown Rice      0.22
...

The default of fill will impute the NA based on the previous and nearest non-NA row. So it is important to make sure that each brown rice record is exactly the next row of the associated white rice record.

Answer 2

I assume that your dataset is of class data.frame and that it's named dat.

I believe the following code will do it. It splits the df into lists of 2 or 1 rows (the last row in your example is missing Brown Rice). Then it checks if any of these lists have 2 rows and if the nutrients of Brown Rice are NA. If so it assigns the value of White Rice. Then, collects the resulting list back in a data.frame.

sp <- split(dat, dat$nutrient.component.)
res <- lapply(sp, function(x){
            if(nrow(x) == 2 & is.na(x$nutrients[x$grain == "Brown Rice"]))
                x$grain[x$grain == "Brown Rice"] <- "White Rice"
            x
            }
        )

rm(sp)   # tidy up

res <- do.call(rbind, res)
res

Answer 3

The zoo package has some useful functions to deal with NA:

library(data.table)
setDT(DT)[, nutrients := zoo::na.aggregate(nutrients), by = nutrient.component][]

                  nutrient.component      grain nutrients
 1:        Beta-carotene (<U+00B5>g) White Rice      0.00
 2:        Beta-carotene (<U+00B5>g) Brown Rice      0.00
 3:                     Calcium (mg) White Rice     28.00
 4:                     Calcium (mg) Brown Rice     23.00
 5:                Carbohydrates (g) White Rice     80.00
 6:                Carbohydrates (g) Brown Rice     77.00
 7:                      Copper (mg) White Rice      0.22
 8:                      Copper (mg) Brown Rice      0.22
 9:                      Energy (kJ) White Rice   1528.00
10:                      Energy (kJ) Brown Rice   1549.00
11:                          Fat (g) White Rice      0.66
12:                          Fat (g) Brown Rice      2.92
13:                        Fiber (g) White Rice      1.30
14:                        Fiber (g) Brown Rice      3.50
15:    Folate Total (B9) (<U+00B5>g) White Rice      8.00
16:    Folate Total (B9) (<U+00B5>g) Brown Rice     20.00
17:                        Iron (mg) White Rice      0.80
18:                        Iron (mg) Brown Rice      1.47
19:    Lutein+zeaxanthin (<U+00B5>g) White Rice      0.00
20:    Lutein+zeaxanthin (<U+00B5>g) Brown Rice      0.00
...

Note rows 2, 8, and 20.

data.table is used here because it updates DT in place which avoids copying the whole table to save memory and time.