The goal of mde is to
ease exploration of missingness.
Loading the package
recode_as_naAs the name might imply, this converts any value or vector of values
to NA i.e. we take a value such as “missing” or “NA” (not a
real NA according to R) and convert it to R’s
known handler for missing values (NA).
To use the function out of the box (with default arguments), one simply does something like:
dummy_test <- data.frame(ID = c("A","B","B","A"),
values = c("n/a",NA,"Yes","No"))
# Convert n/a and no to NA
head(recode_as_na(dummy_test, value = c("n/a","No")))
#> ID values
#> 1 A <NA>
#> 2 B <NA>
#> 3 B Yes
#> 4 A <NA>Great, but I want to do so for specific columns not the entire
dataset. You can do this by providing column names to
subset_cols.
another_dummy <- data.frame(ID = 1:5, Subject = 7:11,
Change = c("missing","n/a",2:4 ))
# Only change values at the column Change
head(recode_as_na(another_dummy, subset_cols = "Change", value = c("n/a","missing")))
#> ID Subject Change
#> 1 1 7 <NA>
#> 2 2 8 <NA>
#> 3 3 9 2
#> 4 4 10 3
#> 5 5 11 4To recode columns using RegEx,one
can provide pattern_type and a target pattern.
Currently supported pattern_types are
starts_with, ends_with, contains
and regex. See docs for more details.:
# only change at columns that start with Solar
head(recode_as_na(airquality,value=190,pattern_type="starts_with",pattern="Solar"))
#> Ozone Solar.R Wind Temp Month Day
#> 1 41 NA 7.4 67 5 1
#> 2 36 118 8.0 72 5 2
#> 3 12 149 12.6 74 5 3
#> 4 18 313 11.5 62 5 4
#> 5 NA NA 14.3 56 5 5
#> 6 28 NA 14.9 66 5 6# recode at columns that start with O or S(case sensitive)
head(recode_as_na(airquality,value=c(67,118),pattern_type="starts_with",pattern="S|O"))
#> Ozone Solar.R Wind Temp Month Day
#> 1 41 190 7.4 67 5 1
#> 2 36 NA 8.0 72 5 2
#> 3 12 149 12.6 74 5 3
#> 4 18 313 11.5 62 5 4
#> 5 NA NA 14.3 56 5 5
#> 6 28 NA 14.9 66 5 6# use my own RegEx
head(recode_as_na(airquality,value=c(67,118),pattern_type="regex",pattern="(?i)^(s|o)"))
#> Ozone Solar.R Wind Temp Month Day
#> 1 41 190 7.4 67 5 1
#> 2 36 NA 8.0 72 5 2
#> 3 12 149 12.6 74 5 3
#> 4 18 313 11.5 62 5 4
#> 5 NA NA 14.3 56 5 5
#> 6 28 NA 14.9 66 5 6recode_as_na_ifThis function allows one to deliberately introduce missing values if
a column meets a certain threshold of missing values. This is similar to
amputation but is much more basic. It is only provided here
because it is hoped it may be useful to someone for whatever reason.
head(recode_as_na_if(airquality,sign="gt", percent_na=20))
#> Ozone Solar.R Wind Temp Month Day
#> 1 NA 190 7.4 67 5 1
#> 2 NA 118 8.0 72 5 2
#> 3 NA 149 12.6 74 5 3
#> 4 NA 313 11.5 62 5 4
#> 5 NA NA 14.3 56 5 5
#> 6 NA NA 14.9 66 5 6recode_as_na_strThis allows recoding as NA based on a string match.
partial_match <- data.frame(A=c("Hi","match_me","nope"), B=c(NA, "not_me","nah"))
recode_as_na_str(partial_match,"ends_with","ME", case_sensitive=FALSE)
#> A B
#> 1 Hi <NA>
#> 2 <NA> <NA>
#> 3 nope nahrecode_as_na_forFor all values greater/less/less or equal/greater or equal than some
value, can I convert them to NA?!
Yes You Can! All we have to do is use
recode_as_na_for:
head(recode_as_na_for(airquality,criteria="gt",value=25))
#> Ozone Solar.R Wind Temp Month Day
#> 1 NA NA 7.4 NA 5 1
#> 2 NA NA 8.0 NA 5 2
#> 3 12 NA 12.6 NA 5 3
#> 4 18 NA 11.5 NA 5 4
#> 5 NA NA 14.3 NA 5 5
#> 6 NA NA 14.9 NA 5 6To do so at specific columns, pass an optional
subset_cols character vector:
recode_na_asSometimes, for whatever reason, one would like to replace
NAs with whatever value they would like.
recode_na_as provides a very simple way to do just
that.
head(recode_na_as(airquality))
#> Ozone Solar.R Wind Temp Month Day
#> 1 41 190 7.4 67 5 1
#> 2 36 118 8.0 72 5 2
#> 3 12 149 12.6 74 5 3
#> 4 18 313 11.5 62 5 4
#> 5 0 0 14.3 56 5 5
#> 6 28 0 14.9 66 5 6
# use NaN
head(recode_na_as(airquality, value=NaN))
#> Ozone Solar.R Wind Temp Month Day
#> 1 41 190 7.4 67 5 1
#> 2 36 118 8.0 72 5 2
#> 3 12 149 12.6 74 5 3
#> 4 18 313 11.5 62 5 4
#> 5 NaN NaN 14.3 56 5 5
#> 6 28 NaN 14.9 66 5 6As a “bonus”, you can manipulate the data only at specific columns as shown here:
head(recode_na_as(airquality, value=0, subset_cols="Ozone"))
#> Ozone Solar.R Wind Temp Month Day
#> 1 41 190 7.4 67 5 1
#> 2 36 118 8.0 72 5 2
#> 3 12 149 12.6 74 5 3
#> 4 18 313 11.5 62 5 4
#> 5 0 NA 14.3 56 5 5
#> 6 28 NA 14.9 66 5 6The above also supports custom recoding similar to
recode_na_as:
head(mde::recode_na_as(airquality, value=0, pattern_type="starts_with",pattern="Solar"))
#> Ozone Solar.R Wind Temp Month Day
#> 1 41 190 7.4 67 5 1
#> 2 36 118 8.0 72 5 2
#> 3 12 149 12.6 74 5 3
#> 4 18 313 11.5 62 5 4
#> 5 NA 0 14.3 56 5 5
#> 6 28 0 14.9 66 5 6column_based_recodeEver needed to change values in a given column based on the
proportions of NAs in other columns(row-wise)?!. The goal
of column_based_recode is to achieve just that. Let’s see
how we could do this with a simple example:
head(column_based_recode(airquality, values_from = "Wind", values_to="Wind", pattern_type = "regex", pattern = "Solar|Ozone"))
#> Ozone Solar.R Wind Temp Month Day
#> 1 41 190 7.4 67 5 1
#> 2 36 118 8.0 72 5 2
#> 3 12 149 12.6 74 5 3
#> 4 18 313 11.5 62 5 4
#> 5 NA NA 0.0 56 5 5
#> 6 28 NA 14.9 66 5 6custom_na_recodeThis allows recoding NA values with common stats
functions such as
mean,max,min,sd.
To use default values:
head(custom_na_recode(airquality))
#> Ozone Solar.R Wind Temp Month Day
#> 1 41.00000 190.0000 7.4 67 5 1
#> 2 36.00000 118.0000 8.0 72 5 2
#> 3 12.00000 149.0000 12.6 74 5 3
#> 4 18.00000 313.0000 11.5 62 5 4
#> 5 42.12931 185.9315 14.3 56 5 5
#> 6 28.00000 185.9315 14.9 66 5 6To use select columns:
head(custom_na_recode(airquality,func="mean",across_columns=c("Solar.R","Ozone")))
#> Ozone Solar.R Wind Temp Month Day
#> 1 41.00000 190.0000 7.4 67 5 1
#> 2 36.00000 118.0000 8.0 72 5 2
#> 3 12.00000 149.0000 12.6 74 5 3
#> 4 18.00000 313.0000 11.5 62 5 4
#> 5 42.12931 185.9315 14.3 56 5 5
#> 6 28.00000 185.9315 14.9 66 5 6To use a function from another package to perform replacements:
To perform a forward fill with dplyr’s
lead:
# use lag for a backfill
head(custom_na_recode(airquality,func=dplyr::lead ))
#> Ozone Solar.R Wind Temp Month Day
#> 1 41 190 7.4 67 5 1
#> 2 36 118 8.0 72 5 2
#> 3 12 149 12.6 74 5 3
#> 4 18 313 11.5 62 5 4
#> 5 23 99 14.3 56 5 5
#> 6 28 19 14.9 66 5 6To perform replacement by group:
some_data <- data.frame(ID=c("A1","A1","A1","A2","A2", "A2"),A=c(5,NA,0,8,3,4),B=c(10,0,0,NA,5,6),C=c(1,NA,NA,25,7,8))
head(custom_na_recode(some_data,func = "mean", grouping_cols = "ID"))
#> # A tibble: 6 × 4
#> ID A B C
#> <chr> <dbl> <dbl> <dbl>
#> 1 A1 5 10 1
#> 2 A1 2.5 0 1
#> 3 A1 0 0 1
#> 4 A2 8 5.5 25
#> 5 A2 3 5 7
#> 6 A2 4 6 8Across specific columns:
head(custom_na_recode(some_data,func = "mean", grouping_cols = "ID", across_columns = c("C", "A")))
#> # A tibble: 6 × 4
#> ID A B C
#> <chr> <dbl> <dbl> <dbl>
#> 1 A1 5 10 1
#> 2 A1 2.5 0 1
#> 3 A1 0 0 1
#> 4 A2 8 NA 25
#> 5 A2 3 5 7
#> 6 A2 4 6 8recode_na_ifGiven a data.frame object, one can recode
NAs as another value based on a grouping variable. In the
example below, we replace all NAs in all columns with 0s if
the ID is A2 or A3
some_data <- data.frame(ID=c("A1","A2","A3", "A4"),
A=c(5,NA,0,8), B=c(10,0,0,1),
C=c(1,NA,NA,25))
head(recode_na_if(some_data,grouping_col="ID", target_groups=c("A2","A3"),
replacement= 0))
#> # A tibble: 4 × 4
#> ID A B C
#> <chr> <dbl> <dbl> <dbl>
#> 1 A1 5 10 1
#> 2 A2 0 0 0
#> 3 A3 0 0 0
#> 4 A4 8 1 25drop_na_ifSuppose you wanted to drop any column that has a percentage of
NAs greater than or equal to a certain value?
drop_na_if does just that.
We can drop any columns that have greater than or equal(gteq) to 24%
of the values missing from airquality:
head(drop_na_if(airquality, sign="gteq",percent_na = 24))
#> Solar.R Wind Temp Month Day
#> 1 190 7.4 67 5 1
#> 2 118 8.0 72 5 2
#> 3 149 12.6 74 5 3
#> 4 313 11.5 62 5 4
#> 5 NA 14.3 56 5 5
#> 6 NA 14.9 66 5 6The above also supports less than or equal to(lteq),
equal to(eq), greater than(gt) and less
than(lt).
To keep certain columns despite fitting the target
percent_na criteria, one can provide an optional
keep_columns character vector.
head(drop_na_if(airquality, percent_na = 24, keep_columns = "Ozone"))
#> Ozone Solar.R Wind Temp Month Day
#> 1 41 190 7.4 67 5 1
#> 2 36 118 8.0 72 5 2
#> 3 12 149 12.6 74 5 3
#> 4 18 313 11.5 62 5 4
#> 5 NA NA 14.3 56 5 5
#> 6 28 NA 14.9 66 5 6Compare the above result to the following:
head(drop_na_if(airquality, percent_na = 24))
#> Solar.R Wind Temp Month Day
#> 1 190 7.4 67 5 1
#> 2 118 8.0 72 5 2
#> 3 149 12.6 74 5 3
#> 4 313 11.5 62 5 4
#> 5 NA 14.3 56 5 5
#> 6 NA 14.9 66 5 6To drop groups that meet a set missingness criterion, we proceed as follows.
grouped_drop <- structure(list(ID = c("A", "A", "B", "A", "B"),
Vals = c(4, NA, NA, NA, NA), Values = c(5, 6, 7, 8, NA)),
row.names = c(NA, -5L), class = "data.frame")
# Drop all columns for groups that meet a percent missingness of greater than or
# equal to 67
drop_na_if(grouped_drop,percent_na = 67,sign="gteq",
grouping_cols = "ID")
#> # A tibble: 3 × 3
#> ID Vals Values
#> <chr> <dbl> <dbl>
#> 1 A 4 5
#> 2 A NA 6
#> 3 A NA 8drop_row_ifThis is similar to drop_na_if but does operations
rowwise not columnwise. Compare to the example above:
# Drop rows with at least two NAs
head(drop_row_if(airquality, sign="gteq", type="count" , value = 2))
#> Dropped 2 rows.
#> Ozone Solar.R Wind Temp Month Day
#> 1 41 190 7.4 67 5 1
#> 2 36 118 8.0 72 5 2
#> 3 12 149 12.6 74 5 3
#> 4 18 313 11.5 62 5 4
#> 6 28 NA 14.9 66 5 6
#> 7 23 299 8.6 65 5 7To drop based on percentages:
# Drops 42 rows
head(drop_row_if(airquality, type="percent", value=16, sign="gteq",
as_percent=TRUE))
#> Dropped 42 rows.
#> Ozone Solar.R Wind Temp Month Day
#> 1 41 190 7.4 67 5 1
#> 2 36 118 8.0 72 5 2
#> 3 12 149 12.6 74 5 3
#> 4 18 313 11.5 62 5 4
#> 7 23 299 8.6 65 5 7
#> 8 19 99 13.8 59 5 8For more details, please see the documentation of
drop_row_if.
drop_na_atThis provides a simple way to drop missing values only at specific columns. It currently only returns those columns with their missing values removed. See usage below. Further details are given in the documentation. It is currently case sensitive.
head(drop_na_at(airquality,pattern_type = "starts_with","O"))
#> Ozone
#> 1 41
#> 2 36
#> 3 12
#> 4 18
#> 5 28
#> 6 23drop_all_naThis drops columns where all values are missing.
test2 <- data.frame(ID= c("A","A","B","A","B"), Vals = c(4,rep(NA, 4)))
drop_all_na(test2, grouping_cols="ID")
#> # A tibble: 3 × 2
#> ID Vals
#> <chr> <dbl>
#> 1 A 4
#> 2 A NA
#> 3 A NAAlternatively, we can drop groups where all variables are all NA.
test2 <- data.frame(ID= c("A","A","B","A","B"), Vals = rep(NA, 5))
head(drop_all_na(test2, grouping_cols = "ID"))
#> # A tibble: 0 × 2
#> # ℹ 2 variables: ID <chr>, Vals <lgl>dict_recodeIf one would like to recode column values using a “dictionary”,
dict_recode provides a simple way to do that. For example,
if one would like to convert NA values in
Solar.R to 520 and those in Ozone to 42, one
simply calls the following:
head(dict_recode(airquality, use_func="recode_na_as",
patterns = c("solar", "ozone"),
pattern_type="starts_with", values = c(520,42)))
#> Ozone Solar.R Wind Temp Month Day
#> 1 41 190 7.4 67 5 1
#> 2 36 118 8.0 72 5 2
#> 3 12 149 12.6 74 5 3
#> 4 18 313 11.5 62 5 4
#> 5 42 520 14.3 56 5 5
#> 6 28 520 14.9 66 5 6recode_as_value for example as shown below
head(recode_as_value(airquality, value=c(67,118),replacement=NA,
pattern_type="starts_with",pattern="S|O"))
#> Ozone Solar.R Wind Temp Month Day
#> 1 41 190 7.4 67 5 1
#> 2 36 NA 8.0 72 5 2
#> 3 12 149 12.6 74 5 3
#> 4 18 313 11.5 62 5 4
#> 5 NA NA 14.3 56 5 5
#> 6 28 NA 14.9 66 5 6The above is a more general function that can do what the other functions do and may be more useful for development purposes.
Please note that the mde project is released with a Contributor
Code of Conduct. By contributing to this project, you agree to abide
by its terms.
For further exploration, please
browseVignettes("mde").
To raise an issue, please do so here
Thank you, feedback is always welcome :)