2022-01-31
The goal of mde is to ease exploration of missingness.
Installation
CRAN release
install.packages("mde")Stable Development version
devtools::install_github("Nelson-Gon/mde")
devtools::install_github("Nelson-Gon/mde", build_vignettes=TRUE)Unstable Development version
devtools::install_github("Nelson-Gon/mde@develop")Loading the package
library(mde)
#> Welcome to mde. This is mde version 0.3.2.
#> Please file issues and feedback at https://www.github.com/Nelson-Gon/mde/issues
#> Turn this message off using 'suppressPackageStartupMessages(library(mde))'
#> Happy Exploration :)Exploring missingness
To get a simple missingness report, use na_summary:
na_summary(airquality)
#> variable missing complete percent_complete percent_missing
#> 1 Day 0 153 100.00000 0.000000
#> 2 Month 0 153 100.00000 0.000000
#> 3 Ozone 37 116 75.81699 24.183007
#> 4 Solar.R 7 146 95.42484 4.575163
#> 5 Temp 0 153 100.00000 0.000000
#> 6 Wind 0 153 100.00000 0.000000To sort this summary by a given column :
na_summary(airquality,sort_by = "percent_complete")
#> variable missing complete percent_complete percent_missing
#> 3 Ozone 37 116 75.81699 24.183007
#> 4 Solar.R 7 146 95.42484 4.575163
#> 1 Day 0 153 100.00000 0.000000
#> 2 Month 0 153 100.00000 0.000000
#> 5 Temp 0 153 100.00000 0.000000
#> 6 Wind 0 153 100.00000 0.000000If one would like to reset (drop) row names, then one can set row_names to TRUE This may especially be useful in cases where rownames are simply numeric and do not have much additional use.
na_summary(airquality,sort_by = "percent_complete", reset_rownames = TRUE)
#> variable missing complete percent_complete percent_missing
#> 1 Ozone 37 116 75.81699 24.183007
#> 2 Solar.R 7 146 95.42484 4.575163
#> 3 Day 0 153 100.00000 0.000000
#> 4 Month 0 153 100.00000 0.000000
#> 5 Temp 0 153 100.00000 0.000000
#> 6 Wind 0 153 100.00000 0.000000To sort by percent_missing instead:
na_summary(airquality, sort_by = "percent_missing")
#> variable missing complete percent_complete percent_missing
#> 1 Day 0 153 100.00000 0.000000
#> 2 Month 0 153 100.00000 0.000000
#> 5 Temp 0 153 100.00000 0.000000
#> 6 Wind 0 153 100.00000 0.000000
#> 4 Solar.R 7 146 95.42484 4.575163
#> 3 Ozone 37 116 75.81699 24.183007To sort the above in descending order:
na_summary(airquality, sort_by="percent_missing", descending = TRUE)
#> variable missing complete percent_complete percent_missing
#> 3 Ozone 37 116 75.81699 24.183007
#> 4 Solar.R 7 146 95.42484 4.575163
#> 1 Day 0 153 100.00000 0.000000
#> 2 Month 0 153 100.00000 0.000000
#> 5 Temp 0 153 100.00000 0.000000
#> 6 Wind 0 153 100.00000 0.000000To exclude certain columns from the analysis:
na_summary(airquality, exclude_cols = c("Day", "Wind"))
#> variable missing complete percent_complete percent_missing
#> 1 Month 0 153 100.00000 0.000000
#> 2 Ozone 37 116 75.81699 24.183007
#> 3 Solar.R 7 146 95.42484 4.575163
#> 4 Temp 0 153 100.00000 0.000000To include or exclude via regex match:
na_summary(airquality, regex_kind = "inclusion",pattern_type = "starts_with", pattern = "O|S")
#> variable missing complete percent_complete percent_missing
#> 1 Ozone 37 116 75.81699 24.183007
#> 2 Solar.R 7 146 95.42484 4.575163
na_summary(airquality, regex_kind = "exclusion",pattern_type = "regex", pattern = "^[O|S]")
#> variable missing complete percent_complete percent_missing
#> 1 Day 0 153 100 0
#> 2 Month 0 153 100 0
#> 3 Temp 0 153 100 0
#> 4 Wind 0 153 100 0To get this summary by group:
test2 <- data.frame(ID= c("A","A","B","A","B"), Vals = c(rep(NA,4),"No"),ID2 = c("E","E","D","E","D"))
na_summary(test2,grouping_cols = c("ID","ID2"))
#> # A tibble: 2 x 7
#> ID ID2 variable missing complete percent_complete percent_missing
#> <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 B D Vals 1 1 50 50
#> 2 A E Vals 3 0 0 100
na_summary(test2, grouping_cols="ID")
#> Warning in na_summary.data.frame(test2, grouping_cols = "ID"): All non grouping
#> values used. Using select non groups is currently not supported
#> # A tibble: 4 x 6
#> ID variable missing complete percent_complete percent_missing
#> <chr> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 A Vals 3 0 0 100
#> 2 A ID2 0 3 100 0
#> 3 B Vals 1 1 50 50
#> 4 B ID2 0 2 100 0get_na_counts
This provides a convenient way to show the number of missing values column-wise. It is relatively fast(tests done on about 400,000 rows, took a few microseconds.)
To get the number of missing values in each column of airquality, we can use the function as follows:
get_na_counts(airquality)
#> Ozone Solar.R Wind Temp Month Day
#> 1 37 7 0 0 0 0The above might be less useful if one would like to get the results by group. In that case, one can provide a grouping vector of names in grouping_cols.
test <- structure(list(Subject = structure(c(1L, 1L, 2L, 2L), .Label = c("A",
"B"), class = "factor"), res = c(NA, 1, 2, 3), ID = structure(c(1L,
1L, 2L, 2L), .Label = c("1", "2"), class = "factor")), class = "data.frame", row.names = c(NA,
-4L))
get_na_counts(test, grouping_cols = "ID")
#> # A tibble: 2 x 3
#> ID Subject res
#> <fct> <int> <int>
#> 1 1 0 1
#> 2 2 0 0percent_missing
This is a very simple to use but quick way to take a look at the percentage of data that is missing column-wise.
percent_missing(airquality)
#> Ozone Solar.R Wind Temp Month Day
#> 1 24.18301 4.575163 0 0 0 0We can get the results by group by providing an optional grouping_cols character vector.
percent_missing(test, grouping_cols = "Subject")
#> # A tibble: 2 x 3
#> Subject res ID
#> <fct> <dbl> <dbl>
#> 1 A 50 0
#> 2 B 0 0To exclude some columns from the above exploration, one can provide an optional character vector in exclude_cols.
percent_missing(airquality,exclude_cols = c("Day","Temp"))
#> Ozone Solar.R Wind Month
#> 1 24.18301 4.575163 0 0sort_by_missingness
This provides a very simple but relatively fast way to sort variables by missingness. Unless otherwise stated, this does not currently support arranging grouped percents.
Usage:
sort_by_missingness(airquality, sort_by = "counts")
#> variable percent
#> 1 Wind 0
#> 2 Temp 0
#> 3 Month 0
#> 4 Day 0
#> 5 Solar.R 7
#> 6 Ozone 37To sort in descending order:
sort_by_missingness(airquality, sort_by = "counts", descend = TRUE)
#> variable percent
#> 1 Ozone 37
#> 2 Solar.R 7
#> 3 Wind 0
#> 4 Temp 0
#> 5 Month 0
#> 6 Day 0To use percentages instead:
sort_by_missingness(airquality, sort_by = "percents")
#> variable percent
#> 1 Wind 0.000000
#> 2 Temp 0.000000
#> 3 Month 0.000000
#> 4 Day 0.000000
#> 5 Solar.R 4.575163
#> 6 Ozone 24.183007Recoding as NA
recode_as_na
As 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_if
This 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_str
This 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_for
For 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:
head(recode_as_na_for(airquality, value=40,subset_cols=c("Solar.R","Ozone"), criteria="gt"))
#> Ozone Solar.R Wind Temp Month Day
#> 1 NA NA 7.4 67 5 1
#> 2 36 NA 8.0 72 5 2
#> 3 12 NA 12.6 74 5 3
#> 4 18 NA 11.5 62 5 4
#> 5 NA NA 14.3 56 5 5
#> 6 28 NA 14.9 66 5 6Recoding NA as
recode_na_as
Sometimes, 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_recode
Ever 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_recode
This 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 x 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 x 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_if
Given 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 x 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 25Dropping NAs
drop_na_if
Suppose 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 x 3
#> ID Vals Values
#> <chr> <dbl> <dbl>
#> 1 A 4 5
#> 2 A NA 6
#> 3 A NA 8drop_row_if
This 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_at
This 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_na
This 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 x 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(test, grouping_cols = "ID"))
#> # A tibble: 4 x 3
#> Subject res ID
#> <fct> <dbl> <fct>
#> 1 A NA 1
#> 2 A 1 1
#> 3 B 2 2
#> 4 B 3 2dict_recode
If 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 6Please 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 :)
