This is regarding latest tidyr release. I am trying pivot_wider & pivot_longer function from library(tidyr) (Update 1.0.0)
I was trying to obtain normal iris dataset when I run below but instead I get nested sort of 3X5 dimension tibble, not sure whats happening (I read https://tidyr.tidyverse.org/articles/pivot.html) but still not sure how to avoid this
library(tidyr)
iris %>% pivot_longer(-Species,values_to = "count") %>%
pivot_wider(names_from = name, values_from = count)
Expected Output: Normal Iris dataset (150 X 5 dimension)
Edit: I read below that if I wrap around unnest() I get expected output. I am not able to understand why to unnest it when we did not nest it anywhere. Any basic help would be appreciated. Want to understand the concept of what went wrong.
As I learnt from Akrun & other helpful friends & post
(Not a bug or anything)
spread(., name, count) throws an error because we have multiple rows for each species x name. pivot_wider does a better job by providing a list-columns instead. If we add unique ID to each row then it works fine.
library(tidyverse)
iris %>%
rowid_to_column() %>%
pivot_longer(-c(rowid, Species), values_to = "count") %>%
pivot_wider(names_from = name, values_from = count) %>%
select(-rowid)
pivot_wider(), unlike nest(), allows us to aggregate multiple values when the rows are not given a unique identifier.
The default is to use list to aggregate and to be verbose about it.
To expand the output we could use unnest() as already suggested but it's more idiomatic to use unchop() because we're not trying to expand a horizontal dimensionality in the nested values.
So to sum it all up to get back your initial data (except it'll be a tibble) you can do:
library(tidyr)
iris %>%
pivot_longer(-Species,values_to = "count") %>%
print() %>%
pivot_wider(names_from = name,
values_from = count,
values_fn = list(count=list)) %>%
print() %>%
unchop(everything()) %>%
print() %>%
all.equal(iris)
#> # A tibble: 600 x 3
#> Species name count
#> <fct> <chr> <dbl>
#> 1 setosa Sepal.Length 5.1
#> 2 setosa Sepal.Width 3.5
#> 3 setosa Petal.Length 1.4
#> 4 setosa Petal.Width 0.2
#> 5 setosa Sepal.Length 4.9
#> 6 setosa Sepal.Width 3
#> 7 setosa Petal.Length 1.4
#> 8 setosa Petal.Width 0.2
#> 9 setosa Sepal.Length 4.7
#> 10 setosa Sepal.Width 3.2
#> # ... with 590 more rows
#> # A tibble: 3 x 5
#> Species Sepal.Length Sepal.Width Petal.Length Petal.Width
#> <fct> <list<dbl>> <list<dbl>> <list<dbl>> <list<dbl>>
#> 1 setosa [50] [50] [50] [50]
#> 2 versicolor [50] [50] [50] [50]
#> 3 virginica [50] [50] [50] [50]
#> # A tibble: 150 x 5
#> Species Sepal.Length Sepal.Width Petal.Length Petal.Width
#> <fct> <dbl> <dbl> <dbl> <dbl>
#> 1 setosa 5.1 3.5 1.4 0.2
#> 2 setosa 4.9 3 1.4 0.2
#> 3 setosa 4.7 3.2 1.3 0.2
#> 4 setosa 4.6 3.1 1.5 0.2
#> 5 setosa 5 3.6 1.4 0.2
#> 6 setosa 5.4 3.9 1.7 0.4
#> 7 setosa 4.6 3.4 1.4 0.3
#> 8 setosa 5 3.4 1.5 0.2
#> 9 setosa 4.4 2.9 1.4 0.2
#> 10 setosa 4.9 3.1 1.5 0.1
#> # ... with 140 more rows
#> [1] TRUE
Created on 2019-09-15 by the reprex package (v0.3.0)
Related
If I add a new row to the iris dataset with:
iris <- as_tibble(iris)
> iris %>%
add_row(.before=0)
# A tibble: 151 × 5
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
<dbl> <dbl> <dbl> <dbl> <chr>
1 NA NA NA NA <NA> <--- Good!
2 5.1 3.5 1.4 0.2 setosa
3 4.9 3.0 1.4 0.2 setosa
It works. So, why can't I add a new row on top of each "subset" with:
iris %>%
group_by(Species) %>%
add_row(.before=0)
Error: is.data.frame(df) is not TRUE
If you want to use a grouped operation, you need do like JasonWang described in his comment, as other functions like mutate or summarise expect a result with the same number of rows as the grouped data frame (in your case, 50) or with one row (e.g. when summarising).
As you probably know, in general do can be slow and should be a last resort if you cannot achieve your result in another way. Your task is quite simple because it only involves adding extra rows in your data frame, which can be done by simple indexing, e.g. look at the output of iris[NA, ].
What you want is essentially to create a vector
indices <- c(NA, 1:50, NA, 51:100, NA, 101:150)
(since the first group is in rows 1 to 50, the second one in 51 to 100 and the third one in 101 to 150).
The result is then iris[indices, ].
A more general way of building this vector uses group_indices.
indices <- seq(nrow(iris)) %>%
split(group_indices(iris, Species)) %>%
map(~c(NA, .x)) %>%
unlist
(map comes from purrr which I assume you have loaded as you have tagged this with tidyverse).
A more recent version would be using group_modify() instead of do().
iris %>%
as_tibble() %>%
group_by(Species) %>%
group_modify(~ add_row(.x,.before=0))
#> # A tibble: 153 x 5
#> # Groups: Species [3]
#> Species Sepal.Length Sepal.Width Petal.Length Petal.Width
#> <fct> <dbl> <dbl> <dbl> <dbl>
#> 1 setosa NA NA NA NA
#> 2 setosa 5.1 3.5 1.4 0.2
#> 3 setosa 4.9 3 1.4 0.2
With a slight variation, this could also be done:
library(purrr)
library(tibble)
iris %>%
group_split(Species) %>%
map_dfr(~ .x %>%
add_row(.before = 1))
# A tibble: 153 x 5
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
<dbl> <dbl> <dbl> <dbl> <fct>
1 NA NA NA NA NA
2 5.1 3.5 1.4 0.2 setosa
3 4.9 3 1.4 0.2 setosa
4 4.7 3.2 1.3 0.2 setosa
5 4.6 3.1 1.5 0.2 setosa
6 5 3.6 1.4 0.2 setosa
7 5.4 3.9 1.7 0.4 setosa
8 4.6 3.4 1.4 0.3 setosa
9 5 3.4 1.5 0.2 setosa
10 4.4 2.9 1.4 0.2 setosa
# ... with 143 more rows
This also can be used for grouped data frame, however, it's a bit verbose:
library(dplyr)
iris %>%
group_by(Species) %>%
summarise(Sepal.Length = c(NA, Sepal.Length),
Sepal.Width = c(NA, Sepal.Width),
Petal.Length = c(NA, Petal.Length),
Petal.Width = c(NA, Petal.Width),
Species = c(NA, Species))
I'm trying to mutate a new variable from sort of row calculation,
say rowSums as below
iris %>%
mutate_(sumVar =
iris %>%
select(Sepal.Length:Petal.Width) %>%
rowSums)
the result is that "sumVar" is truncated to its first value(10.2):
Source: local data frame [150 x 6]
Groups: <by row>
Sepal.Length Sepal.Width Petal.Length Petal.Width Species sumVar
1 5.1 3.5 1.4 0.2 setosa 10.2
2 4.9 3.0 1.4 0.2 setosa 10.2
3 4.7 3.2 1.3 0.2 setosa 10.2
4 4.6 3.1 1.5 0.2 setosa 10.2
5 5.0 3.6 1.4 0.2 setosa 10.2
6 5.4 3.9 1.7 0.4 setosa 10.2
..
Warning message:
Truncating vector to length 1
Should it be rowwise applied? Or what's the right verb to use in these kind of calculations.
Edit:
More specifically, is there any way to realize the inline custom function with dplyr?
I'm wondering if it is possible do something like:
iris %>%
mutate(sumVar = colsum_function(Sepal.Length:Petal.Width))
This is more of a workaround but could be used
iris %>% mutate(sumVar = rowSums(.[1:4]))
As written in comments, you can also use a select inside of mutate to get the columns you want to sum up, for example
iris %>%
mutate(sumVar = rowSums(select(., contains("Sepal")))) %>%
head
or
iris %>%
mutate(sumVar = select(., contains("Sepal")) %>% rowSums()) %>%
head
You can use rowwise() function:
iris %>%
rowwise() %>%
mutate(sumVar = sum(c_across(Sepal.Length:Petal.Width)))
#> # A tibble: 150 x 6
#> # Rowwise:
#> Sepal.Length Sepal.Width Petal.Length Petal.Width Species sumVar
#> <dbl> <dbl> <dbl> <dbl> <fct> <dbl>
#> 1 5.1 3.5 1.4 0.2 setosa 10.2
#> 2 4.9 3 1.4 0.2 setosa 9.5
#> 3 4.7 3.2 1.3 0.2 setosa 9.4
#> 4 4.6 3.1 1.5 0.2 setosa 9.4
#> 5 5 3.6 1.4 0.2 setosa 10.2
#> 6 5.4 3.9 1.7 0.4 setosa 11.4
#> 7 4.6 3.4 1.4 0.3 setosa 9.7
#> 8 5 3.4 1.5 0.2 setosa 10.1
#> 9 4.4 2.9 1.4 0.2 setosa 8.9
#> 10 4.9 3.1 1.5 0.1 setosa 9.6
#> # ... with 140 more rows
"c_across() uses tidy selection syntax so you can to succinctly select many variables"'
Finally, if you want, you can use %>% ungroup at the end to exit from rowwise.
A more complicated way would be:
iris %>% select(Sepal.Length:Petal.Width) %>%
mutate(sumVar = rowSums(.)) %>% left_join(iris)
Adding #docendodiscimus's comment as an answer. +1 to him!
iris %>% mutate(sumVar = rowSums(select(., contains("Sepal"))))
I am using this simple solution, which is a more robust modification of the answer by Davide Passaretti:
iris %>% select(Sepal.Length:Petal.Width) %>%
transmute(sumVar = rowSums(.)) %>% bind_cols(iris, .)
(But it requires a defined row order, which should be fine, unless you work with remote datasets perhaps..)
You can also use a grep in place of contains or matches, just in case you need to get fancy with the regular expressions (matches doesn't seem to much like negative lookaheads and the like in my experience).
iris %>% mutate(sumVar = rowSums(select(., grep("Sepal", names(.)))))
As requested, transforming my commment into an answer:
For operations like sum that already have an efficient vectorised row-wise alternative, the proper way is currently:
df %>% mutate(total = rowSums(across(where(is.numeric))))
across can take anything that select can (e.g. rowSums(across(Sepal.Length:Petal.Width)) also works).
Scroll down the row-wise vignette to find this and have a look at across
library(tidyverse)
df <- iris %>%
group_by(Species) %>%
mutate(Petal.Dim = Petal.Length * Petal.Width,
rank = rank(desc(Petal.Dim))) %>%
mutate(new_col = rank == 4, Sepal.Width)
table <- df %>%
filter(rank == 4) %>%
select(Species, new_col = Sepal.Width)
correct_df <- left_join(df, table, by = "Species")
df
#> # A tibble: 150 x 8
#> # Groups: Species [3]
#> Sepal.Length Sepal.Width Petal.Length Petal.Width Species Petal.Dim
#> <dbl> <dbl> <dbl> <dbl> <fct> <dbl>
#> 1 5.1 3.5 1.4 0.2 setosa 0.280
#> 2 4.9 3 1.4 0.2 setosa 0.280
#> 3 4.7 3.2 1.3 0.2 setosa 0.26
#> 4 4.6 3.1 1.5 0.2 setosa 0.3
#> 5 5 3.6 1.4 0.2 setosa 0.280
#> 6 5.4 3.9 1.7 0.4 setosa 0.68
#> 7 4.6 3.4 1.4 0.3 setosa 0.42
#> 8 5 3.4 1.5 0.2 setosa 0.3
#> 9 4.4 2.9 1.4 0.2 setosa 0.280
#> 10 4.9 3.1 1.5 0.1 setosa 0.15
#> # ... with 140 more rows, and 2 more variables: rank <dbl>, new_col <lgl>
I'm basically looking for new_col to show the value that corresponds with rank = 4 from the Sepal.Width column. In this case, those values would be 3.9, 3.3, and 3.8. I'm envisioning this similar to a VLookup, or Index/Match in Excel.
When ever I think "now I need to use VLOOKUP like I did in the past in Excel" I find the left_join() function helpful. It's also part of the dplyr package. Instead of "looking up" values in one table in another table, it's easier for R to just make one bigger table where one table remains unchanged (here the "left" one or the first term you put in the function) and the other is added using a column or columns they have in common as an index.
In your specific example, I can't entirely understand what you want new_col to have in it. If you want to do Excel-style VLOOKUP in R, then left_join() is the best starting point.
The question is not clear since it does not mention the purpose of a Vlookup or Index/Match like operation from Excel.
Also, you don't mention what value should "new_col" have if rank is not equal to 4.
Assuming the value is NA, the below solution with a simple ifelse would work:
df <- iris %>%
group_by(Species) %>%
mutate(Petal.Dim = Petal.Length * Petal.Width,
rank = rank(desc(Petal.Dim))) %>%
ungroup() %>%
mutate(new_col = ifelse(rank == 4, Sepal.Width,NA))
df
I try to use gather and spread functions in tidyverse package, but it throws an error in spread function
library(caret)
dataset<-iris
# gather function is to convert wide data to long data
dataset_gather<-dataset %>% tidyr::gather(key=Type,value = Values,1:4)
head(dataset_gather)
# spead is the opposite of gather
This code below throws an error like this Error: Duplicate identifiers for rows
dataset_spead<- dataset_gather%>%tidyr::spread(key = Type,value = Values)
Added later: Sorry #alistaire, only saw your comment on the original post after posting this response.
As far as I understand Error: Duplicate identifiers for rows..., it occurs when you have values with the same identifier. For example in the original 'iris' dataset, the first five rows of Species = setosa all have a Petal.Width of 0.2, and three rows of Petal.Length have values of 1.4. Gathering those data isn't an issue, but when you try spread them, the function doesn't know what belongs to what. That is, which 0.2 Petal.Width and 1.4 Petal.Length belongs to which row of setosa.
The (tidyverse) solution I use in those circumstances is to create a unique marker for each row of data at the gather stage so that the function can keep track which duplicate data belong to which rows when you want to spread again. See example below:
# Load packages
library(dplyr)
library(tidyr)
# Get data
dataset <- iris
# View dataset
head(dataset)
#> Sepal.Length Sepal.Width Petal.Length Petal.Width Species
#> 1 5.1 3.5 1.4 0.2 setosa
#> 2 4.9 3.0 1.4 0.2 setosa
#> 3 4.7 3.2 1.3 0.2 setosa
#> 4 4.6 3.1 1.5 0.2 setosa
#> 5 5.0 3.6 1.4 0.2 setosa
#> 6 5.4 3.9 1.7 0.4 setosa
# Gather data
dataset_gathered <- dataset %>%
# Create a unique identifier for each row
mutate(marker = row_number(Species)) %>%
# Gather the data
gather(key = Type, value = Values, 1:4)
# View gathered data
head(dataset_gathered)
#> Species marker Type Values
#> 1 setosa 1 Sepal.Length 5.1
#> 2 setosa 2 Sepal.Length 4.9
#> 3 setosa 3 Sepal.Length 4.7
#> 4 setosa 4 Sepal.Length 4.6
#> 5 setosa 5 Sepal.Length 5.0
#> 6 setosa 6 Sepal.Length 5.4
# Spread it out again
dataset_spread <- dataset_gathered %>%
# Group the data by the marker
group_by(marker) %>%
# Spread it out again
spread(key = Type, value = Values) %>%
# Not essential, but remove marker
ungroup() %>%
select(-marker)
# View spread data
head(dataset_spread)
#> # A tibble: 6 x 5
#> Species Petal.Length Petal.Width Sepal.Length Sepal.Width
#> <fctr> <dbl> <dbl> <dbl> <dbl>
#> 1 setosa 1.4 0.2 5.1 3.5
#> 2 setosa 1.4 0.2 4.9 3.0
#> 3 setosa 1.3 0.2 4.7 3.2
#> 4 setosa 1.5 0.2 4.6 3.1
#> 5 setosa 1.4 0.2 5.0 3.6
#> 6 setosa 1.7 0.4 5.4 3.9
(and as ever, thanks to Jenny Bryan for the reprex package)
We can do this with data.table
library(data.table)
dcast(melt(setDT(dataset, keep.rownames = TRUE), id.var = c("rn", "Species")), rn + Species ~ variable)
If I add a new row to the iris dataset with:
iris <- as_tibble(iris)
> iris %>%
add_row(.before=0)
# A tibble: 151 × 5
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
<dbl> <dbl> <dbl> <dbl> <chr>
1 NA NA NA NA <NA> <--- Good!
2 5.1 3.5 1.4 0.2 setosa
3 4.9 3.0 1.4 0.2 setosa
It works. So, why can't I add a new row on top of each "subset" with:
iris %>%
group_by(Species) %>%
add_row(.before=0)
Error: is.data.frame(df) is not TRUE
If you want to use a grouped operation, you need do like JasonWang described in his comment, as other functions like mutate or summarise expect a result with the same number of rows as the grouped data frame (in your case, 50) or with one row (e.g. when summarising).
As you probably know, in general do can be slow and should be a last resort if you cannot achieve your result in another way. Your task is quite simple because it only involves adding extra rows in your data frame, which can be done by simple indexing, e.g. look at the output of iris[NA, ].
What you want is essentially to create a vector
indices <- c(NA, 1:50, NA, 51:100, NA, 101:150)
(since the first group is in rows 1 to 50, the second one in 51 to 100 and the third one in 101 to 150).
The result is then iris[indices, ].
A more general way of building this vector uses group_indices.
indices <- seq(nrow(iris)) %>%
split(group_indices(iris, Species)) %>%
map(~c(NA, .x)) %>%
unlist
(map comes from purrr which I assume you have loaded as you have tagged this with tidyverse).
A more recent version would be using group_modify() instead of do().
iris %>%
as_tibble() %>%
group_by(Species) %>%
group_modify(~ add_row(.x,.before=0))
#> # A tibble: 153 x 5
#> # Groups: Species [3]
#> Species Sepal.Length Sepal.Width Petal.Length Petal.Width
#> <fct> <dbl> <dbl> <dbl> <dbl>
#> 1 setosa NA NA NA NA
#> 2 setosa 5.1 3.5 1.4 0.2
#> 3 setosa 4.9 3 1.4 0.2
With a slight variation, this could also be done:
library(purrr)
library(tibble)
iris %>%
group_split(Species) %>%
map_dfr(~ .x %>%
add_row(.before = 1))
# A tibble: 153 x 5
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
<dbl> <dbl> <dbl> <dbl> <fct>
1 NA NA NA NA NA
2 5.1 3.5 1.4 0.2 setosa
3 4.9 3 1.4 0.2 setosa
4 4.7 3.2 1.3 0.2 setosa
5 4.6 3.1 1.5 0.2 setosa
6 5 3.6 1.4 0.2 setosa
7 5.4 3.9 1.7 0.4 setosa
8 4.6 3.4 1.4 0.3 setosa
9 5 3.4 1.5 0.2 setosa
10 4.4 2.9 1.4 0.2 setosa
# ... with 143 more rows
This also can be used for grouped data frame, however, it's a bit verbose:
library(dplyr)
iris %>%
group_by(Species) %>%
summarise(Sepal.Length = c(NA, Sepal.Length),
Sepal.Width = c(NA, Sepal.Width),
Petal.Length = c(NA, Petal.Length),
Petal.Width = c(NA, Petal.Width),
Species = c(NA, Species))