Can anyone tell me an elegant solution to achieve the same result with less code? As far as I know, there is no "un-filter" in R.
test1 <- dat_long%>%
filter(time == "0month") %>%
merge(blood_m1, by="ID")
test2 <- dat_long%>%
filter(time == "3month") %>%
merge(blood_m2, by="ID")
test3 <- dat_long%>%
filter(time == "4month") %>%
merge(blood_m3, by="ID")
test_long <- test3 %>%
bind_rows(test2 )%>%
bind_rows(test1 )
Basically, I want to achieve the "test_long" df by generating a single object and all connect with %>%. Thanks!
I think you want a cleaner blood_all lookup table to begin with, here's a suggestion :
library(dplyr)
blood_all <-
# create named list
list("0month" = blood_m1, "3month" = blood_m2, "4month", blood_m3) %>%
# bind into a single tibble, placing names into "time" column
bind_rows(, .id = "time")
test <- dat_long %>%
merge(blood, by=c("ID", "time")) # or inner_join to keep it tidyverse
Related
I have a bunch of excel files that I have loaded into R as separate dataframes. I now need to change the structure/layout of every one of these data frames. I have done all of this separately, but it is becoming very time consuming. I am not sure how there is a better way to accomplish this. My guess would be that I need to combine them all into a list and then create some type of loop to go through every data frame in that list. I need to be able to remove rows and columns from the edge, add 'row' the top left cell that is currently empty, and then follow that pivot_longer, mutate, and select functions that I have listed below that I have done separately.
names(df)[1] <- 'row'
df <- df %>%
pivot_longer((!row), names_to = "plateColumn", values_to = "Broth_t0")
df <- df %>%
mutate(wellID = paste0(row, plateColumn)) %>%
select(-c(row, plateColumn))
I have tried what is below and I get an error, does anyone have a better way that what I am currently doing to accomplish this?
for(x in seq_along(files.list)){
names(files.list)[1] <- 'row'
df <- df %>%
pivot_longer((!row), names_to = "plateColumn", values_to = "Broth_t0")
df <- df %>%
mutate(wellID = paste0(row, plateColumn)) %>%
select(-c(row, plateColumn))
}
If you have a vector of filenames my_files, I think this will work
library(tidyverse)
library(readxl)
prepare_df <- function(df) {
# make changes to df
names(df)[1] <- 'row'
df <- df %>%
pivot_longer((!row), names_to = "plateColumn", values_to = "Broth_t0")
df <- df %>%
mutate(wellID = paste0(row, plateColumn)) %>%
select(-c(row, plateColumn))
return(df)
}
names(my_files) <- my_files # often useful if the vector we're mapping over has names
dfs <- map(my_files, read_excel) # read into a list of data frames
dfs <- map(dfs, prepare_df) # prepare each one
df <- bind_rows(dfs, .id = "file") # if you prefer one data frame instead
Simple question. Considering the data frame below, I want to count distinct IDs: one for all records and one after filtering on status. However, the %>% doesn't seem to work here. I just want to have a single value as ouput (so for total this should be 10, for closed it should be 5), not a dataframe . Both # lines don't work
dat <- data.frame (ID = as.factor(c(1:10)),
status = as.factor(rep(c("open","closed"))))
total <- n_distinct(dat$ID)
#closed <- dat %>% filter(status == "closed") %>% n_distinct(dat$ID)
#closed <- dat %>% filter(status == "closed") %>% n_distinct(ID)
n_distinct expects a vector as input, you are passing a dataframe. You can do :
library(dplyr)
dat %>%
filter(status == "closed") %>%
summarise(n = n_distinct(ID))
# n
#1 5
Or without using filter :
dat %>% summarise(n = n_distinct(ID[status == "closed"]))
You can add %>% pull(n) to above if you want a vector back and not a dataframe.
An option with data.table
library(data.table)
setDT(dat)[status == "closed"][, .(n = uniqueN(ID))]
I am looking to make four graphs in ggplot each containing 7 data-series each of which is marked as a group in my data frame. I therefore need a way to filter my single long data frame by the 7 group keys. I want my code to work something like this:
library(tidyverse)
df <- mtcars[0:2]
df <- tibble::rownames_to_column(df, "groups")
grouped_df <- df %>% group_by(groups)
conditions = group_keys(grouped_df)[[1]]
subplot_1_data <- grouped_df %>% filter(groups == AMC Javelin) ## this works
subplot_2_data <- grouped_df %>% filter(conditions[6:10]) ##does not work
subplot_3_data <- grouped_df %>% filter(groups == conditions[11:15]) ## does not work
i want to generate three ggplot graphs 1 with subplot_1_data and another with subplot_2_data and a third with subplot_3_data
I am struggling to achieve this. any hint on how to get multiple groups into 1 dataframe for plotting would be appreciated.
What you are looking for is x %in% c("a", "b") instead of == when filtering using a vector.
library(tidyverse)
df <- mtcars[0:2] %>%
tibble::rownames_to_column("groups") %>%
group_by(groups)
conditions <- group_keys(grouped_df)$groups
subplot_1_data <- df %>% filter(groups == "AMC Javelin")
subplot_2_data <- df %>% filter(groups %in% conditions[6:10])
subplot_3_data <- df %>% filter(groups %in% conditions[11:15])
I am trying to build a summary table of a data frame like DataProfile below.
The idea is to transform each column into a row and add variables for count, nulls, not nulls, unique, and add additional mutations of those variables.
It seems like there should be a better faster way to do this. Is there a function that does this?
#trying to write the functions within dplyr & magrittr framework
library(tidyverse)
mtcars[2,2] <- NA # Add a null to test completeness
#
total <- mtcars %>% summarise_all(funs(n())) %>% melt
nulls <- mtcars %>% summarise_all(funs(sum(is.na(.)))) %>% melt
filled <- mtcars %>% summarise_all(funs(sum(!is.na(.)))) %>% melt
uniques <- mtcars %>% summarise_all(funs(length(unique(.)))) %>% melt
mtcars %>% summarise_all(funs(n_distinct(.))) %>% melt
#Build a Data Frame from names of mtcars and add variables with mutate
DataProfile <- as.data.frame(names(mtcars))
DataProfile <- DataProfile %>% mutate(Total = total$value,
Nulls = nulls$value,
Filled = filled $value,
Complete = Filled/Total,
Cardinality = uniques$value,
Uniqueness = Cardinality/Total,
Distinctness = Cardinality/Filled)
DataProfile
#These are other attempts with Base R, but they are harder to read and don't play well with summarise_all
sapply(mtcars, function(x) length(unique(x[!is.na(x)]))) %>% melt
rapply(mtcars,function(x)length(unique(x))) %>% melt
The summarise_all() function can process more than one function at a time, so you can consolidate code by doing it in one pass then formatting your data to get to the type of "profile" per variable that you want.
library(tidyverse)
mtcars[2,2] <- NA # Add a null to test completeness
DataProfile <- mtcars %>%
summarise_all(funs("Total" = n(),
"Nulls" = sum(is.na(.)),
"Filled" = sum(!is.na(.)),
"Cardinality" = length(unique(.)))) %>%
melt() %>%
separate(variable, into = c('variable', 'measure'), sep="_") %>%
spread(measure, value) %>%
mutate(Complete = Filled/Total,
Uniqueness = Cardinality/Total,
Distinctness = Cardinality/Filled)
DataProfile
I have a data.frame where I assign each column.name a vector of variables:
dat1 <- data.frame(a=1:5,b=1:5,c=1:5)
I want to create a new data.frame but instead of assigning each column individually, I want to assign them all at once. For example, if I wanted to rename them all:
dat.new <- data.frame(paste(names(dat1),'1',sep='') = dat1)
This obviously doens't work. Is there a way to make it work?
I understand I can just rename using names(), but the scenario where this actually seems useful is if combining multiple data sets that share the same col.names (and in which I don't want to simply rbind):
dat1 <- data.frame(a=1:5,b=1:5,c=1:5)
dat2 <- data.frame(a=6:10,b=6:10,c=6:10)
dat.new <- data.frame(paste(names(dat1),'1',sep='') = dat1, paste(names(dat1),'2',sep='') = dat2)
library(dplyr)
library(tidyr)
library(magrittr)
Ok, here's the first part:
dat2 =
dat1 %>%
setNames(names(.) %>%
paste0("1") )
Here's the second part. The reshaping is a bit complex but more flexible, especially if you have row id's already with different amounts of rows:
list(dat1, dat2) %>%
bind_rows(.id = "number") %>%
group_by(number) %>%
mutate(id = 1:n()) %>%
gather(variable, value, -number, -id) %>%
unite(new_variable, variable, number) %>%
spread(new_variable, value)