I need to split my data so that when I use the facet_wrap I have the top 50 percentile for each year.
Here is a sample of my data:
# A tibble: 10,519 x 3
Species Abundance Year
<chr> <dbl> <chr>
1 Astropecten irregularis 2 2009
2 Asterias rubens 14 2009
3 Echinus esculentus 1 2009
4 Pagurus prideaux 1 2009
5 Raja clavata 1 2009
6 Astropecten irregularis 4 2009
7 Asterias rubens 47 2009
8 Henricia sp. 2 2009
9 Ophiura ophiura 8 2009
10 Solaster endeca 1 2009
# ... with 10,509 more rows
My current strategy is this:
Data <- All_years %>%
group_by(Species, Year) %>%
summarise(Abundance = sum(Abundance, na.rm = TRUE)) %>%
filter(quantile(Abundance, 0.50)<Abundance) %>%
filter(Abundance > 50)
The issue is that this gives me the top 50 percentile for the whole set while I would like it to give me the top 50 for each year so I can then display it with a facet_wrap in ggplot.
Related
Below is my dataset, which contains four columns id, year, quarter, and price.
df <- data.frame(id = c(1,2,1,2),
year = c(2010,2010,2011,2011),
quarter = c("2010-q1","2010-q2","2011-q1","2011-q2"),
price = c(10,50,10,50))
Now I want to expand this dataset for 2012 and 2013. First, I want to copy rows for 2010 and 2011 and paste them below, and after that, replace these values for years and quarters with 2012 and 2013 and also quarters with 2012-q1,2012-q2,2013-q1 and 2013-q2.
So can anybody help me with how to solve this and prepare the table as the table below?
df %>%
mutate(year = year + 2, quarter = paste0(year, "-q", id)) %>%
bind_rows(df, .)
id year quarter price
1 1 2010 2010-q1 10
2 2 2010 2010-q2 50
3 1 2011 2011-q1 10
4 2 2011 2011-q2 50
5 1 2012 2012-q1 10
6 2 2012 2012-q2 50
7 1 2013 2013-q1 10
8 2 2013 2013-q2 50
I am trying to extract the team with the maximum number of wins each year in women's college basketball, and I am currently stuck with having the number of wins for each year for each team, and I want only the team with the maximum number of wins in each year.
winsbyyear <- WomenCBnewdf %>%
group_by(Year,Team)%>%
summarise(totalwinsyr = sum(Outcome))
Output currently looks like this, but I am expecting to see each year only once with the team with the maximum number of wins in the subsequent columns
Year Team totalwinsyr
<fct> <chr> <dbl>
1 2014 AbileneChristian 10
2 2014 AirForce 0
3 2014 Akron 18
4 2014 Alabama 10
5 2014 AlabamaAM 3
6 2014 AlabamaHuntsville 0
7 2014 AlabamaMobile 0
8 2014 AlabamaSt 15
9 2014 AlaskaAnchorage 1
10 2014 AlbanyNY 16
How to select the rows with maximum values in each group with dplyr?
I have already looked here but I could not find any resources to help with a group_by() with multiple values
Create a new column with the number of wins and then filter:
winsbyyear <- WomenCBnewdf %>%
group_by(Year,Team)%>%
mutate(totalwinsyr = sum(Outcome)) %>%
filter(totalwinsyr == max(totalwinsyr))
I am working on creating conditional averages for a large data set that involves # of flu cases seen during the week for several years. The data is organized as such:
What I want to do is create a new column that tabulates that average number of cases for that same week in previous years. For instance, for the row where Week.Number is 1 and Flu.Year is 2017, I would like the new row to give the average count for any year with Week.Number==1 & Flu.Year<2017. Normally, I would use the case_when() function to conditionally tabulate something like this. For instance, when calculating the average weekly volume I used this code:
mutate(average = case_when(
Flu.Year==2016 ~ mean(chcc$count[chcc$Flu.Year==2016]),
Flu.Year==2017 ~ mean(chcc$count[chcc$Flu.Year==2017]),
Flu.Year==2018 ~ mean(chcc$count[chcc$Flu.Year==2018]),
Flu.Year==2019 ~ mean(chcc$count[chcc$Flu.Year==2019]),
),
However, since there are four years of data * 52 weeks which is a lot of iterations to spell out the conditions for. Is there a way to elegantly code this in dplyr? The problem I keep running into is that I want to call values in counts column based on Week.Number and Flu.Year values in other rows conditioned on the current value of Week.Number and Flu.Year, and I am not sure how to accomplish that. Please let me know if there is further information / detail I can provide.
Thanks,
Steven
dat <- tibble( Flu.Year = rep(2016:2019,each = 52), Week.Number = rep(1:52,4), count = sample(1000, size=52*4, replace=TRUE) )
It's bad-form and, in some cases, an error when you use $-indexing within dplyr verbs.
I think a better way to get that average field is to group_by(Flu.Year) and calculate it straight-up.
library(dplyr)
set.seed(42)
dat <- tibble(
Flu.Year = sample(2016:2020, size=100, replace=TRUE),
count = sample(1000, size=100, replace=TRUE)
)
dat %>%
group_by(Flu.Year) %>%
mutate(average = mean(count)) %>%
# just to show a quick summary
slice(1:3) %>%
ungroup()
# # A tibble: 15 x 3
# Flu.Year count average
# <int> <int> <dbl>
# 1 2016 734 578.
# 2 2016 356 578.
# 3 2016 411 578.
# 4 2017 217 436.
# 5 2017 453 436.
# 6 2017 920 436.
# 7 2018 963 558
# 8 2018 609 558
# 9 2018 536 558
# 10 2019 943 543.
# 11 2019 740 543.
# 12 2019 536 543.
# 13 2020 627 494.
# 14 2020 218 494.
# 15 2020 389 494.
An alternative approach is to generate a summary table (just one row per year) and join it back in to the original data.
dat %>%
group_by(Flu.Year) %>%
summarize(average = mean(count))
# # A tibble: 5 x 2
# Flu.Year average
# <int> <dbl>
# 1 2016 578.
# 2 2017 436.
# 3 2018 558
# 4 2019 543.
# 5 2020 494.
dat %>%
group_by(Flu.Year) %>%
summarize(average = mean(count)) %>%
full_join(dat, by = "Flu.Year")
# # A tibble: 100 x 3
# Flu.Year average count
# <int> <dbl> <int>
# 1 2016 578. 734
# 2 2016 578. 356
# 3 2016 578. 411
# 4 2016 578. 720
# 5 2016 578. 851
# 6 2016 578. 822
# 7 2016 578. 465
# 8 2016 578. 679
# 9 2016 578. 30
# 10 2016 578. 180
# # ... with 90 more rows
The result, after chat:
tibble( Flu.Year = rep(2016:2018,each = 3), Week.Number = rep(1:3,3), count = 1:9 ) %>%
arrange(Flu.Year, Week.Number) %>%
group_by(Week.Number) %>%
mutate(year_week.average = lag(cumsum(count) / seq_along(count)))
# # A tibble: 9 x 4
# # Groups: Week.Number [3]
# Flu.Year Week.Number count year_week.average
# <int> <int> <int> <dbl>
# 1 2016 1 1 NA
# 2 2016 2 2 NA
# 3 2016 3 3 NA
# 4 2017 1 4 1
# 5 2017 2 5 2
# 6 2017 3 6 3
# 7 2018 1 7 2.5
# 8 2018 2 8 3.5
# 9 2018 3 9 4.5
We can use aggregate from base R
aggregate(count ~ Flu.Year, data, FUN = mean)
I have tried to find a solution via similar topics, but haven't found anything suitable. This may be due to the search terms I have used. If I have missed something, please accept my apologies.
Here is a excerpt of my data UN_ (the provided sample should be sufficient):
country year sector UN
AT 1990 1 1.407555
AT 1990 2 1.037137
AT 1990 3 4.769618
AT 1990 4 2.455139
AT 1990 5 2.238618
AT 1990 Total 7.869005
AT 1991 1 1.484667
AT 1991 2 1.001578
AT 1991 3 4.625927
AT 1991 4 2.515453
AT 1991 5 2.702081
AT 1991 Total 8.249567
....
BE 1994 1 3.008115
BE 1994 2 1.550344
BE 1994 3 1.080667
BE 1994 4 1.768645
BE 1994 5 7.208295
BE 1994 Total 1.526016
BE 1995 1 2.958820
BE 1995 2 1.571759
BE 1995 3 1.116049
BE 1995 4 1.888952
BE 1995 5 7.654881
BE 1995 Total 1.547446
....
What I want to do is, to add another row with UN_$sector = Residual. The value of residual will be (UN_$sector = Total) - (the sum of column UN for the sectors c("1", "2", "3", "4", "5")) for a given year AND country.
This is how it should look like:
country year sector UN
AT 1990 1 1.407555
AT 1990 2 1.037137
AT 1990 3 4.769618
AT 1990 4 2.455139
AT 1990 5 2.238618
----> AT 1990 Residual TO BE CALCULATED
AT 1990 Total 7.869005
As I don't want to write many, many lines of code I'm looking for a way to automate this. I was told about loops, but can't really follow the concept at the moment.
Thank you very much for any type of help!!
Best,
Constantin
PS: (for Parfait)
country year sector UN ETS
UK 2012 1 190336512 NA
UK 2012 2 18107910 NA
UK 2012 3 8333564 NA
UK 2012 4 11269017 NA
UK 2012 5 2504751 NA
UK 2012 Total 580957306 NA
UK 2013 1 177882200 NA
UK 2013 2 20353347 NA
UK 2013 3 8838575 NA
UK 2013 4 11051398 NA
UK 2013 5 2684909 NA
UK 2013 Total 566322778 NA
Consider calculating residual first and then stack it with other pieces of data:
# CALCULATE RESIDUALS BY MERGED COLUMNS
agg <- within(merge(aggregate(UN ~ country + year, data = subset(df, sector!='Total'), sum),
aggregate(UN ~ country + year, data = subset(df, sector=='Total'), sum),
by=c("country", "year")),
{UN <- UN.y - UN.x
sector = 'Residual'})
# ROW BIND DIFFERENT PIECES
final_df <- rbind(subset(df, sector!='Total'),
agg[c("country", "year", "sector", "UN")],
subset(df, sector=='Total'))
# ORDER ROWS AND RESET ROWNAMES
final_df <- with(final_df, final_df[order(country, year, as.character(sector)),])
row.names(final_df) <- NULL
Rextester demo
final_df
# country year sector UN
# 1 AT 1990 1 1.407555
# 2 AT 1990 2 1.037137
# 3 AT 1990 3 4.769618
# 4 AT 1990 4 2.455139
# 5 AT 1990 5 2.238618
# 6 AT 1990 Residual -4.039062
# 7 AT 1990 Total 7.869005
# 8 AT 1991 1 1.484667
# 9 AT 1991 2 1.001578
# 10 AT 1991 3 4.625927
# 11 AT 1991 4 2.515453
# 12 AT 1991 5 2.702081
# 13 AT 1991 Residual -4.080139
# 14 AT 1991 Total 8.249567
# 15 BE 1994 1 3.008115
# 16 BE 1994 2 1.550344
# 17 BE 1994 3 1.080667
# 18 BE 1994 4 1.768645
# 19 BE 1994 5 7.208295
# 20 BE 1994 Residual -13.090050
# 21 BE 1994 Total 1.526016
# 22 BE 1995 1 2.958820
# 23 BE 1995 2 1.571759
# 24 BE 1995 3 1.116049
# 25 BE 1995 4 1.888952
# 26 BE 1995 5 7.654881
# 27 BE 1995 Residual -13.643015
# 28 BE 1995 Total 1.547446
I think there are multiple ways you can do this. What I may recommend is to take advantage of the tidyverse suite of packages which includes dplyr.
Without getting too far into what dplyr and tidyverse can achieve, we can talk about the power of dplyr's inline commands group_by(...), summarise(...), arrange(...) and bind_rows(...) functions. Also, there are tons of great tutorials, cheat sheets, and documentation on all tidyverse packages.
Although it is less and less relevant these days, we generally want to avoid for loops in R. Therefore, we will create a new data frame which contains all of the Residual values then bring it back into your original data frame.
Step 1: Calculating all residual values
We want to calculate the sum of UN values, grouped by country and year. We can achieve this by this value
res_UN = UN_ %>% group_by(country, year) %>% summarise(UN = sum(UN, na.rm = T))
Step 2: Add sector column to res_UN with value 'residual'
This should yield a data frame which contains country, year, and UN, we now need to add a column sector which the value 'Residual' to satisfy your specifications.
res_UN$sector = 'Residual'
Step 3 : Add res_UN back to UN_ and order accordingly
res_UN and UN_ now have the same columns and they can now be added back together.
UN_ = bind_rows(UN_, res_UN) %>% arrange(country, year, sector)
Piecing this all together, should answer your question and can be achieved in a couple lines!
TLDR:
res_UN = UN_ %>% group_by(country, year) %>% summarise(UN = sum(UN, na.rm = T))`
res_UN$sector = 'Residual'
UN_ = bind_rows(UN_, res_UN) %>% arrange(country, year, sector)
I would like like to calculate the median not only for different groups of my data, but also the median over all groups and store the result in a single data.frame. While accomplishing each of these tasks separately is easy, I have not found a clean way to do both at the same time.
Right now, what I'm doing is calculate both statistics separately; then join the results; then tidy the data if necessary. Here's an example of what this may look like if I wanted to know the median delay per day and per month:
library(dplyr)
library(hflights)
data(hflights)
# Calculate both statistics separately
per_day <- hflights %>%
group_by(Year, Month, DayofMonth) %>%
summarise(Delay = mean(ArrDelay, na.rm = TRUE)) %>%
mutate(Interval = "Daily")
per_month <- hflights %>%
group_by(Year, Month) %>%
summarise(Delay = mean(ArrDelay, na.rm = TRUE)) %>%
mutate(Interval = "Monthly", DayofMonth = NA)
# Join into a single data.frame
my_summary <- full_join(per_day, per_month,
by = c("Year", "Month", "DayofMonth", "Interval", "Delay"))
my_summary
# Source: local data frame [377 x 5]
# Groups: Year, Month
#
# Year Month DayofMonth Delay Interval
# 1 2011 1 1 10.067642 Daily
# 2 2011 1 2 10.509745 Daily
# 3 2011 1 3 6.038627 Daily
# 4 2011 1 4 7.970740 Daily
# 5 2011 1 5 4.172650 Daily
# 6 2011 1 6 6.069909 Daily
# 7 2011 1 7 3.907295 Daily
# 8 2011 1 8 3.070140 Daily
# 9 2011 1 9 17.254325 Daily
# 10 2011 1 10 11.040388 Daily
# .. ... ... ... ... ...
Are there better ways to do this?
(Note that in many cases one could easily progressively roll up summaries as pointed out in the Introduction to dplyr. However, this doesn't work for statistics like median, mean etc.)
As a one-off table. This is fairly straightforward in data.table:
require(data.table)
setDT(hflights)[,{
mo_del <- mean(ArrDelay,na.rm=TRUE)
.SD[,.(DailyDelay = mean(ArrDelay,na.rm=TRUE),MonthlyDelay = mo_del),by=DayofMonth]
},by=.(Year,Month)]
# Year Month DayofMonth DailyDelay MonthlyDelay
# 1: 2011 1 1 10.0676417 4.926065
# 2: 2011 1 2 10.5097451 4.926065
# 3: 2011 1 3 6.0386266 4.926065
# 4: 2011 1 4 7.9707401 4.926065
# 5: 2011 1 5 4.1726496 4.926065
# ---
# 361: 2011 12 14 1.0293610 5.013244
# 362: 2011 12 17 -0.1049822 5.013244
# 363: 2011 12 24 -4.1457490 5.013244
# 364: 2011 12 25 -2.2976827 5.013244
# 365: 2011 12 31 46.4846491 5.013244
How it works. The basic syntax is DT[i,j,by].
With by=.(Year,Month), all operations in j are done per "by group."
We can nest another "by group" using the data.table of the current Subset of Data, .SD.
To return columns in j we use .(colname1=col1,colname2=col2,...).
Creating new variables. Alternately, we could create new variables in hflights using := in j.
hflights[,DailyDelay := mean(ArrDelay,na.rm=TRUE),.(Year,Month,DayofMonth)]
hflights[,MonthlyDelay := mean(ArrDelay,na.rm=TRUE),.(Year,Month)]
Then we can view the summary table:
hflights[,.GRP,.(Year,Month,DayofMonth,DailyDelay,MonthlyDelay)]
# Year Month DayofMonth DailyDelay MonthlyDelay .GRP
# 1: 2011 1 1 10.0676417 4.926065 1
# 2: 2011 1 2 10.5097451 4.926065 2
# 3: 2011 1 3 6.0386266 4.926065 3
# 4: 2011 1 4 7.9707401 4.926065 4
# 5: 2011 1 5 4.1726496 4.926065 5
# ---
# 361: 2011 12 14 1.0293610 5.013244 361
# 362: 2011 12 17 -0.1049822 5.013244 362
# 363: 2011 12 24 -4.1457490 5.013244 363
# 364: 2011 12 25 -2.2976827 5.013244 364
# 365: 2011 12 31 46.4846491 5.013244 365
(Something needed to be put in j here, so I used the "by group" code, .GRP.)