I have a rather large dataframe with 13 variables. Here is the first line just to give an idea:
prov_code nuts1 nuts1name nuts2 nuts2name prov_geoorder prov_name NUTS_ID EDAD year ORDER graphs value prov_geo
1. 15 1 NW 11 Galicia 1 La Corunna ES111 11 1975 1 1 0.000000000 La Corunna
I would like to obtain the maximum for a certain set of variables according to a combination of variables year ORDER and prov_code (ie, f_all being my data.frame: f_all[(f_all$year==1975)&(f_all$ORDER==1)&(f_all$prov_code=="1"),] ). The goal is to repeat the operation in order to obtain a new data frame containing all the maximum values for each year, ORDER, prov_code.
Is there a simple and quick way to do this?
Thanks for any suggestion on the matter,
There are several way of doing this, for example the one #James mentions. I want to suggest using plyr:
library(ply)
ddply(f_all, .(year, ORDER, prov_code), summarise, mx_value = max(value))
Alternatively, if you have a lot of data, data.table provides similar functionality, but is much much faster in that case.
Related
I am working on a project for school in R that is looking at swimming data compiled up of 8 different teams looking at each of the 13 events, over 6 years. I have over 8700 rows of data that I have appended and am trying to find out how to draw the specific means that I am looking for. For example, I would like to look at the progression of mean times for team 1 for event 3 for men. Thanks!
You can subset your data-frame to only include those variables, e.g.
ss = subset(df, team == 1 & event == 3)
mean(ss$times)
I have the following data frame:
group_id date_show date_med
1 1976-02-07 1971-04-14
1 1976-02-09 1976-12-11
1 2011-03-02 1970-03-22
2 1993-08-04 1997-06-13
2 2008-07-25 2006-09-01
2 2009-06-18 2005-11-12
3 2009-06-18 1999-11-03
I want to subset my data frame in such a way that the new data frame only shows the rows in which the values of date_show are further than 10 days apart but this condition should only be applied per group. I.e. if the values in the date_show column are less than 10 days apart but the group_ids are different, I need to keep both entries. What I want my result to look like based on the above table is:
group_id date_show date_med
1 1976-02-07 1971-04-14
1 2011-03-02 1970-03-22
2 1993-08-04 1997-06-13
2 2008-07-25 2006-09-01
2 2009-06-18 2005-11-12
3 2009-06-18 1999-11-03
Which row gets deleted isn't important because the reason why I'm subsetting in the first place is to calculate the number of rows I am left with after applying this criteria.
I've tried playing around with the diff function but I'm not sure how to go about it in the simplest possible way because this problem is already within another sapply function so I'm trying to avoid any kind of additional loop (in this case by group_id).
The df I'm working with has around 100 000 rows. Ideally, I would like to do this with base R because I have no rights to install any additional packages on the machine I'm working on but if this is not possible (or if solving this with an additional package would be significantly better), I can try and ask my admin to install it.
Any tips would be appreciated!
I'm quite a newbie in R so I was interested in the optimality of my solution. Even if it works it could be (a bit) long and I wanted your advice to see if the "way I solved it" is "the best" and it could help me to learn new techniques and functions in R.
I have a dataset on students identified by their id and I have the school where they are matched and the score they obtained at a specific test (so for short: 3 variables id,match and score).
I need to construct the following table: for students in between two percentiles of score, I need to calculate the average score (between students) of the average score of the students of the school they are matched to (so for each school I take the average score of the students matched to it and then I calculate the average of this average for percentile classes, yes average of a school could appear twice in this calculation). In English it allows me to answer: "A student belonging to the x-th percentile in terms of score will be in average matched to a school with this average quality".
Here is an example in the picture:
So in that case, if I take the median (15) for the split (rather than percentiles) I would like to obtain:
[0,15] : 9.5
(15,24] : 20.25
So for students having a score between 0 and 15 I take the average of the average score of the school they are matched to (note that b average will appears twice but that's ok).
Here how I did it:
match <- c(a,b,a,b,c)
score <- c(18,4,15,8,24)
scoreQuant <- cut(score,quantile(score,probs=seq(0,1,0.1),na.rm=TRUE))
AvgeSchScore <- tapply(score,match,mean,na.rm=TRUE)
AvgScore <- 0
for(i in 1:length(score)) {
AvgScore[i] <- AvgeSchScore[match[i]]
}
results <- tapply(AvgScore,scoreQuant,mean,na.rm = TRUE)
If you have a more direct way of doing it.. Or I think the bad point is 3) using a loop, maybe apply() is better ? But I'm not sure how to use it here (I tried to code my own function but it crashed so I "bruted force it").
Thanks :)
The main fix is to eliminate the for loop with:
AvgScore <- AvgeSchScore[match]
R allows you to subset in ways that you cannot in other languages. The tapply function outputs the names of the factor that you grouped by. We are using those names for match to subset AvgeScore.
data.table
If you would like to try data.table you may see speed improvements.
library(data.table)
match <- c("a","b","a","b","c")
score <- c(18,4,15,8,24)
dt <- data.table(id=1:5, match, score)
scoreQuant <- cut(dt$score,quantile(dt$score,probs=seq(0,1,0.1),na.rm=TRUE))
dt[, AvgeScore := mean(score), match][, mean(AvgeScore), scoreQuant]
# scoreQuant V1
#1: (17.4,19.2] 16.5
#2: NA 6.0
#3: (12.2,15] 16.5
#4: (7.2,9.4] 6.0
#5: (21.6,24] 24.0
It may be faster than base R. If the value in the NA row bothers you, you can delete it after.
I'm new to R and I am having some trouble iterating through the unique element of a vector. I have a dataframe "School" with 700 different teachers. Each teacher has around 40 students.
I want to be able to loop through each teacher, create a graphs for the mean score of his/her students' over time, save the graphs in a folder and automatically email that folder to that teacher.
I'm just getting started and am having trouble setting up the for-loop. In Stata, I know how to loop through each unique element in a list, but am having trouble doing that in R. Any help would be appreciated.
School$Teacher School$Student School$ScoreNovember School$ScoreDec School$TeacherEmail
A 1 35 45 A#school.org
A 2 43 65 A#school.org
B 1 66 54 B#school.org
A 3 97 99 A#school.org
C 1 23 45 C#school.org
Your question seems a bit vague and it looks like you want us to write your whole project. Could you share what you have done so far and where exactly you are struggling?
see ?subset
School=data.frame(Teacher=c("A","B"), ScoreNovember=10:11, ScoreDec=13:14)
for (teacher in unique(School$Teacher)) {
teacher_df=subset(School, Teacher==teacher)
MeanScoreNovember=mean(teacher_df$ScoreNovember)
MeanScoreDec =mean(teacher_df$ScoreDec)
# do your plot
# send your email
}
I think you have 3 questions, which will need separate questions, how do I:
Create graphs
Automatically email output
Compute a subset mean based on group
For the 3rd one, I like using the plyr package, other people will recommend data.table or dplyrpackages. You can also use aggregate from base. To get a teacher's mean:
library(plyr)
ddply(School,.(Teacher),summarise,Nov_m=mean(ScoreNovember))
If you want per student per teacher, etc. just add between the columns, like:
library(plyr)
ddply(School,.(Teacher,Student),summarise,Nov_m=mean(ScoreNovember))
You could do that for each score column (and then chart it) if your data was long rather than wide you could also add the date ('November', 'Dec') as a group in the brackets, or:
library(plyr)
ddply(School,.(Teacher,Student),summarise,Nov_m=mean(ScoreNovember),Dec_m=mean(ScoreDec))
See if that helps with the 3rd, but look at splitting your questions up too.
First of all, I apologize for the title. I really don't know how to succinctly explain this issue in one sentence.
I have a dataframe where each row represents some aspect of a hospital visit by a patient. A single patient might have thousands of rows for dozens of hospital visits, and each hospital visit could account for several rows.
One column is Medical.Record.Number, which corresponds to Patient IDs, and the other is Patient.ID.Visit, which corresponds to an ID for an individual hospital visit. I am trying to calculate the number of hospital visits each each patient has had.
For example:
Medical.Record.Number Patient.ID.Visit
AAAXXX 1111
AAAXXX 1112
AAAXXX 1113
AAAZZZ 1114
AAAZZZ 1114
AAABBB 1115
AAABBB 1116
would produce the following:
Medical.Record.Number Number.Of.Visits
AAAXXX 3
AAAZZZ 1
AAABBB 2
The solution I am currently using is the following, where "data" is my dataframe:
#this function returns the number of unique hospital visits associated with the
#supplied record number
countVisits <- function(record.number){
visits.by.number <- data$Patient.ID.Visit[which(data$Medical.Record.Number
== record.number)]
return(length(unique(visits.by.number)))
}
recordNumbers <- unique(data$Medical.Record.Number)
visits <- integer()
for (record in recordNumbers){
visits <- c(visits, countVisits(record))
}
visit.counts <- data.frame(recordNumbers, visits)
This works, but it is pretty slow. I am dealing with potentially millions of rows of data, so I'd like something efficient. From what little I know about R, I know there's usually a faster way to do things without using a for-loop.
This essentially looks like a table() operation after you take out duplicates. First, some sample data
#sample data
dd<-read.table(text="Medical.Record.Number Patient.ID.Visit
AAAXXX 1111
AAAXXX 1112
AAAXXX 1113
AAAZZZ 1114
AAAZZZ 1114
AAABBB 1115
AAABBB 1116", header=T)
then you could do
tt <- table(Medical.Record.Number=unique(dd)$Medical.Record.Number)
as.data.frame(tt, responseName="Number.Of.Visits") #to get a data.frame rather than named vector (table)
# Medical.Record.Number Number.Of.Visits
# 1 AAABBB 2
# 2 AAAXXX 3
# 3 AAAZZZ 1
Or you could also think of this as an aggregation problem
aggregate(Patient.ID.Visit~Medical.Record.Number, dd, function(x) length(unique(x)))
# Medical.Record.Number Patient.ID.Visit
# 1 AAABBB 2
# 2 AAAXXX 3
# 3 AAAZZZ 1
There are many ways to do this, #MrFlick provided handful of perfectly valid approaches. Personally I'm fond of the data.table package. Its faster on large data frames and I find the logic to be more intuitive than the base functions. I'd check it out if you are having problems with execution time.
library(data.table)
med.dt <- data.table(med_tbl)
num.visits.dt <- med.dt[ , num_visits = length(unique(Patient.ID.Visit)),
by = Medical.Record.Number]
data.Table should be much faster than data.frame on a large tables.