I have a dataset with survey score results for 3 hospitals over a number of years. This survey contains 2 questions.
The dataset looks like this -
set.seed(1234)
library(dplyr)
library(tidyr)
dataset= data.frame(Hospital=c(rep('A',10),rep('B',8),rep('C',6)),
YearN=c(2015,2016,2017,2018,2019,
2015,2016,2017,2018,2019,
2015,2016,2017,2018,
2015,2016,2017,2018,
2015,2016,2017,
2015,2016,2017),
Question=c(rep('Overall Satisfaction',5),
rep('Overall Cleanliness',5),
rep('Overall Satisfaction',4),
rep('Overall Cleanliness',4),
rep('Overall Satisfaction',3),
rep('Overall Cleanliness',3)),
ScoreYearN=c(rep(runif(24,min = 0.6,max = 1))),
TotalYearN=c(rep(round(runif(24,min = 1000,max = 5000),0))))
MY OBJECTIVE
To add two columns to the dataset such that -
The first column contains the score for the given question in the given
hospital for the previous year
The second column contains the total number of respondents for the given question in the given hospital for the previous year
MY ATTEMPT
I called the first column ScoreYearN-1 and the second column TotalYearN-1
I used the lag function to create the new columns that contain the lagged values from the existing columns.
library(dplyr)
library(tidyr)
dataset$`ScoreYearN-1`=lag(dataset$ScoreYearN)
dataset$`TotalYearN-1`=lag(dataset$TotalYearN)
Which gives me a resulting dataset where I have the desired outcome for the first five rows only (these rows correspond to the first Hospital-Question combination).
The remaining rows do not account for this grouping, and hence the 2015 'N-1' values take on the values of the previous group.
I'm not sure this is the best way to go about this problem. If you have any better suggestions, I'm happy to consider them.
Any help will be greatly appreciated.
You're close! Just use dplyr to group by hospital
dataset_lagged <- dataset %>%
group_by(Hospital,Question) %>%
mutate(`ScoreYearN-1` = lag(ScoreYearN),
`TotalYearN-1` = lag(TotalYearN))
Related
I have a large dataset, lets call it df1 (4226 observations X 186 variables)
I used a package called naniar to assess missingness, and created a dataset that shows, for each observation, what the percentage of missing data is. I then filtered the dataset, to show me only the observations (rows), in which there was less then 50% of missing data. Then, I created a dataset of just the row number of all rows that fit the missingness criteria, we can call this df2
Now, I want to create a subset of dataset df1 using the data in df2 (2044 observations X 1 variable).
Can anyone help me here?
I have tried something like:
df3 <- df2[df2$row %in% df1]
to get matched pairs due to PSM ("Matchit"-Package and Method = full) i need to specifiy my command for my longitudinal data frame. Every Case has several obeservations but i only need the first observation per patient to be included in the Matching. So the matching should be based on every patients' first observation but my later analysis should include the complete dataset of each patient with all observations.
Has anyone an idea how to achieve this?
I tried using a data subset (first observation per patient) but wasn't able to get the matching included in the data set (with all observations per patient) using "Match.data".
Thanks in advance
Simon (desperately writing his masters thesis)
My udnerstanding is that you want to create matches at just the first time point but have those matches be identified for each unit at all time points. Fortunatly, this is pretty straightforward: just perform the matching at the first time point and then merge the matched dataset with the full dataset. Here is how this might look. Let's say your original long dataset is d and has an ID column id and a time column time.
m <- matchit(treat ~ X1 + X2, data = subset(d, time == 1), method = "full")
md1 <- match.data(m)
d <- merge(d, md1[c("id", "subclass", "weights")], by = "id", all.x = TRUE)
Your new dataset should have two new columns, subclass and weights, which contain the matching subclass and matching weight for each unit. Rows with identical IDs (i.e., rows corresponding to the same unit at multiple time points) will have the same value of subclass and weight.
I have a dataset with repeated measures: measurements nested within participants (ID) nested in groups. A variable G (with range 0-100) was measured on the group-level. I want to create a new column that shows:
The first day on which the maximum value of G was reached in a group coded as zero.
How many days each measurement (in this same group) occurred before or after the day on which the maximum was reached. For example: a measurement taken 2 days before the maximum is then coded -2, and a measurement 5 days after the maximum is coded as 5.
Here is an example of what I'm aiming for: Example
I highlighted the days on which the maximum value of G was reached in the different groups. The column 'New' is what I'm trying to get.
I've been trying with dplyr and I managed to get for each group the maximum with group_by, arrange(desc), slice. I then recoded those maxima into zero and joined this dataframe with my original dataframe. However, I cannot manage to do the 'sequence' of days leading up to/ days from the maximum.
EDIT: sorry I didn't include a reprex. I used this code so far:
To find the maximum value: First order by date
data <- data[with(data, order(G, Date)),]
Find maximum and join with original data:
data2 <- data %>%
dplyr::group_by(Group) %>%
arrange(desc(c(G)), .by_group=TRUE) %>%
slice(1) %>%
ungroup()
data2$New <- data2$G
data2 <- data2 %>%
dplyr::select(c("ID", "New", "Date"))
data3 <- full_join(data, data2, by=c("ID", "Date"))
data3$New[!is.na(data3$New)] <- 0
This gives me the maxima coded as zero and all the other measurements in column New as NA but not yet the number of days leading up to this, and the number of days since. I have no idea how to get to this.
It would help if you would be able to provide the data using dput() in your question, as opposed to using an image.
It looked like you wanted to group_by(Group) in your example to compute number of days before and after the maximum date in a Group. However, you have ID of 3 and Group of A that suggests otherwise, and maybe could be clarified.
Here is one approach using tidyverse I hope will be helpful. After grouping and arranging by Date, you can look at the difference in dates comparing to the Date where G is maximum (the first maximum detected in date order).
Also note, as.numeric is included to provide a number, as the result for New is a difftime (e.g., "7 days").
library(tidyverse)
data %>%
group_by(Group) %>%
arrange(Date) %>%
mutate(New = as.numeric(Date - Date[which.max(G)]))
I am trying to identify the value of the variable in an R data frame conditioning on the value of another variable, but unable to do it.
Basically, I am giving 3 different Dose of vaccine to three groups of animals (5 animal per group ( Total )) and recording results as Protec which means the number of protected animals in each group. From the Protec, I am calculating the proportion of protection (Protec/Total as Prop for each Dose group. For example
library(dplyr)
Dose=c(1,0.25,0.0625);Dose #Dose or Dilution
Protec=c(5,4,3);Protec
Total=c(rep(5,3));Total
df=as.data.frame(cbind(Dose,Protec,Total));df
df=df %>% mutate(Prop=Protec/Total);df
Question is, what is the log10 of minimum value of Dose for which Prop==1, which can be found using the following code
X0=log10(min(df$Dose[df$Prop1==1.0]));X0
The result should be X0=0
If the Protec=c(5,5,3), the Prop becomes c(1.0,1.0,0.6) then the X0 should be -0.60206.
If the Protec=c(5,5,5), the Prop becomes c(1.0,1.0,1.0), For which I want X0=0.
if the Protec=c(5,4,5), the Prop becomes c(1.0,0.8,1.0), then also I want X0=0 because I consider them as unordered and take the highest dose for calculating X0
I think it requires if function but the conditions for which I don't know how to write the code.
can someone explain how to do it in R?. thanking you in advance
We can use mutate_at to create apply the calculation on multiple columns that have column name starting with 'Protec'
library(dplyr)
df1 <- df %>%
mutate_at(vars(starts_with("Protec")), list(Prop = ~./Total))
I have budget data on a set of districts. I also have a district, DH, that had 2 additional regions merged into it after 2012. The budget values are given separately in the data frame for the year 2011 for the three parts that were later merged into one. I want to add those values into the district DH's values for the year 2011.
I know I can use column sums, but I don't know how to use column sum for all variables using the if/else condition
columnSums(df) if District==1 | District==2
The above code is definitely not going to work because it is not in the correct form, but this is the basic gist of the code I want to use to sum all variables for the districts 1 and 2 and add it to the values of the district 'DH'.
You have to alter the district column or do create a new one that identifies the districts that belong together. Here is some pseudo code:
library(dplyr)
df %>%
mutate(District = if_else(District == 2, 1, District)) %>%
group_by(District) %>%
summarise(col_to_sum = sum(col_to_sum))