In R, I have a matrix: matClust4 which holds all vectors that are in cluster 4 after executing the kmeans algorithm.
matClust4 has dimensions 27 X 31 and has the rownames attribute set for each vector.
What I would like to do is give another attribute to each row vector in matClust4
I would prefer to use the apply function. I would like to try something like this:
apply(matClust4, 1, function(v) SOME_ATTRIBUTE(v) = idClust4)
#where idClust4 is some previous calculated result
How can I create/use an attribute of matClust4 to do this?
You woud not need to use apply for that purpose if the to-be-assigned values had already been computed (and had the same number of elements as matClust4 had rows. You should just assign an R attribute with:
attr(matClust4, 'SOME_ATTRIBUTE') = idClust4
This is how Frank Harrell creates value labels for datasets he imports from SAS. You do need to be careful that reordering or alterations of the dataframe could upset the association with the vector, since there would be enforcement of consistency by [<- or sort or order.
Related
Looking for a vectorized base R solution for my own edification. I'm assigning a value to a column in a data frame based on a value in another column in the data frame.
My solution creates a named vector of possible codes, looks up the code in the original column, subsets the named list by the value found, and assigns the resulting name to the new column. I'm sure there's a way to do exactly this using the named vector I created that doesn't need a for loop; is it some version of apply?
dplyr is great and useful and I'm not looking for a solution that uses it.
# reference vector for assigning more readable text to this table
tempAssessmentCodes <- setNames(c(600,301,302,601,303,304,602,305,306,603,307,308,604,309,310,605,311,312,606,699),
c("base","3m","6m","6m","9m","12m","12m","15m","18m","18m","21m","24m","24m","27m","30m","30m",
"33m","36m","36m","disch"))
for(i in 1:nrow(rawDisp)){
rawDisp$assessText[i] <- names(tempAssessmentCodes)[tempAssessmentCodes==rawDisp$assessment[i]]
}
The standard way is to use match():
rawDisp$assessText <- names(tempAssessmentCodes)[match(rawDisp$assessment, tempAssessmentCodes)]
For each y element match(x, y) will find a corresponding element index in x. Then we use the names of y for replacing values with names.
Personally, I do it the opposite way - make tempAssesmentCodes have names that correspond to old codes, and values correspond to new codes:
codes <- setNames(names(tempAssessmentCodes), tempAssessmentCodes)
Then simply select elements from the new codes using the names (old codes):
rawDisp$assessText <- codes[as.character(rawDisp$assessment)]
Consider the following simulation snippet:
k <- 1:5
x <- seq(0,10,length.out = 100)
dsts <- lapply(1:length(k), function(i) cbind(x=x, distri=dchisq(x,k[i]),i) )
dsts <- do.call(rbind,dsts)
why does this code throws an error (dsts is matrix):
subset(dsts,i==1)
#Error in subset.matrix(dsts, i == 1) : object 'i' not found
Even this one:
colnames(dsts)[3] <- 'iii'
subset(dsts,iii==1)
But not this one (matrix coerced as dataframe):
subset(as.data.frame(dsts),i==1)
This one works either where x is already defined:
subset(dsts,x> 500)
The error occurs in subset.matrix() on this line:
else if (!is.logical(subset))
Is this a bug that should be reported to R Core?
The behavior you are describing is by design and is documented on the ?subset help page.
From the help page:
For data frames, the subset argument works on the rows. Note that subset will be evaluated in the data frame, so columns can be referred to (by name) as variables in the expression (see the examples).
In R, data.frames and matrices are very different types of objects. If this is causing a problem, you are probably using the wrong data structure for your data. Matrices are really only necessary if you meed matrix arithmetic. If you are thinking of your columns as different attributes for a row observations, then you should be storing your data in a data.frame in the first place. You could store all your values in a simple vector where every three values represent one observation, but that would also be a poor choice of data structure for your data. I'm not sure if you were trying to be more efficient by choosing a matrix but it seems like just the wrong choice.
A data.frame is stored as a named list while a matrix is stored as a dimensioned vector. A list can be used as an environment which makes it easy to evaluate variable names in that context. The biggest difference between the two is that data.frames can hold columns of different classes (numerics, characters, dates) while matrices can only hold values of exactly one data.type. You cannot always easily convert between the two without a loss of information.
Thinks like $ only work with data.frames as well.
dd <- data.frame(x=1:10)
dd$x
mm <- matrix(1:10, ncol=1, dimnames=list(NULL, "x"))
mm$x # Error
If you want to subset a matrix, you are better off using standard [ subsetting rather than the sub setting function.
dsts[ dsts[,"i"]==1, ]
This behavior has been a part of R for a very long time. Any changes to this behavior is likely to introduce breaking changes to existing code that relies on variables being evaluated in a certain context. I think the problem lies with whomever told you to use a matrix in the first place. Rather than cbind(), you should have used data.frame()
I am trying to change the final correcttot function from a for loop to apply, but have been running into issues in trying to get the apply function to take the underlying values in df, the array which I will be applying it to.
correcttot<-function(v,p,r){
df<-expand.grid(i=1:10,j=1:10,k=1:10,l=1:10,m=2:10,n=2:10,o=1:10))
df$correct3<-0
df$correct3<- apply(df, 1:7, function(x)
percentcorrect((x$i)/10,(x$j)/10,(x$k)*20,(x$l)*20,x$m,x$n,x$o,v,p,r)
)
df$correct3
}
newvec2<-correcttot(v,p,r)
The second argument of apply is not the column numbers, it's the number of the dimension. Your data frame only has two dimensions: rows (1) and columns (2).
For your analysis, set the second argument to 1 indicating you're applying the function to each row.
Dear Friends I would appreciate if someone can help me in some question in R.
I have a data frame with 8 variables, lets say (v1,v2,...,v8).I would like to produce groups of datasets based on all possible combinations of these variables. that is, with a set of 8 variables I am able to produce 2^8-1=63 subsets of variables like {v1},{v2},...,{v8}, {v1,v2},....,{v1,v2,v3},....,{v1,v2,...,v8}
my goal is to produce specific statistic based on these groupings and then compare which subset produces a better statistic. my problem is how can I produce these combinations.
thanks in advance
You need the function combn. It creates all the combinations of a vector that you provide it. For instance, in your example:
names(yourdataframe) <- c("V1","V2","V3","V4","V5","V6","V7","V8")
varnames <- names(yourdataframe)
combn(x = varnames,m = 3)
This gives you all permutations of V1-V8 taken 3 at a time.
I'll use data.table instead of data.frame;
I'll include an extraneous variable for robustness.
This will get you your subsetted data frames:
nn<-8L
dt<-setnames(as.data.table(cbind(1:100,matrix(rnorm(100*nn),ncol=nn))),
c("id",paste0("V",1:nn)))
#should be a smarter (read: more easily generalized) way to produce this,
# but it's eluding me for now...
#basically, this generates the indices to include when subsetting
x<-cbind(rep(c(0,1),each=128),
rep(rep(c(0,1),each=64),2),
rep(rep(c(0,1),each=32),4),
rep(rep(c(0,1),each=16),8),
rep(rep(c(0,1),each=8),16),
rep(rep(c(0,1),each=4),32),
rep(rep(c(0,1),each=2),64),
rep(c(0,1),128)) *
t(matrix(rep(1:nn),2^nn,nrow=nn))
#now get the correct column names for each subset
# by subscripting the nonzero elements
incl<-lapply(1:(2^nn),function(y){paste0("V",1:nn)[x[y,][x[y,]!=0]]})
#now subset the data.table for each subset
ans<-lapply(1:(2^nn),function(y){dt[,incl[[y]],with=F]})
You said you wanted some statistics from each subset, in which case it may be more useful to instead specify the last line as:
ans2<-lapply(1:(2^nn),function(y){unlist(dt[,incl[[y]],with=F])})
#exclude the first row, which is null
means<-lapply(2:(2^nn),function(y){mean(ans2[[y]])})
I am currently working on a code which applies to various datasets from an experiment which looks at a wide range of variables which might not be present in every repetition. My first step is to create an empty dataset with all the possible variables, and then write a function which retains columns that are in the dataset being inputted and delete the rest. Here is an example of how I want to achieve this:-
x<-c("a","b","c","d","e","f","g")
y<-c("c","f","g")
Is there a way of removing elements of x that aren't present in y and/or retaining values of x that are present in y?
For your first question: "My first step is to create an empty dataset with all the possible variables", I would use factor on the concatenation of all the vectors, for example:
all_vect = c(x, y)
possible = levels(factor(all_vect))
Then, for the second part " write a function which retains columns that are in the dataset being inputted and delete the rest", I would write:
df[,names(df)%in%possible]
As akrun wrote, use intersect(x,y) or
> x[x %in% y]