I'm coming because, I don't need help to realize the exercise, but I need help on an error that I can't fix..
This is the subject:
In R the more appropriate indicator for missing data is “NA” (not available). Therefore, replace each occurrence of “?” with “NA”.
a. For this exercise, create an R data frame for the mammographic data using only datapoints that have no missing values. This can be done using the complete.cases function which inputs a data frame and returns a Boolean vector v, where v[i] equals TRUE iff the i the data-frame sample is complete (meaning it does not possess an NA). For example, if the data-frame is stored in mammogram.frame, then mammogram2.frame = mammogram.frame[complete.cases(mammogram.frame),] creates a new data frame called mammogram2.frame that has all the complete mammogram data samples.
So I coded that:
mammogram = read.table("https://archive.ics.uci.edu/ml/machine-learning-databases/mammographic-masses/mammographic_masses.data",
sep=",",
col.names=c("Birads","Age","Shape","Margin","Density","Severity"),
fill=TRUE,
strip.white=TRUE)
#Replace N/A by -1
mammogram2.frame = mammogram.frame[complete.cases(mammogram.frame),]
#Display data frame
mammogram2
However I get this error:
> mammogram2.frame = mammogram.frame[complete.cases(mammogram.frame),]
Error: object 'mammogram.frame' not found
I can't find on internet any solution about it, I tried lot of stuff but the missing values are still '?'
Thank
Related
In my data frame I am trying to sort the data in descending order. I am using the below line of code for sorting my data and it works as intended.
CNS25VOL <- CNS25VOL[order(-CNS25VOL$MATVOL22), ]
However if I refer to the same column by it's index number, the code throws an error
CNS25VOL <- CNS25VOL[order(-CNS25VOL[, 2]), ]
Error thrown is
Error in CNS25VOL[, 2] : incorrect number of dimensions
While I do have a solution to what I am intending to do, but issue I see is if all of a sudden name of my column changes the code won't work. I know that their position will stay same in the data frame.
How can we handle it.
order(-CNS25VOL[, 2]) order here does expect a vector which you try to construct via the [] in CNS25VOL[, 2]. Normal dataframes will return a vector consisting only of the 2nd column. A tibble however will return a tibble with only one column.
You can reproduce the behaviour of normal data.frames with the drop = FALSE argument to [] as in
CNS25VOL[, 2, drop = TRUE]
Try to always be aware whether you are using a standard data.frame or a tibble or a data.table because they look very similar and are not in the details. Also see https://tibble.tidyverse.org/reference/subsetting.html
dplyr functions tend to give you a tibble back even if you fed them a classical data.frame.
I would like to perform a HCPC on the columns of my dataset, after performing a CA. For some reason I also have to specify at the start, that all of my columns are of type 'factor', just to loop over them afterwards again and convert them to numeric. I don't know why exactly, because if I check the type of each column (without specifying them as factor) they appear to be numeric... When I don't load and convert the data like this, however, I get an error like the following:
Error in eigen(crossprod(t(X), t(X)), symmetric = TRUE) : infinite or
missing values in 'x'
Could this be due to the fact that there are columns in my dataset that only contain 0's? If so, how come that it works perfectly fine by reading everything in first as factor and then converting it to numeric before applying the CA, instead of just performing the CA directly?
The original issue with the HCPC, then, is the following:
# read in data; 40 x 267 data frame
data_for_ca <- read.csv("./data/data_clean_CA_complete.csv",row.names=1,colClasses = c(rep('factor',267)))
# loop over first 267 columns, converting them to numeric
for(i in 1:267)
data_for_ca[[i]] <- as.numeric(data_for_ca[[i]])
# perform CA
data.ca <- CA(data_for_ca,graph = F)
# perform HCPC for rows (i.e. individuals); up until here everything works just fine
data.hcpc <- HCPC(data.ca,graph = T)
# now I start having trouble
# perform HCPC for columns (i.e. variables); use their coordinates that are stocked in the CA-object that was created earlier
data.cols.hcpc <- HCPC(data.ca$col$coord,graph = T)
The code above shows me a dendrogram in the last case and even lets me cut it into clusters, but then I get the following error:
Error in catdes(data.clust, ncol(data.clust), proba = proba, row.w =
res.sauv$call$row.w.init) : object 'data.clust' not found
It's worth noting that when I perform MCA on my data and try to perform HCPC on my columns in that case, I get the exact same error. Would anyone have any clue as how to fix this or what I am doing wrong exactly? For completeness I insert a screenshot of the upper-left corner of my dataset to show what it looks like:
Thanks in advance for any possible help!
I know this is old, but because I've been troubleshooting this problem for a while today:
HCPC says that it accepts a data frame, but any time I try to simply pass it $col$coord or $colcoord from a standard ca object, it returns this error. My best guess is that there's some metadata it actually needs/is looking for that isn't in a data frame of coordinates, but I can't figure out what that is or how to pass it in.
The current version of FactoMineR will actually just allow you to give HCPC the whole CA object and tell it whether to cluster the rows or columns. So your last line of code should be:
data.cols.hcpc <- HCPC(data.ca, cluster.CA = "columns", graph = T)
Question:
I have a data.frame (hlth) that consists of 49 vectors - a mix of numeric(25:49) and factor(1:24). I am trying to randomly select 50 rows, then calculate column means only for the numeric columns (dropping the other values), and then place the random row mean(s) into a new data.frame (beta). I would then like to iterate this process 1000 times.
I have attempted this process but the values that get returned are identical and the new means will not enter the new data.frame
Here is a few rows and columns of the data.frame(hlth)
DateIn adgadj Sex VetMedCharges pwtfc
1/01/2006 3.033310 STEER 0.00 675.1151
1/10/1992 3.388245 STEER 2540.33 640.2261
1/10/1995 3.550847 STEER 572.78 607.6200
1/10/1996 2.893707 HEIFER 549.42 425.5217
1/10/1996 3.647233 STEER 669.18 403.8238
The code I have used thus far:
set.seed[25]
beta<-data.frame()
net.row<-function(n=50){
netcol=sample(1:nrow(hlth),size=n ,replace=TRUE)
rNames <- row.names(hlth)
subset(hlth,rNames%in%netrow,select=c(25:49))
colMeans(s1,na.rm=TRUE,dims=1)
}
beta$net.row=replicate(1000,net.row()); net.row
The two issues, that I have detected, are:
1) Returns the same value(s) each iteration
2) "Error during wrap-up: object of type 'closure' is not subsettable" when the beta$netrow
Any suggestions would be appreciated!!!
Just adding to my comment (and firstly pasting it):
netcol=sample(1:nrow(hlth),size=n ,replace=TRUE) should presumably by netrow = ... and the error is a scoping problem - R is trying to subset the function beta, presumably again, because it can't find netRowMeans in the data.frame you've defined, moves on to the global environment and throws an error there.
There are also a couple of other things. You don't assign subset(hlth,rNames%in%netrow,select=c(25:49)) to a variable, which I think you mean to assign to s1, so colMeans is probably running on something you've set in the global environment.
If you want to pass a variable directly in to the data frame beta in that manner, you'll have to initialise beta with the right number of columns and number of rows - the column means you've passed out will be a vector of (1 x 25), so won't fit in a single column. You would probably be better of initalising a matrix called mat or something (to avoid confusion with scoping errors masking the actual error messages) with 25 columns and 1000 rows.
EDIT: Question has been edited slightly since I posted this, but most points still stand.
I have a question regarding the aggregation of imputed data as created by the R-package 'mice'.
As far as I understand it, the 'complete'-command of 'mice' is applied to extract the imputed values of, e.g., the first imputation. However, when running a total of ten imputations, I am not sure, which imputed values to extract. Does anyone know how to extract the (aggregate) imputed data across all imputations?
Since I would like to enter the data into MS Excel and perform further calculations in another software tool, such a command would be very helpful.
Thank you for your comments. A simple example (from 'mice' itself) can be found below:
R> library("mice")
R> nhanes
R> imp <- mice(nhanes, seed = 23109) #create imputation
R> complete(imp) #extraction of the five imputed datasets (row-stacked matrix)
How can I aggregate the five imputed data sets and extract the imputed values to Excel?
I had similar issue.
I used the code below which is good enough to numeric vars.
For others I thought about randomly choose one of the imputed results (because averaging can disrupt it).
My offered code is (for numeric):
tempData <- mice(data,m=5,maxit=50,meth='pmm',seed=500)
completedData <- complete(tempData, 'long')
a<-aggregate(completedData[,3:6] , by = list(completedData$.id),FUN= mean)
you should join the results back.
I think the 'Hmisc' is a better package.
if you already found nicer/ more elegant/ built in solution - please share with us.
You should use complete(imp,action="long") to get values for each imputation. If you see ?complete, you will find
complete(x, action = 1, include = FALSE)
Arguments
x
An object of class mids as created by the function mice().
action
If action is a scalar between 1 and x$m, the function returns the data with imputation number action filled in. Thus, action=1 returns the first completed data set, action=2 returns the second completed data set, and so on. The value of action can also be one of the following strings: 'long', 'broad', 'repeated'. See 'Details' for the interpretation.
include
Flag to indicate whether the orginal data with the missing values should be included. This requires that action is specified as 'long', 'broad' or 'repeated'.
So, the default is to return the first imputed values. In addition, the argument action can also be a string: long, broad, and repeated. If you enter long, it will give you the data in long format. You can also set include = TRUE if you want the original missing data.
ok, but still you have to choose one imputed dataset for further analyses... I think the best option is to analyze using your complete(imp,action="long") and pool the results afterwards.fit <- with(data=imp,exp=lm(bmi~hyp+chl))
pool(fit)
but I also assume its not forbidden to use just one of the imputed datasets ;)
New to R and having problem with a very simple task! I have read a few columns of .csv data into R, the contents of which contains of variables that are in the natural numbers plus zero, and have missing values. After trying to use the non-parametric package, I have two problems: first, if I use the simple command bw=npregbw(ydat=y, xdat=x, na.omit), where x and y are column vectors, I get the error that "number of regression data and response data do not match". Why do I get this, as I have the same number of elements in each vector?
Second, I would like to call the data ordered and tell npregbw this, using the command bw=npregbw(ydat=y, xdat=ordered(x)). When I do that, I get the error that x must be atomic for sort.list. But how is x not atomic, it is just a vector with natural numbers and NA's?
Any clarifications would be greatly appreciated!
1) You probably have a different number of NA's in y and x.
2) Can't be sure about this, since there is no example. If it is of following type:
x <- c(3,4,NA,2)
Then ordered(x) should work fine. Please provide an example of your case.
EDIT: You of course tried bw=npregbw(ydat=y, xdat=x)? ordered() makes your vector an ordered factor (see ?ordered), which is not an atomic vector (see 2.1.1 link and ?factor)
EDIT2: So the problem was the way of subsetting data. Note the difference in various ways of subsetting. data$x and data[,i] (where i = column number of column x) give you vectors, while data[c("x")] and data[i] give a data frame. Functions expect vectors, unless they call for data = (your data). In that case they work with column names