RandomForestSRC error and vimp - random-forest

I am trying to perform a randomforest survival analysis according to the RANDOMFORESTSRC vignette in R. I have a data frame containing 59 variables - where 14 of them are numeric and the rest are factors. 2 of the numeric ones are TIME (days till death) and DIED (0/1 dead or not). I'm running into 2 problems:
trainrfsrc<- rfsrc(Surv(TIME, DIED) ~ .,
data = train, nsplit = 10, na.action = "na.impute")
trainrfsrc gives: Error rate: 17.07%
works fine, however exploring the error rate such as:
plot(gg_error(trainrfsrc))+ coord_cartesian(y = c(.09,.31))
returns:
geom_path: Each group consists of only one observation. Do you need to adjust the group aesthetic?
or:
a<-(gg_error(trainrfsrc))
a
error ntree 1 NA 1 2 NA 2 3 NA 3 4 NA 4 5 NA 5 6 NA 6 7 NA 7 8 NA 8 9 NA 9 10 NA 10
NA for all 1000 trees.how come there's no error rate for each number of trees tried?
the second problem is when trying to explore the most important variables using VIMP such as:
plot(gg_vimp(trainrfsrc)) + theme(legend.position = c(.8,.2))+ labs(fill = "VIMP > 0")
it returns:
In gg_vimp.rfsrc(trainrfsrc) : rfsrc object does not contain VIMP information. Calculating...
Any ideas? Thanks

Setting the err.block=1 (or some integer between 1 and ntree) should fix the problem of returning NA for error. You can check the help file under rfsrc to read more about err.block.

Related

missing data in time series

As im so new to this field and im trying to explore the data for a time series, and find the missing values and count them and study a distribution of their length and fill in these gaps, the thing is i have, let's say 10 file.txt and for each file i have 2 columns as follows:
C1 C2
944 0
920 1
920 2
928 3
912 7
920 8
920 9
880 10
888 11
920 12
944 13
and so on... lets say till 100 and not necessarily the 10 files have the same number of observations.
so here for example the missing values and not necessarily appears in all files that i have, missing value are: 4,5 and 6 in C2 and the corresponding 1st column C1(measured in milliseconds, so the value of 928ms is not a time neighbor of 912ms). So i want to find those gaps(the total missing values in all 10 files) and show a histogram of their lengths.
i wrote a piece of code in R, but the problem is that i don't get the exact total number that i should have for the missing values.
path = "files path"
out.file<-data.frame(TS = 0, Index = 0, File = '')
file.names <- dir(path, pattern =".txt")
for(i in 1:length(file.names)){
file <- cbind(read.table(file.names[i],
header=F,
sep ="\t",
stringsAsFactors=FALSE),
file.names[i])
colnames(file) <- c('TS', 'Index', 'File')
out.file <- rbind(out.file, file)
}
d = dim(out.file)[1]
misDa = 0
for(i in 2:(d-1)){
if(abs(out.file$Index[i]-out.file$Index[i+1]) > 1)
misDa = misDa+1
}
Hard to give specific hints without having a more extensive example of your data that contains some of the actual NAs.
If you are using R (like it seems) the naniar and the imputeTS packages offer nice functions for missing data visualizations.
Some examples from the naniar package, which is especially good for multivariate data (more plot examples):
Some examples from the imputeTS package, which is especially good for time series data (additional plot examples):

Clustering to achieve heterogeneous groups

I want to group 100 users based on a categorical variable (which can be low, medium, or high). The group size should be 3. I want to get the maximal heterogeneity within groups, assuming that users are distributed equally. I wonder if I can use some clustering algorithm to group based on the dissimilarity? Any suggestions?
I don't believe you need a clustering algorithm to group the data based upon a categorical variable.
Based on you question, I think this should work.
# Code
from sklearn.model_selection import train_test_split
group1, group23 = train_test_split(data, test_size=2/3., stratify=data['lab'])
group2, group3 = train_test_split(group23, test_size=1/2., stratify=group23['lab'])
Stratify makes sure that the maximum heterogeneity is maintained for the given categorical value.
# Sample output
print(data)
val1 val2 lab
0 1 1 L
1 2 2 L
2 3 3 L
3 4 4 M
4 5 5 M
5 6 6 M
6 7 7 H
7 8 8 H
8 9 9 H
print(group1)
val1 val2 lab
4 5 5 M
1 2 2 L
6 7 7 H
print(group2)
val1 val2 lab
8 9 9 H
2 3 3 L
3 4 4 M
print(group3)
val1 val2 lab
0 1 1 L
7 8 8 H
5 6 6 M
train_test_split() Documentation

GLMM glmer and glmmADMB - comparison error

I am trying to compare if there are differences in the number of obtained seeds in five different populations with different applied treatments, and having maternal plant and paternal plant as random effects. First I tried to fit a glmer model.
dat <-dat [,c(12,7,6,13,8,11)]
dat$parents<-factor(paste(dat$mother,dat$father,sep="_"))
compareTreat <- function(d)
{
d$treatment <-factor(d$treatment)
print (tapply(d$pop,list(d$pop,d$treatment),length))
print(summary(fit<-glmer(seed_no~treatment+(1|pop/mother)+
(1|pop/father),data=d,family="poisson")))
}
Then, I compared two treatments in two populations (pop 64 and pop 121, in that case). The other populations do not have this particular treatments, so I get NA values for those.
compareTreat(subset(dat,treatment%in%c("IE 5x","IE 7x")&pop%in%c(64,121)))
This is the output:
IE 5x IE 7x
10 NA NA
45 NA NA
64 31 27
121 33 28
144 NA NA
Generalized linear mixed model fit by maximum likelihood (Laplace
Approximation) [glmerMod]
Family: poisson ( log )
Formula: seed_no ~ treatment + (1 | pop/mother) + (1 | pop/father)
Data: d
AIC BIC logLik deviance df.resid
592.5 609.2 -290.2 580.5 113
Scaled residuals:
Min 1Q Median 3Q Max
-1.8950 -0.8038 -0.2178 0.4440 1.7991
Random effects:
Groups Name Variance Std.Dev.
father.pop (Intercept) 3.566e-01 5.971e-01
mother.pop (Intercept) 9.456e-01 9.724e-01
pop (Intercept) 1.083e-10 1.041e-05
pop.1 (Intercept) 1.017e-10 1.008e-05
Number of obs: 119, groups: father:pop, 81; mother:pop, 24; pop, 2
Fixed effects:
Estimate Std. Error z value Pr(>|z|)
(Intercept) 0.74664 0.24916 2.997 0.00273 **
treatmentIE 7x -0.05789 0.17894 -0.324 0.74629
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Correlation of Fixed Effects:
(Intr)
tretmntIE7x -0.364
It seems there are no differences between treatments. But as there are many zeros in the data, a zero-inflated model would be worthy to try. I tried with glmmabmd, and I wrote the script like this:
compareTreat<-function(d)
{
d$treatment<-factor(d$treatment)
print(tapply(d$pop,list(d$pop,d$treatment), length))
print(summary(fit_zip<-glmmadmb(seed_no~treatment + (1|pop/mother)+
(1|pop/father),data=d,family="poisson", zeroInflation=TRUE)))
}
Then I compared again the treatments. Here I have not changed the code.
compareTreat(subset(dat,treatment%in%c("IE 5x","IE 7x")&pop%in%c(64,121)))
But in that case, the output is
IE 5x IE 7x
10 NA NA
45 NA NA
64 31 27
121 33 28
144 NA NA
Error in pop:father : NA/NaN argument
In addition: Warning messages:
1: In pop:father :
numerical expression has 119 elements: only the first used
2: In pop:father :
numerical expression has 119 elements: only the first used
3: In eval(parse(text = x), data) : NAs introduced by coercion
Called from: eval(parse(text = x), data)
I tried to change everything I came up with, but I still don't know where the problem is.
If I remove the (1|pop/father) from the glmmadmb script, the model runs, but it feels not correct. I wonder if the mistake is in the loop prior to the glmmadmb but it worked OK in the glmer model, or if it is in the comparison itself after the model. I tried as well to remove NAs with na.omit in case that was an issue, but it did not make a difference. Why does the script stop and does not continue running?
I am a student beginner with RStudio, my version is 3.4.2, called Short Summer. If someone with experience could point me in the right direction I would be very grateful!
H.

Missing Values per participant in a repeated measures design using SPSS

I've got a dataset with repeated measures that looks roughly like this:
ID v1 v2 v3 v4
1 3 4 2 NA
1 2 NA 6 7
2 4 3 6 4
2 NA 2 7 9
. . . . .
n . . . .
What I want to know is how many NAs are there for each participants over the variables v1 - v4 (e.g. participant 1 is missing 2 of 8 responses)?
Missing Values are always displayed per Variable not per participant so how do I do this? Maybe there is a way using the AGGREGATE command with ID as BREAK?
Use COUNT to count the missing values as a new variable and then aggregate by the Id or split files by I'd and freq.

Clustering unique datasets based on similarities (equality)

I just entered into the space of data mining, machine learning and clustering. I'm having special problem, and do not know which technique to use it for solving it.
I want to perform clustering of observations (objects or whatever) on specific data format. All variables in each observation is numeric. My data input looks like this:
1 2 3 4 5 6
1 3 5 7
2 9 10 11 12 13 14
45 1 22 23 24
Let's say that n represent row (observation, or 1D vector,..) and m represents column (variable index in each vector). n could be very large number, and 0 < m < 100. Also main point is that same observation (row) cannot have identical values (in 1st row, one value could appear only once).
So, I want to somehow perform clustering where I'll put observations in one cluster based on number of identical values which contain each row/observation.
If there are two rows like:
1
1 2 3 4 5
They should be clustered in same cluster, if there are no match than for sure not. Also number of each rows in one cluster should not go above 100.
Sick problem..? If not, just for info that I didn't mention time dimension. But let's skip that for now.
So, any directions from you guys,
Thanks and best regards,
JDK
Its hard to recommend anything since your problem is totally vague, and we have no information on the data. Data mining (and in particular explorative techniques like clustering) is all about understanding the data. So we cannot provide the ultimate answer.
Two things for you to consider:
1. if the data indicates presence of species or traits, Jaccard similarity (and other set based metrics) are worth a try.
2. if absence is less informative, maybe you should be mining association rules, not clusters
Either way, without understanding your data these numbers are as good as random numbers. You can easily cluster random numbers, and spend weeks to get the best useless result!
Can your problem be treated as a Bag-of-words model, where each article (observation row) has no more than 100 terms?
Anyway, I think your have to give more information and examples about "why" and "how" you want to cluster these data. For example, we have:
1 2 3
2 3 4
2 3 4 5
1 2 3 4
3 4 6
6 7 8
9 10
9 11
10 12 13 14
What is your expected clustering? How many clusters are there in this clustering? Only two clusters?
Before you give more information, according to you current description, I think you do not need a cluster algorithm, but a structure of connected components. The first round you process the dataset to get the information of connected components, and you need a second round to check each row belong to which connected components. Take the example above, first round:
1 2 3 : 1 <- 1, 1 <- 2, 1 <- 3 (all point linked to the smallest point to
represent they are belong to the same cluster of the smallest point)
2 3 4 : 2 <- 4 (2 and 3 have already linked to 1 which is <= 2, so they do
not need to change)
2 3 4 5 : 2 <- 5
1 2 3 4 : 1 <- 4 (in fact this change are not essential because we have
1 <- 2 <- 4, but change this can speed up the second round)
3 4 6 : 3 <- 6
6 7 8 : 6 <- 7, 6 <- 8
9 10 : 9 <- 9, 9 <- 10
9 11 : 9 <- 11
10 11 12 13 14 : 10 <- 12, 10 <- 13, 10 <- 14
Now we have a forest structure to represent the connected components of points. The second round you can easily pick up one point in each row (the smallest one is the best) and trace its root in the forest. The rows which have the same root are in the same, in your words, cluster. For example:
1 2 3 : 1 <- 1, cluster root 1
2 3 4 5 : 1 <- 1 <- 2, cluster root 1
6 7 8 : 1 <- 1 <- 3 <- 6, cluster root 1
9 10 : 9 <- 9, cluster root 9
10 11 12 13 14 : 9 <- 9 <- 10, cluster root 9
This process takes O(k) space where k is the number of points, and O(nm + nh) time, where r is the height of the forest structure, where r << m.
I am not sure if this is the result you want.

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