I am trying to use svm() to classify my data. A sample of my data is as follows:
ID call_YearWeek week WeekCount oc
x 2011W01 1 0 0
x 2011W02 2 1 1
x 2011W03 3 0 0
x 2011W04 4 0 0
x 2011W05 5 1 1
x 2011W06 6 0 0
x 2011W07 7 0 0
x 2011W08 8 1 1
x 2011W09 9 0 0
x 2011W10 10 0 0
x 2011W11 11 0 0
x 2011W12 12 1 1
x 2011W13 13 1 1
x 2011W14 14 1 1
x 2011W15 15 0 0
x 2011W16 16 2 1
x 2011W17 17 0 0
x 2011W18 18 0 0
x 2011W19 19 1 1
The third column shows week of the year. The 4th column shows number of calls in that week and the last column is a binary factor (if a call was received in that week or not). I used the following lines of code:
train <- data[1:105,]
test <- data[106:157,]
model <- svm(oc~week,data=train)
plot(model,train,week)
plot(model,train)
none of the last two lines work. they dont show any plots and they return no error. I wonder why this is happening.
Thanks
Seems like there are two problems here, first is that not all svm types are supported by plot.svm -- only the classification methods are, and not the regression methods. Because your response is numeric, svm() assumes you want to do regression so it chooses "eps-regression" by default. If you want to do classification, change your response to a factor
model <- svm(factor(oc)~week,data=train)
which will then use "C-classification" by default.
The second problem is that there does not seem to be a univariate predictor plot implemented. It seems to want two variables (one for x and one for y).
It may be better to take a step back and describe exactly what you want your plot to look like.
Related
I have a dataset with four variables (df)
household
group
income
post
1
0
20'000
0
1
0
22'000
1
2
1
10'000
0
2
1
20'000
1
3
0
20'000
0
3
0
21'000
1
4
1
9'000
0
4
1
16'000
1
5
1
8'000
0
5
1
18'000
1
6
0
22'000
0
6
0
26'000
1
7
1
12'000
0
7
1
24'000
1
8
0
24'000
0
8
0
27'000
1
Group is a binary variable and is 1, when household got support from state. and post variable is also binary and is 1, when it is after some household got support from state.
Now I would like to run a before vs after regression that estimates the group effect by comparing post-period and before period for the supported group. I would like to put the dependent variable in logs, to have the effect in percentage, so the impact of state support on income.
I used that code, but I don't know if it is right to get the answer?
library("fixest")
feols(log(income) ~ group + post,data=df) %>% etable()
Is there another way?
If you are looking for the classic 2x2 design your code was almost correct. Change '+' with '*'. This tell us that the supported group increased the income with 7 250 more than the group which not received support.
comparing = feols(income ~ group * post,data)
comparing_log = feols(log(income) ~ group * post,data)
etable(comparing,comparing_log)
PS: The interpretation of the coefficient as percentage change is a good approximation for small numbers. The correct formula for % change is: exp(beta)-1. In this case it is exp(0.5829)-1 = 0.7912.
So the change here is 79,12%.
There is a problem in DataCamp about computing the probability of winning an NBA series. Cavs and the Warriors are playing a seven game championship series. The first to win four games wins the series. They each have a 50-50 chance of winning each game. If the Cavs lose the first game, what is the probability that they win the series?
Here is how DataCamp computed the probability using Monte Carlo simulation:
B <- 10000
set.seed(1)
results<-replicate(B,{x<-sample(0:1,6,replace=T) # 0 when game is lost and 1 when won.
sum(x)>=4})
mean(results)
Here is a different way they computed the probability using simple code:
# Assign a variable 'n' as the number of remaining games.
n<-6
# Assign a variable `outcomes` as a vector of possible game outcomes: 0 indicates a loss and 1 a win for the Cavs.
outcomes<-c(0,1)
# Assign a variable `l` to a list of all possible outcomes in all remaining games. Use the `rep` function on `list(outcomes)` to create list of length `n`.
l<-rep(list(outcomes),n)
# Create a data frame named 'possibilities' that contains all combinations of possible outcomes for the remaining games.
possibilities<-expand.grid(l) # My comment: note how this produces 64 combinations.
# Create a vector named 'results' that indicates whether each row in the data frame 'possibilities' contains enough wins for the Cavs to win the series.
rowSums(possibilities)
results<-rowSums(possibilities)>=4
# Calculate the proportion of 'results' in which the Cavs win the series.
mean(results)
Question/Problem:
They both produce approximately the same probability of winning the series ~ 0.34. However, there seems to be a flaw in the the concept and the code design. For example, the code (sampling six times) allows for combinations such as the following:
G2 G3 G4 G5 G6 G7 rowSums
0 0 0 0 0 0 0 # Series over after G4 (Cavs lose). No need for game G5-G7.
0 0 0 0 1 0 1 # Series over after G4 (Cavs lose). Double counting!
0 0 0 0 0 1 1 # Double counting!
...
1 1 1 1 0 0 4 # No need for game G6 and G7.
1 1 1 1 0 1 5 # Double counting! This is the same as 1,1,1,1,0,0.
0 1 1 1 1 1 5 # No need for game G7.
1 1 1 1 1 1 6 # Series over after G5 (Cavs win). Double counting!
> rowSums(possibilities)
[1] 0 1 1 2 1 2 2 3 1 2 2 3 2 3 3 4 1 2 2 3 2 3 3 4 2 3 3 4 3 4 4 5 1 2 2 3 2 3 3 4 2 3 3 4 3 4 4 5 2 3 3 4 3 4 4 5 3 4 4 5 4 5 5 6
As you can see, these are never possible. After winning the first four of the remaining six games, no more games should be played. Similarly, after losing the first three games of the remaining six games, no more games should be played. So these combinations shouldn't be included in the computation of the probability of winning the series. There is double counting for some of the combinations.
Here is what I did to omit some of the combinations that are not possible in real life.
outcomes<-c(0,1)
l<-rep(list(outcomes),6)
possibilities<-expand.grid(l)
possibilities<-possibilities %>% mutate(rowsums=rowSums(possibilities)) %>% filter(rowsums<=4)
But then I am not able to omit the other unnecessary combinations. For example, I want to remove two of these three: (a) 1,0,0,0,0,0 (b) 1,0,0,0,0,1 (c) 1,0,0,0,1,1. This is because no more games will be played after losing three times in a row. And they are basically double counting.
There are too many conditions for me to be able to filter them individually. There has to be a more efficient and intuitive way to do this. Can someone provide me with some hints on how to solve this whole mess?
Here is a way:
library(dplyr)
outcomes<-c(0,1)
l<-rep(list(outcomes),6)
possibilities<-expand.grid(l)
possibilities %>%
mutate(rowsums=rowSums(cur_data()),
anti_sum = rowSums(!cur_data())) %>%
filter(rowsums<=4, anti_sum <= 3)
We use the fact that r can coerce into a logical where 0 will be false. See sum(!0) as a short example.
I am trying to train a model using bstTree method and print out the confusion matrix. adverse_effects is my class attribute.
set.seed(1234)
splitIndex <- createDataPartition(attended_num_new_bstTree$adverse_effects, p = .80, list = FALSE, times = 1)
trainSplit <- attended_num_new_bstTree[ splitIndex,]
testSplit <- attended_num_new_bstTree[-splitIndex,]
ctrl <- trainControl(method = "cv", number = 5)
model_bstTree <- train(adverse_effects ~ ., data = trainSplit, method = "bstTree", trControl = ctrl)
predictors <- names(trainSplit)[names(trainSplit) != 'adverse_effects']
pred_bstTree <- predict(model_bstTree$finalModel, testSplit[,predictors])
plot.roc(auc_bstTree)
conf_bstTree= confusionMatrix(pred_bstTree,testSplit$adverse_effects)
But I get the error 'Error in confusionMatrix.default(pred_bstTree, testSplit$adverse_effects) :
The data must contain some levels that overlap the reference.'
max(pred_bstTree)
[1] 1.03385
min(pred_bstTree)
[1] 1.011738
> unique(trainSplit$adverse_effects)
[1] 0 1
Levels: 0 1
How can I fix this issue?
> head(trainSplit)
type New_missed Therapytypename New_Diesease gender adverse_effects change_in_exposure other_reasons other_medication
5 2 1 14 13 2 0 0 0 0
7 2 0 14 13 2 0 0 0 0
8 2 0 14 13 2 0 0 0 0
9 2 0 14 13 2 1 0 0 0
11 2 1 14 13 2 0 0 0 0
12 2 0 14 13 2 0 0 0 0
uvb_puva_type missed_prev_dose skintypeA skintypeB Age DoseB DoseA
5 5 1 1 1 22 3.000 0
7 5 0 1 1 22 4.320 0
8 5 0 1 1 22 4.752 0
9 5 0 1 1 22 5.000 0
11 5 1 1 1 22 5.000 0
12 5 0 1 1 22 5.000 0
I had similar problem, which refers to this error. I used function confusionMatrix:
confusionMatrix(actual, predicted, cutoff = 0.5)
An I got the following error: Error in confusionMatrix.default(actual, predicted, cutoff = 0.5) : The data must contain some levels that overlap the reference.
I checked couple of things like:
class(actual) -> numeric
class(predicted) -> integer
unique(actual) -> plenty values, since it is probability
unique(predicted) -> 2 levels: 0 and 1
I concluded, that there is problem with applying cutoff part of the function, so I did it before by:
predicted<-ifelse(predicted> 0.5,1,0)
and run the confusionMatrix function, which works now just fine:
cm<- confusionMatrix(actual, predicted)
cm$table
which generated correct outcome.
One takeaway for your case, which might improve interpretation once you make code working:
you mixed input values for your confusion matrix(as per confusionMatrix package documetation), instead of:
conf_bstTree= confusionMatrix(pred_bstTree,testSplit$adverse_effects)
you should have written:
conf_bstTree= confusionMatrix(testSplit$adverse_effects,pred_bstTree)
As said it will most likely help you interpret confusion matrix, once you figure out way to make it work.
Hope it helps.
max(pred_bstTree) [1] 1.03385
min(pred_bstTree) [1] 1.011738
and errors tells it all. Plotting ROC is simply checking the effect of different threshold points. Based on threshold rounding happens e.g. 0.7 will be converted to 1 (TRUE class) and 0.3 will be go 0 (FALSE class); in case threshold is 0.5. Threshold values are in range of (0,1)
In your case regardless of threshold you will always get all observations into TRUE class as even minimum prediction is greater than 1. (Thats why #phiver was wondering if you are doing regression instead of classification) . Without any zero in prediction there is no level in 'prediction' which coincide with zero level in adverse_effects and hence this error.
PS: It will be difficult to tell root cause of error without you posting your data
I downloaded the R package RVAideMemoire in order to use the G.test.
> head(bio)
Date Trt Treated Control Dead DeadinC AliveinC
1 23Ap citol 1 3 1 0 13
2 23Ap cital 1 5 3 1 6
3 23Ap gerol 0 3 0 0 9
4 23Ap mix 0 5 0 0 8
5 23Ap cital 0 5 1 0 13
6 23Ap cella 0 5 0 1 4
So, I make subsets of the data to look at each treatment, because the G.test result will need to be pooled for each one.
datamix<-subset(bio, Trt=="mix")
head(datamix)
Date Trt Treated Control Dead DeadinC AliveinC
4 23Ap mix 0 5 0 0 8
8 23Ap mix 0 5 1 0 8
10 23Ap mix 0 2 3 0 5
20 23Ap mix 0 0 0 0 18
25 23Ap mix 0 2 1 0 15
28 23Ap mix 0 1 0 0 12
So for the G.test(x) to work if x is a matrix, it must be constructed as 2 columns containing numbers, with 1 row per population. If I use the apply() function I can run the G,test on each row if my data set contains only two columns of numbers. I want to look only at the treated and control for example, but I'm not sure how to omit columns so the G.test can ignore the headers, and other columns. I've tried using the following but I get an error:
apply(datamix, 1, G.test)
Error in match.fun(FUN) : object 'G.test' not found
I have also thought about trying to use something like this rather than creating subsets.
by(bio, Trt, rowG.test)
The G.test spits out this, when you compare two numbers.
G-test for given probabilities
data: counts
G = 0.6796, df = 1, p-value = 0.4097
My other question is, is there someway to add all the df and G values that I get for each row (once I'm able to get all these numbers) for each treatment? Is there also some way to have R report the G, df and p-values in a table to be summed rather than like above for each row?
Any help is hugely appreciated.
You're really close. This seems to work (hard to tell with such a small sample though).
by(bio,bio$Trt,function(x)G.test(as.matrix(x[,3:4])))
So first, the indices argument to by(...) (the second argument) is not evaluated in the context of bio, so you have to specify bio$Trt instead of just Trt.
Second, this will pass all the columns of bio, for each unique value of bio$Trt, to the function specified in the third argument. You need to extract only the two columns you want (columns 3 and 4).
Third, and this is a bit subtle, passing x[,3:4] to G.test(...) causes it to fail with an unintelligible error. Looking at the code, G.test(...) requires a matrix as it's first argument, whereas x[,3:4] in the code above is a data.frame. So you need to convert with as.matrix(...).
I have an imputed dataset that I'm analysing, and I'm trying to draw boxplots, but I can't wrap my head around the proper procedure.
my data (a sample, original has 20 observations per imputation and 13 vars per group, all values range from 0 to 25):
.imp .id FTE_RM FTE_PD OMZ_RM OMZ_PD
1 1 25 25 24 24
1 2 4 0 2 6
1 3 11 5 3 2
1 4 12 3 3 3
2 1 20 15 15 15
2 2 4 1 2 3
2 3 0 0 0 6
2 4 20 0 0 0
.imp signifies the imputation round, .id the identifer for each observartion.
I want to draw all the FTE_* variables in a single plot (and the `OMZ_* in another), but wonder what to do with all the imputations, can I just include all values? The imputated data now has 500 observations. With for instance an ANOVA I'd need to average the ANOVA results by 5 to get back to 20 observations. But is this needed for a boxplot as well, since I only deal with medians, means, max. and min.?
Such as:
data_melt <- melt(df[grep("^FTE_", colnames(df))])
ggplot(data_melt, aes(x=variable, y=value))+geom_boxplot()
I've played a couple of times with ggplot, but consider myself a complete newbie.
I assume you want to keep the identifier for .imp and .id after melting so rather put:
data_melt <- melt(df,c(".imp",".id"))
For completeness of the dataframe it probably helps to introduce a column that identifies the type - FTE vs. OMZ:
data_melt$type <- ifelse(grepl("FTE",data_melt$variable),"FTE","OMZ")
Having this data.frame you can, for example, facet on the type (alternatively you can just use a simple filter statement on data_melt to restrict to one type):
ggplot(data_melt, aes(x=variable, y=value))+geom_boxplot()+facet_wrap(~type,scales="free_x")
This would look like this.
EDIT: fixed the data mess-up