I set up two identical models in lme (R) and apply it to two different dependent variables. However, in one of the models one of the predictors is renamed, a 1 is added to the name. I assume this means, that the predictor is somehow adjusted, but I do not know what is going on and how to suppress this behaviour? Could you please provide me with some information on this or a hint on where to find help on this topic?
Thank you!
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I created a Random-Forest Regression model for time-series data in R that have three predictors and one output variable.
Is there a way to find (perhaps in more absolute terms) how changes in a specific variable affect the prediction output?
I know about variable importance, I am not trying to find the variables that have the biggest effect instead I am trying to see if I pick input variable X_1 and increase its value (or decrease it) how that would change the prediction output.
Does it even makes sense to do this? or is it even possible with a random-forest model? Rereading my question a few times it made me dubious, but any insight/recommendation would be greatly appreciated.
I would guess what this question is actually about is called exploratory data analysis (EDA). For starters, I would calculate the correlations between the variables to get a feeling for the strength of the [linear] relationship between two variables. Further, I would look at scatter plots between the variables to get a feeling for the relationships. Depending on the variables [linear] regression could tell how an increase in variable x1 would affect variable x2.
I am trying to understand how to run PERMANOVA using Adonis2 in R to analyse some data that I have collected. I have been looking online, but as it often happens, explanations are a bit convoluted, so I am asking for your help, if you can help me. I have got some fish and coral groups as columns, as well as 3 independent variables (reef age, depth, and material). Snapshot of my dataset structure I think I have understood that p-values are not the only important bit of the output, and that the R2 values indicate how much each variable contributes to the model. Is there something wrong or that I am missing here? Also, I think I understood that I should check for homogeneity of variance, but I have not understood, again, if I should check for it on each variable independently, or if I should include them all in the same bit of code (which does not seem to work). Here are the bit of code that I am using to run the PERMANOVA (1), and the one that I am trying to use to assess homogeneity of variance - which does not work (2).
(1) adonis2(species ~ Age+Material+Depth,data=data.var,by="margin)
'Species' is the subset of the dataset including all the species'count, while 'data.var'is the subset including the 3 independent variables. Also what is the difference in using '+' or '' in the code? When I use '' it gives me - 'Error in qr.X(object$CCA$QR) :
need larger value of 'ncol' as pivoting occurred'. What does this mean?
(2) variance.check<-betadisper(species.distance,data.var, type=c("centroid"), bias.adjust= FALSE)
'species.distance' is a matrix calculated through 'vegdist' using Bray-Curtis method. I used 'data.var'to check variance on all the 3 independent variables, but it does not work, while it works if I check them independently (3). Why is that?
(3) variance.check<-betadisper(species.distance, data$Depth, type=c("centroid"), bias.adjust= FALSE)
Thank you in advance for your responses, and for your help. It will really help me to get my head around it (and sorry for the many questions).
I am considerably new to statistics and self-learnt R so please bear with me if my question appears silly:
I am doing a multivariate panel regression by country-months. I want to find out how much I should lag my dependent variable by, in relation to my independent variable(s), using a statistical method (as opposed to just using theory).
According to answers I found on other forums, it appears (I don't actually know whether this is appropriate for my purpose and any other suggestions would be very welcome) I should be using the function VARselect(). I am however confused where in the formula I should insert my independent variable and dependent variable, as well where to indicate the country and time variable.
Any help would be greatly appreciated!
I'm fairly new to R and am currently trying to find the best model to predict my dependent variable from a number of predictor variables. I have 20 precictor variables and I want to see which ones I should include in my model and which ones I should exclude.
I am currently just running models with different predictor variables in each and comparing them to see which one has the lowest AIC, but this is taking a really long time. Is there an easier way to do this?
Thank you in advance.
This is more of a theoretical question actually...
In principle, if all of the predictors are actually exogenous to the model, they can all be included together and assuming you have enough data (N >> 20) and they are not too similar (which could give rise to multi-collinearity), that should help prediction. In practice, you need to think about whether each of (or any of) your predictors are actually exogenous to the model (that is, independent of the error term in the model). If they are not, then they will impart a bias on the estimates. (Also, omitting explanatory variables that are actually necessary imparts a bias.)
If predictive accuracy (even spurious in-sample accuracy) is the goal, then techniques like LASSO (as mentioned in the comments) could also help.
I have a huge data which has about 2,000 variables and about 10,000 observations.
Initially, I wanted to run a regression model for each one with 1999 independent variables and then do stepwise model selection.
Therefore, I would have 2,000 models.
However, unfortunately R presented errors because of lack of memory..
So, alternatively, I have tried to remove some independent variables which are low correlation value- maybe lower than .5-
With variables which are highly correlated with each dependent variable, I would like to run regression model..
I tried to do follow codes, even melt function doesn't work because of memory issue.. oh god..
test<-data.frame(X1=rnorm(50,mean=50,sd=10),
X2=rnorm(50,mean=5,sd=1.5),
X3=rnorm(50,mean=200,sd=25))
test$X1[10]<-5
test$X2[10]<-5
test$X3[10]<-530
corr<-cor(test)
diag(corr)<-NA
corr[upper.tri(corr)]<-NA
melt(corr)
#it doesn't work with my own data..because of lack of memory.
Please help me.. and thank you so much in advance..!
In such a situation if might be worth trying sparsity inducing techniques such as the Lasso. Here a sparse subset of variables is selected by constraining the sum of absolute values of the regression coefficients.
This will give you a reduced subset of variables which are the most relevant (and due to the nature of the Lasso algorithm also the most correlated, which was what you were looking for)
In R you can use the LARS package and information about the Lasso can be found here:
http://www-stat.stanford.edu/~tibs/lasso.html
Also a very good resource is: http://www-stat.stanford.edu/~tibs/ElemStatLearn/