similar to: substitute games with randomForest::partialPlot

All, I'm trying to set up a function which calls the partialPlot function but am getting an error that I can't seem to solve. Here's a simplified version of the function and error... > pplot <- function(rf,pred.var){partialPlot(x=rf,pred.data=acoust,x.var=pred.var)} > > attach(acoust) > acoust.rf <-

Hi everybody, I used randomForest to regress invertebrates abundances in least impaired river reaches from some environmental parameters. Then I used these models to predict invertebrates abundances in impaired reaches. Now I would like to model the deviation (observation - prediction) with a set of chemical parameters to see if the deviations from predictions could be explained with water

Hello all useRs, I am tring make a simple surface plot ( 2 by 2 terms of a MARS model (with earth package) but I get the follow error message: > plotmo( mars ) Error: bad index (missing column in x?) I don't no how to workround this... :-( I thanks in advanced by some help! Thanks. Cleber ############### > > ### example code: > library( earth ) > data( gasoline,

Dear R Group I had an observation that in some cases, when I use the randomForest model to create partialPlot in R using the package "randomForest" the y-axis displays values that are more than -1! It is a classification problem that i was trying to address. Any insights as to how the y axis can display value more than -1 for some variables? Am i missing something! Thanks Regards

Hola erreros. A ver si alguien podría decirme qué son los dos ejes del plot que resulta de aplicar partialPlot en un Randomforest. Encuentro que: Partial dependence plot gives a graphical depiction of the marginal effect of a variable on the class probability (classification) or response (regression) que nos indica como varía la VR en función de la variable considerada, manteniendo el

Dear R Users, I'm using the randomForest package and would like to generate partial dependence plots, one after another, for a variety of variables: m <- randomForest( s, ... ) varnames <- c( "var1", "var2", "var3", "var4" ) # var1..4 are all in data frame s for( v in varnames ) { partialPlot( x=m, pred.data=s, x.var=v ) } ...but this

Greg, Two thoughts: 1. It might be possible that 'vars' is a reserved word of sorts and if you change the name of your vector RF might be happier 2. A way that works for me is to call importance as follows: sel.imp <- importance(sel.rf, class=NULL, scale=TRUE, type=NULL) and then use the 'names' of the imp data frame to be absolutely clear to RF you are talking about the

Muchas gracias Carlos; ¡tu siempre al pié del cañón! (lo puse el día de reyes a la 1.20h y me contestas a las 2.45h) Una cosa más: si el eje y es la probabilidad ¿por qué va de 0 a 10? En un RF para clasificación me da valores parecidos a los de tu ejemplo, y en otro para regresión, valores de y entre 45 y 55. Para regresión, el último parámetro no puede ser una categoría, como

Stephen, thanks for your effort. The more appropriate list for this discussion is probably R-devel (as far as I understand it) so I've moved the discussion there. Related topics have already been discussed in the past. Specifically, I remember contributions by Paul Johnson ("rockchalk" package) and John Fox ("effects" and "car" package) as their packages

Dear all, Version 4.3-0 of the randomForest package is now available on CRAN (in source; binaries will follow in due course). There are some interface changes and a few new features, as well as bug fixes. For those who had used previous versions, the important things to note are: 1. there's a namespace now, and 2. some functions have been renamed. The list of changes since 4.0-7 (last

Dear all, Version 4.3-0 of the randomForest package is now available on CRAN (in source; binaries will follow in due course). There are some interface changes and a few new features, as well as bug fixes. For those who had used previous versions, the important things to note are: 1. there's a namespace now, and 2. some functions have been renamed. The list of changes since 4.0-7 (last

Hello, I am running randomForest models on a number of species. I would like to be able to automate the printing of dependence plots for the most important variables in each model, but I am unable to figure out how to enter the variable names into my code. I had originally thought to extract them from the $importance matrix after sorting by metric (e.g. %IncMSE), but the importance matrix is n

Hi, I'm trying to make a partial plot with package randomForest in R. After I perform my random forest object I type partialPlot(data.rforest, pred.data=act2, x.var=centroid, "C") where data.rforest is my randomforest object, act2 is the original dataset, centroid is one of the predictor and C is one of the classes in my response variable. Whatever predictor or response class I

? data=read.table("http://statcourse.com/research/boston.csv", , sep=",", header = TRUE) ? library(rpart) ? fit=rpart (MV~ CRIM+ZN+INDUS+CHAS+NOX+RM+AGE+DIS+RAD+TAX+ PT+B+LSTAT) Please: Show me the tree. Mark -------- Original Message -------- Subject: Re: [R] help with rpart From: "Stephen Milborrow" <[1]milbo at sonic.net>

Dear list, can someone explain to me why deparse(substitute(x)) does not seem to work when x is of a user-defined S3 class? In my actual problem, my print method is part of a package, and the method is registered in the NAMESPACE, if that should make a difference. > print.testclass <- function(x,...){ xname <- deparse(substitute(x)) cat("Your object name

(earlier I sent it as html by mistake). Hi, How can I get from C an object name used as a function argument? I have sample code in C that gives me access to the name of the function being called: SEXP xname(SEXP x) { const char *fun_name = CHAR(PRINTNAME(CAR(x))); x = CDR(x); const char *arg_name = isNull(TAG(x)) ? "" : CHAR(PRINTNAME(TAG(x)));

Greetings R developers, R will run a little faster when executing "pure R" code if the function R_CheckStack() is modified. With the modification, the following code for example runs 15% faster (compared to a virgin R-2.5.1 on my Windows XP machine): N = 1e7 foo <- function(x) { for (i in 1:N) x <- x + 1 x }

Hi all, As I reported earlier (with a typo in the work [BUG]) client certification validation *does not* work even if you do everything exactly according to all documentation and attempts at helpful advice. I have seen this issue with both startssl.com and self-signed certificates, and based on what I've seen from searching the web, this is a problem that has gotten little attention because

Hello, I need to draw a partial dependence bar graph. My the my predictor vectors are continous and so is the response variable. Iam using the partialPlot function of the randomForest package. I get a line graph. How can I edit it to get a bar graph instead? (partialPlot(randomForest object ,data-matrix, number of predictor vectors, "Temp")) -- Daudi Jjingo [[alternative HTML

Full_Name: Stephen Milborrow Version: R 2.8.0 OS: Windows XP Submission from: (NULL) (81.159.65.46) Under certain conditions, R 2.8.0 incorrectly echoes integer literals without the "L" suffix. R 2.7.2 is ok. To reproduce, create two files as follows: a.R containing: source("b.R", echo=TRUE) b.R containing: x <- 1L Now execute: Rterm --vanilla --silent <a.R This