Displaying 20 results from an estimated 1000 matches similar to: "evaluation of 2 matrices: categorical comparison"
2006 Dec 11
1
cohen kappa for two-way table
Greetings,
I am a bit confused by the results returned by the functions:
cohen.kappa {concord}
classAgreement {e1071}
when using a two-way table.
for example, if I have an matrix A, and a similar matrix B (same
dimensions), then:
matrix A and B can be found:
http://casoilresource.lawr.ucdavis.edu/drupal/files/a_40.txt
http://casoilresource.lawr.ucdavis.edu/drupal/files/b_40.txt
A <-
2007 May 14
1
cross-validation / sensitivity anaylsis for logistic regression model
Hi,
I have developed a logistic regression model in the form of (factor_1~ numeric
+ factor_2) and would like to perform a cross-validation or some similar
form of sensitivity analysis on this model.
using cv.glm() from the boot package:
# dataframe from which model was built in 'z'
# model is called 'm_geo.lrm'
# as suggested in the man page for a binomial model:
cost <-
2006 May 23
1
standardization of values before call to pam() or clara()
Greetings,
Experimenting with the cluster package, and am starting to scratch my head in
regards to the *best* way to standardize my data. Both functions can
pre-standardize columns in a dataframe. according to the manual:
Measurements are standardized for each variable (column), by subtracting the
variable's mean value and dividing by the variable's mean absolute deviation.
This
2006 Oct 04
2
compiling rgdal package on windows / macos
Greetings:
As I am not a windows user, I cannot try this: is it possible to install rgdal
on windows without having to compile it from source ?
Compilation on MacOS is within my abilities, however each time i try and
install the rgdal package it dies complaining that it cannot find
gdal-config --- which was recently installed with GRASS. I have updated my
PATH environment variable, logged
2006 Oct 25
1
any good way to convert sp class objects to splancs object
Greetings:
are there any simple ways to convert an sp class object to a splancs ppp class
object, outside of reading the coordinates and computing a bounding box?
cheers,
--
Dylan Beaudette
Soils and Biogeochemistry Graduate Group
University of California at Davis
530.754.7341
2005 Nov 28
1
overlay additional axes
Greetings,
I am trying to add an extra labled axis in position 3 (top x-axis), with
numbers that do not match up with the existing axes.
Surely this must be possible, and I am just doing it incorectly.
So far I have tried the following:
#make a plot
plot(TIK, type="l", cex=.25, xlim=c(2,32), ylim=c(0,1600))
#try and add a new axis with different numbers in position 3
2007 Feb 14
1
model diagnostics for logistic regression
Greetings,
I am using both the lrm() {Design} and glm( , family=binomial()) to perform a
a logisitic regression in R. Apart from the typical summary() methods, what
other methods of diagnosing logistic regression models does R provide? i.e.
plotting an 'lm' object, etc.
Secondly, is there any facility to calculate the R^{2)_{L} as suggested by
Menard in "Applied Logistic
2007 May 28
1
off-topic: affine transformation matrix
This may sound like a very naive question, but...
give two lists of coordinate pairs (x,y - Cartesian space) is there any simple
way to compute the affine transformation matrix in R.
I have a set of data which is offset from where i know it should be. I have
coordinates of the current data, and matching coordinates of where the data
should be. I need to compute the composition of the affine
2006 Apr 10
2
passing known medoids to clara() in the cluster package
Greetings,
I have had good success using the clara() function to perform a simple cluster
analysis on a large dataset (1 million+ records with 9 variables).
Since the clara function is a wrapper to pam(), which will accept known medoid
data - I am wondering if this too is possible with clara() ... The
documentation does not suggest that this is possible.
Essentially I am trying to
2007 Feb 27
1
prop.test or chisq.test ..?
Hi everyone,
Suppose I have a count the occurrences of positive results, and the total
number of occurrences:
pos <- 14
total <- 15
testing that the proportion of positive occurrences is greater than 0.5 gives
a p-value and confidence interval:
prop.test( pos, total, p=0.5, alternative='greater')
1-sample proportions test with continuity correction
data: 14 out of
2006 Sep 20
2
mysterious error on compile R 2.3.1
Getting a very strange error with a new install of R from source on x86;
make[3]: Leaving directory `/tmp/R.INSTALL.r20887/cluster/src'
** R
** data
** moving datasets to lazyload DB
Error in factor(c(1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1), :
invalid labels; length 2 should be 1 or 1
Execution halted
ERROR: lazydata failed for package 'cluster'
** Removing
2006 Mar 02
1
extracting RGB values from a colorspace class object
Greetings,
After pouring over the documentation for the 'colorspace' package, I have not
been able to figure out how the plot() method converts colorspace coordinates
to RGB values for display on the screen. I am convert between colorspaces
with the various as() methods... but cannot seem to find a way to extract RGB
(i.e. for displaying on a computer screen) triplets from color space
2007 Jun 26
3
inter-rater agreement index kappa
Is there a function that calculates the inter-rater agreement index
(kappa) in R?
Thanks ../Murli
[[alternative HTML version deleted]]
2011 Jun 22
1
caret's Kappa for categorical resampling
Hello,
When evaluating different learning methods for a categorization problem with
the (really useful!) caret package, I'm getting confusing results from the
Kappa computation. The data is about 20,000 rows and a few dozen columns,
and the categories are quite asymmetrical, 4.1% in one category and 95.9% in
the other. When I train a ctree model as:
model <- train(dat.dts,
2007 Mar 22
3
Cohen's Kappa
Hi,
im little bit confused about Cohen's Kappa and i should be look into the
Kappa function code. Is the easy formula really wrong?
kappa=agreement-chance/(1-chance)
many thanks
christian
###############################################################################
true-negativ:7445
false-positive:3410
false-negativ:347
true-positiv:772
classification-aggrement:68,6%
2008 Sep 07
1
cohen's kappa
Dear all,
I have a question on Cohen's kappa:
Assume I have two datasets, one has 500 objects, 10 methods and the other,
1000 different objects, 20 different methods. Could I compare between the
two datasets to conclude the 10 methods are more "concordant" than the 20
ones by looking at some output, for example, cohen.kappa{concord} ?
One more, could anyone explain in brief,
2006 Jul 31
1
questions regarding spline functions
Greetings,
A couple general questions regarding the use of splines to interpolate depth
profile data.
Here is an example of a set of depths, with associated attributes for a given
soil profile, along with a function for calculating midpoints from a set of
soil horizon boundaries:
#calculate midpoints:
mid <- function(x) {
for( i in 1:length(x)) {
if( i > 1) {
a[i] = (x[i] -
2009 Jan 23
1
lattice: reverse order of panel.lmline, panel.smooth
Hi,
is it possible to reverse the order in which panel.lmline() or panel.smooth()
operation in xyplot() ? This type of situation might occur when plotting some
variable with depth, but the relation we want to describe is variable ~
depth, and not depth ~ variable, as the plotting formula would suggest.
# an example:
d <- 1:100
v <- d * rnorm(100)
xyplot(d ~ v, ylim=c(100,0),
2010 Jul 19
1
possible bug in ape::extract.clade()
Hi,
I was recently splitting some massive phylo class objects with extract.clade()
and noticed what appears to be a bug in how tip labels are copied from the
full tree to the pruned tree. This possible bug was also mentioned here:
http://www.mail-archive.com/r-sig-phylo at r-project.org/msg00537.html
An example:
library(ape)
set.seed(5)
x <- matrix(rnorm(100), ncol=10)
p <-
2007 Dec 17
0
odd error messages coming from val.prob() {Design}
Hi,
after upgrading my R install from 2.5 -> 2.6.1 and performing multiple
iterations of update.packages(), I am getting an odd error when trying to
plot a calibration curve from the val.prob() function in package Design.
when running this function (which used to work) I get the following error
message:
Error in .C("lowess", x = as.double(xy$x[o]), as.double(xy$y[o]), n,