Displaying 20 results from an estimated 2000 matches similar to: "Plots from lda and predict.lda"
2007 Mar 27
1
Jackknife estimates of predict.lda success rate
Dear all
I have used the lda and predict functions to classify a set of objects
of unknown origin. I would like to use a jackknife reclassification to
assess the degree to which the outcomes deviate from that expected by
chance. However, I can't find any function that allows me to do this.
Any suggestions of how to generate the jackknife reclassification to
assess classification accuracy?
2005 Jun 16
1
how to use plot.lda included in MASS package?
Hi there,
I am a master student in Denmark, and apply R to analyze the drug data.
I use the function 'lda' to obtain a linear discriminant object, and
then wish to use 'plot.lda' to do the plot on this object like below.
drug.lda <- lda(Inhibition ~ NET_CHARGE + PKA_1 + MW + MLOGP,
data = drug.class, method = "moment")
plot.lda(drug.lda,
2004 Nov 02
2
lda
Hi !!
I am trying to analyze some of my data using linear discriminant analysis.
I worked out the following example code in Venables and Ripley
It does not seem to be happy with it.
============================
library(MASS)
library(stats)
data(iris3)
ir<-rbind(iris3[,,1],iris3[,,2],iris3[,,3])
ir.species<-factor(c(rep("s",50),rep("c",50),rep("v",50)))
2011 Jun 09
0
(no subject)
> #
>> # Generate the figures (on screen)
>> #
>> # Image generation - function definition
>> pic_onscr<-function(matrix, title, cex_val=1)
> + {x11() + par(mgp=c(5,2,0), # axis margins + # (title,
> labels, line) + mar=c(7,4,4,2), # plot margins (b,l,t,r) +
> las=1) # horizontal labels + plot(matrix, # data to plot +
>
2007 Jun 18
0
discriminant analysis with lda(MASS)
I use Widows, R version 2.4.1
I have 4 questions on lda (MASS) (code is pasted below):
1st. How can I obtain the statistics and p-value associated with
discriminant analysis? Am I supposed to calculate that manually by squaring
the svd value and looking the p value up in a table? I am writing the
following code:
training.mx<-read.table('C:\\Documents and Settings\\silvia\\My
2011 Jun 09
1
what is the mistake?? the coding still not function. no result display
# lda.r
> #
> # Author: Amsha Nahid, Jairus Bowne, Gerard Murray
> # Purpose: Perform Linear Discriminant Analysis (LDA)
> #
> # Input: Data matrix as specified in Data-matrix-format.pdf
> # Output: LDA plot
> #
> # Notes: Missing values (if any) are replaced by the half of the lowest
> # value in the entire data matrix.
>
2011 Jun 21
1
(no subject)
hello,
i already include the error in blue color word.
i hope it can help you to understand my question.
if not burden you, please give me a guide how to correct the error or maybe you
can correct the coding cause error.
thank you.
> # lda.r
> #
> # Author: Amsha Nahid, Jairus Bowne, Gerard Murray
> # Purpose: Perform Linear Discriminant Analysis (LDA)
> #
> #
2004 May 24
1
discriminant analysis
Hi,
I have done different discriminant function analysis of multivariat data. With the CV=True option I was not able to perform the predict() call. What do I have to do? Or is there no possibility at all? You also need the predicted values to produce a plot of the analysis, as far as I know.
Here my code:
pcor.lda2<-lda(pcor~habarea+hcom+isol+flowcov+herbh+inclin+windprot+shrubcov+baregr,
2011 Nov 12
1
Subsetting data leads to funky plots
I'm trying out a basic plot, but something about the way I subset my data
leads to problems with the plot.
Here is the first bit of my data set
year,date,location,quadrat_juvenile,photo_location,photo_exists,genus,count,divers
2005,2005-04-30, 1 Fringing Reef,1, 1 Fringing Reef Coral Transect Pole 1-2
Quadrat 1,t,Acanthastrea,0,HP+MEM
2005,2005-04-30, 1 Fringing Reef,1, 1 Fringing Reef
2009 Aug 05
1
Decision boundaries for lda function?
Hi,
I am using the lda function from the MASS library. I would to find the
decision boundaries of each class and subsequently plot them. I wonder if
anybody can offer any help on this topic?
Below I applied the lda function on a small dataset of mine.
Any help will be much appreciated.
> library(MASS)
>
2005 Apr 28
0
Linear Discriminant Analysis Biplots
Dear R
I'm trying to plot the lda means onto a 2 D plot of discriminant scores.
Preferably I'd like these to be in a larger font compared to the
discriminant scores.
I tried
skull.mean.pred <- predict(skulls.lda, as.data.frame(skulls.lda$means),
dimen=2)
from which I got
skull.mean.pred
$class
[1] 1 2 3 4 5
Levels: 1 2 3 4 5
$posterior
1 2 3 4
2007 Aug 22
1
plotting lda results
Hi all,
I am trying to plot the results of a discriminant analysis done with
lda(MASS) but my groups appear in two different plots (in the same graphics
device) and I want to combine them in one plot. My code looks like:
BirdTrain.lda <- lda(Bdisperser~., data=BirdTrain.mx)
predict(BirdTrain.lda)
plot(BirdTrain.lda)
I have two types of Bdisperser, so I only get one linear discriminant
2004 Jul 12
1
lda()
Hello,
For a simple problem with 1 predictor (x) and 2 classes (0 and 1), the
linear discriminant function should be something like
2(mu_0 - mu_1)/var x + x-independent-terms
where var is the common variance.
2008 Jan 18
0
forming a linear discriminant function from the output of lda()
Hello all-
I am a relatively new user of R and am working through a graduate course
in
Statistics that uses Minitab, SAS and some Matlab. I like using R but
am
having some trouble lining up the output from lda() to that of the other
programs'
results. The dataset below is a modified set of wine data from the
Pinot Noir
data set as an illustration of the 2 group LDA scenario.
Mo Ba
2011 Dec 08
1
lda output missing
Hello everyone,
I am working on a linear discriminant analysis and am having issues finding
the full output of my lda. Specifically, there is no reporting of the
Proportion of Trace that is a normal output of the procedure. I'm using a
csv file and everything is reading in correctly. I've looked and looked and
can't figure out why my output is not complete. Is it something simple that
2009 Nov 18
0
Y axis of 1-D Linear Discriminant Histograms
Hi all.
I would like to understand what are the units defined on the y-axis
when you plot the one-dimensional predictions (histograms) from lda()
(MASS) discriminant function objects?
While the helpfile suggests that a histogram is returned by default,
the presumably proportion-like values for each group seem to add up to
more than 1, and I'm not sure how to interpret the code from
ldahist(),
2003 Feb 01
3
LDA newbie question
Hi,
I have tried the (MASS) LDA example (Iris) that's given on the help
pages but I don't fully understand the results. Perhaps someone could be
so kind to explain it to me.
On the help pages it says as return values:
prior
means
scaling
svd
N
call
What I get as results are
prior
means
coefficients of linear discriminants
proportion of trace
OK, so the first 3 appear to be the same
2000 Mar 08
3
Reading data for discriminant analysis
Dear R users,
I want to do discriminant analysis on my data. I have
successfully followed the discriminant analysis in V & R on
the iris data:
> ir <- rbind (iris3[,,1],iris3[,,2],iris3[,,3])
> ir.species <- c(rep("s",50),rep("c",50),rep("v",50))
> a <- lda(log(ir),ir.species)
> a$svd^2/sum(a$svd^2)
[1] 0.996498601 0.003501399
> a.x <-
2006 Nov 24
2
low-variance warning in lmer
For block effects with small variance, lmer will sometimes
estimate the variance as being very close to zero and issue
a warning. I don't have a problem with this -- I've explored
things a bit with some simulations (see below) and conclude that
this is probably inevitable when trying to incorporate
random effects with not very much data (the means and medians
of estimates are plausibly
2017 Nov 21
2
mystery "158"
This is a simple problem, but a mystery to me.
I'm trying to grab $Family "Scelionidae" from one dataframe and put it into
another dataframe occupied with NA in $Family. The result is a "158" ends
up there instead of Scelionidae.
Simply put fam$Family[1] <- least$Family[1]
If I have made a mistake here, can somebody point it out. I've included
the simple