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Bond, Stephen

2014-Oct-07 13:01 UTC

[R] lattice add a fit

What is the way to add an arbitrary fit from a model to a lattice conditioning
plot ?

For example
xyplot(v1 ~v2 | v3,data=mydata,
        panel=function(...){
            panel.xyplot(...)
            panel.loess(...,col.line="red")
        }
)
Will add a loess smoother. Instead, I want to put a fit from lm (but not a
simple straight line) and the fit has to be done for each panel separately, not
one fit for the full data set, so sth like an lm equivalent of panel.locfit
(there is no panel.lmfit)
Thank you.

Stephen B


	[[alternative HTML version deleted]]

Bert Gunter

2014-Oct-07 13:30 UTC

head link

[R] lattice add a fit

Fit your model in the panel function using lm and plot the fits using
?panel.points, ?panel.lines, etc.

-- Bert

Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374

"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
Clifford Stoll




On Tue, Oct 7, 2014 at 6:01 AM, Bond, Stephen <Stephen.Bond at cibc.com>
wrote:> What is the way to add an arbitrary fit from a model to a lattice
conditioning plot ?
>
> For example
> xyplot(v1 ~v2 | v3,data=mydata,
>         panel=function(...){
>             panel.xyplot(...)
>             panel.loess(...,col.line="red")
>         }
> )
> Will add a loess smoother. Instead, I want to put a fit from lm (but not a
simple straight line) and the fit has to be done for each panel separately, not
one fit for the full data set, so sth like an lm equivalent of panel.locfit
(there is no panel.lmfit)
> Thank you.
>
> Stephen B
>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Bond, Stephen

2014-Oct-07 15:13 UTC

head link

[R] lattice add a fit

Bert,

Can you provide an example how to pass the conditioned data set?

xyplot( x~y | z, data=mydata,
panel=function(...){ 
mod=lm(x~ y+w +q, data=??)
panel.lines(fitted(mod))

}

If I use mydata in place of ?? I get a global fit, not a fit for each level of
z, which is what I want.

Stephen B


-----Original Message-----
From: Bert Gunter [mailto:gunter.berton at gene.com] 
Sent: Tuesday, October 07, 2014 9:30 AM
To: Bond, Stephen
Cc: r-help at R-project.org
Subject: Re: [R] lattice add a fit

Fit your model in the panel function using lm and plot the fits using
?panel.points, ?panel.lines, etc.

-- Bert

Bert Gunter
Genentech Nonclinical Biostatistics
(650) 467-7374

"Data is not information. Information is not knowledge. And knowledge is
certainly not wisdom."
Clifford Stoll




On Tue, Oct 7, 2014 at 6:01 AM, Bond, Stephen <Stephen.Bond at cibc.com>
wrote:> What is the way to add an arbitrary fit from a model to a lattice
conditioning plot ?
>
> For example
> xyplot(v1 ~v2 | v3,data=mydata,
>         panel=function(...){
>             panel.xyplot(...)
>             panel.loess(...,col.line="red")
>         }
> )
> Will add a loess smoother. Instead, I want to put a fit from lm (but 
> not a simple straight line) and the fit has to be done for each panel
separately, not one fit for the full data set, so sth like an lm equivalent of
panel.locfit (there is no panel.lmfit) Thank you.
>
> Stephen B
>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Duncan Mackay

2014-Oct-08 04:15 UTC

head link

[R] lattice add a fit

Hi Stephen

if you want and uncomplicated graph you can do the following
(data is from
https://stat.ethz.ch/pipermail/r-help/2008-December/181887.html
which has an example of smoothing with a panel function a  (follow the
thread))
May be un necessary for what you want

dput(test)
structure(list(x = 1:200, y = c(-0.211833603383945, -1.0415911337336, 
-1.1533075572692, 0.321531497643745, -1.5001298759544, -0.445533260997329, 
1.73404543257509, 0.511295615763455, 0.0996450365533331,
-0.0578911103962697, 
-1.74278762900362, -1.32495298319389, -0.547933881534948, -1.45638427585301,

0.0826868204409038, 0.927578947155782, -0.716769334937502,
0.962399675187835, 
1.54588458200656, -1.00976361360517, 0.557410853590579, 0.168781513971099, 
0.155258858301712, 2.36776473870934, -1.58564441351633, -1.10353350945666, 
0.902787057776989, 0.0683183515567076, -1.14946795040125, -0.90127498047004,

-1.19845352398361, -0.510163823550385, 0.306246343638814,
-0.0678770276660271, 
0.372202425855059, 1.14449122171645, -1.43961215364919, -0.745407767319761, 
-1.08426028148107, -0.911810459312264, 0.254473860506602,
0.0545428435691033, 
0.86939682821168, -0.495822138795001, 0.788983956205307,
-0.0482778318087694, 
0.28444147880148, -2.3449130823549, 0.352139869980497, -0.73670929392907, 
0.152865554816491, 0.466635540442577, -1.34862166637197, -0.371330904577685,

2.04819500702545, -1.03035368989461, -0.808913708097202, -0.899512468883577,

1.32164919515955, -1.90258984438615, -1.43516196895465, 0.0465901079414443, 
-0.050190824605222, -1.28753166678936, 1.15411244955901, -1.37573809203985, 
-1.14829872319585, 1.41625774885229, 0.105763612116132, -0.384659376665841, 
1.78448216497794, -1.1152932761564, -0.0721496590810866, -0.654929692334926,

1.23475033091273, -0.355004059316614, 0.0242929525502168, -1.12014689112359,

0.131516716053627, -1.01789380466415, 1.54412508731677, -0.612498366500995, 
-1.47544725093144, -1.33884056677665, 0.116000294553631, 0.441007318370771, 
0.253328166388004, -0.601324732898278, -0.681872432317887,
-0.638406595370473, 
1.1255146487638, 1.68030106840915, -0.0458152886664351, -0.359702695597414, 
-1.27276961899765, 1.65150890035352, 0.970733803202561, -0.299164223313285, 
0.0863388612193544, -1.56778219134085, -0.934175135343763,
-1.75098468827598, 
-0.350775124642839, -0.497774672576354, 0.771324636489948,
-0.69490617657808, 
-0.776286103585292, 0.0401278987521509, -0.965161644356313,
-0.443562752383677, 
0.482231363899495, 0.299362730723139, -1.13975716906454, 0.750123380303915, 
-0.346046820684503, -0.298660657494398, 1.15743160079942, 1.37831825909263, 
-0.561195292140498, -0.727441974730694, 0.542558262494051, 1.07423749905296,

-0.671511488353386, -0.140489880785358, 1.46724871140033, 0.563360651277434,

1.24069952075524, -0.253423940974, 0.196985403588085, -1.29263886475009, 
-0.700235249467159, 0.386254280503009, -0.489119591847831,
-0.863120570714887, 
0.21167415527797, -0.104722187456112, 0.885271725582058, -1.33715921875481, 
-0.419738882938569, 0.114904893946579, 0.579793678083023, 1.3375478692142, 
0.00553313645797594, -1.0480172540963, -0.293082520385054,
-0.607995018773811, 
0.22269595909434, 0.404577306401601, 0.212081041192621, -1.28370971577478, 
-0.186741150561225, 1.47504624554164, -0.335669248934062,
-0.0752650377217833, 
0.938248892501711, -1.19915518471386, -0.823130111133665, 1.77585103279627, 
-0.726506122852284, -0.854585428953646, 0.18721613856176, 0.664751685525484,

-0.378660174874064, -0.406279864316906, -0.377953114167246,
-0.578277117855972, 
-0.195896309465962, -0.752879703028692, -1.20718148517937,
0.103036243241138, 
0.707569503031958, 0.488185644365067, -0.674354094380548, 1.45780393551308, 
-0.426823625045982, 0.372084624745127, -0.489364737649147, 2.00664228219939,

0.0918083578741706, -0.563102471737825, -0.0372326923340063, 
1.00352069476112, -1.14244200325742, 1.14469060546702, 1.26070182057624, 
0.664616631427959, 0.75021683374034, -1.39029533734557, 0.818844192795068, 
-0.948663137610259, 2.87434018113975, 0.237475434622456, 0.745884070517981, 
1.19494964206119, 0.627396315033843, -0.810728351760724, 1.58246498427057, 
-0.414333063166778, -1.91414027760821, -1.68038800516161), groups
structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 4L, 4L), .Label = c("1", "2",
"3", "4"), class "factor")), .Names =
c("x",
"y", "groups"), row.names = c(NA, -200L), class =
"data.frame")

xyplot(y~x|groups, test, type = c("p","smooth"), span = 0.8,
col.line="red")

span and col.line are not the default values

You will have to make your own panel function for locfit if you want to use
it
I have done it in the past - read the help for 
library(locfit)
?plot.locfit 
and the links
?lattice::prepanel

Regards

Duncan

Duncan Mackay
Department of Agronomy and Soil Science
University of New England
Armidale NSW 2351
Email: home: mackay at northnet.com.au


-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On
Behalf Of Bond, Stephen
Sent: Tuesday, 7 October 2014 23:02
To: r-help at R-project.org
Subject: [R] lattice add a fit

What is the way to add an arbitrary fit from a model to a lattice
conditioning plot ?

For example
xyplot(v1 ~v2 | v3,data=mydata,
        panel=function(...){
            panel.xyplot(...)
            panel.loess(...,col.line="red")
        }
)
Will add a loess smoother. Instead, I want to put a fit from lm (but not a
simple straight line) and the fit has to be done for each panel separately,
not one fit for the full data set, so sth like an lm equivalent of
panel.locfit (there is no panel.lmfit)
Thank you.

Stephen B


	[[alternative HTML version deleted]]

______________________________________________
R-help at r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

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