Re: [R] batch job GLM calculations

2007-01-15 Thread Milton Cezar Ribeiro 
Hi,
   
  Someone help-me on this task some weeks ago, and it is working find to me. I 
use something like:
  -
  findmodels - function(modeltype = lm, dataset, pattern) {
 ls - ls(.GlobalEnv, pattern=pattern)
 mods - ls[sapply(ls, function(x) inherits(get(x), modeltype))]
 if (!missing(dataset)) {
 data.name - function(x) as.character(x$call[[data]])
 mods - mods[sapply(mods, function(x) data.name == dataset)]
 }
 models - lapply(mods, get)
 class(models) - c(ensemble, class(models))
 models
 }
   
  mod_1-glm()
  mod_2-glm()
   
  models-NULL
models- findmodels(pattern=mod_)
  -

  So you can use a for (i in 1:length(models)) to extract the statistics tha 
you want for each model and save it in a file (I´m saving it easily in Access 
using RODBC).
   
  I hope this help,
   
  Miltinho
  Brazil
  
Indermaur Lukas [EMAIL PROTECTED] escreveu:
  Hello

I want to batch job the calculation of many GLM-models, extract some values and 
store them in a file. Almost everything in the script below works (read file, 
extract values and write them to file) except I fail in indexing the GLM with 
the modelstructure it should run. Running GLM's conventionally is no problem.



Conventionally a GLM is calculated as:

--

glm(ZlogHRS ~ ZRi+ZE+ZPROX_MN+ZED+ZAlwd+ZT2+ZW+ZN+Sex+y, family = gaussian, 
data=t.data) 

(just a note: dependent variable is ZlogHRS, while the others are indepent 
variables)



Desired way: sequentially run GLM

-

I want R to take the model structure to take from a vector called 
modelstructure and paste it into the GLM like:

glm(modelstructure[i], family = gaussian, data=t.data).

It would considerably ease my workload if there is a solution to the indexing 
problem within a GLM. I appreciate any hint.

Best regards

Lukas

p.s.

my R skills are rather poor



START 
R-CODE---

# Read file

t.url - 
C://HR_calculations/2005_2006/HR_SIZE/Kandidatenmodelle_Berechnung/inputfiles/

t.tuti - read.table(paste(t.url, All_animals.txt, sep=),header=T)



collect.results - function(x) {

#resets vectors which will be filled

i - 0

AICA - NA;



#put models names hierarchically in vector

modelnames - c(1=global, 2=biotic1, 3=biotic2, 4=abiotic) #keep track 
of changes in model names and number

for (i in 1:length(modelnames)) 

#model structure of the four models given for all models to run

#global

modelstructure - c(

ZlogHRS ~ ZRi+ZE+ZPROX_MN+ZED+ZAlwd+ZT2+ZW+ZN+Sex+y,

#biotic1

ZlogHRS ~ ZRi,

#biotic2

ZlogHRS ~ ZPROX_MN,

#abiotic

ZlogHRS ~ ZE)



ts.model - glm(modelstructure[i], family = gaussian, data=t.data) 



# Extracts some mode results

n[i] - length(resid(ts.model))

AICA[i] - AIC(ts.model)

}

#Writes results to data file

x = data.frame(

modelnames, n, AICA)

write.table(x, paste(t.url, file=Results.txt), sep=\t, quote=F) 

END 
R-CODE---








°°° 
Lukas Indermaur, PhD student 
eawag / Swiss Federal Institute of Aquatic Science and Technology 
ECO - Department of Aquatic Ecology
Überlandstrasse 133
CH-8600 Dübendorf
Switzerland

Phone: +41 (0) 71 220 38 25
Fax : +41 (0) 44 823 53 15 
Email: [EMAIL PROTECTED]
www.lukasindermaur.ch

__
R-help@stat.math.ethz.ch 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.


 __


[[alternative HTML version deleted]]

__
R-help@stat.math.ethz.ch 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.

[R] batch job GLM calculations

2007-01-11 Thread Indermaur Lukas 
Hello

I want to batch job the calculation of many GLM-models, extract some values and 
store them in a file. Almost everything in the script below works (read file, 
extract values and write them to file) except I fail in indexing the GLM with 
the modelstructure it should run. Running GLM's conventionally is no problem.

 

Conventionally a GLM is calculated as:

--

glm(ZlogHRS ~ ZRi+ZE+ZPROX_MN+ZED+ZAlwd+ZT2+ZW+ZN+Sex+y, family = gaussian, 
data=t.data) 

(just a note: dependent variable is ZlogHRS, while the others are indepent 
variables)

 

Desired way: sequentially run GLM

-

I want R to take the model structure to take from a vector called 
modelstructure and paste it into the GLM like:

glm(modelstructure[i], family = gaussian, data=t.data).

It would considerably ease my workload if there is a solution to the indexing 
problem within a GLM. I appreciate any hint.

Best regards

Lukas

p.s.

my R skills are rather poor

 

START 
R-CODE---

# Read file

t.url - 
C://HR_calculations/2005_2006/HR_SIZE/Kandidatenmodelle_Berechnung/inputfiles/

t.tuti - read.table(paste(t.url, All_animals.txt, sep=),header=T)

 

collect.results - function(x) {

#resets vectors which will be filled

i - 0

AICA - NA;

 

#put models names hierarchically in vector

modelnames - c(1=global, 2=biotic1, 3=biotic2, 4=abiotic) #keep track 
of changes in model names and number

for (i in 1:length(modelnames)) 

#model structure of the four models given for all models to run

#global

modelstructure - c(

ZlogHRS ~ ZRi+ZE+ZPROX_MN+ZED+ZAlwd+ZT2+ZW+ZN+Sex+y,

#biotic1

ZlogHRS ~ ZRi,

#biotic2

ZlogHRS ~ ZPROX_MN,

#abiotic

ZlogHRS ~ ZE)

 

ts.model - glm(modelstructure[i], family = gaussian, data=t.data) 

 

# Extracts some mode results

n[i] - length(resid(ts.model))

AICA[i] - AIC(ts.model)

}

#Writes results to data file

x = data.frame(

modelnames, n, AICA)

write.table(x, paste(t.url, file=Results.txt), sep=\t, quote=F) 

END 
R-CODE---

 

 

 

 
°°° 
Lukas Indermaur, PhD student 
eawag / Swiss Federal Institute of Aquatic Science and Technology 
ECO - Department of Aquatic Ecology
Überlandstrasse 133
CH-8600 Dübendorf
Switzerland
 
Phone: +41 (0) 71 220 38 25
Fax: +41 (0) 44 823 53 15 
Email: [EMAIL PROTECTED]
www.lukasindermaur.ch

__
R-help@stat.math.ethz.ch 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.

Re: [R] batch job GLM calculations

2007-01-11 Thread Ken Beath 
as.formula(modelstructure[i]) in the glm function

 Indermaur Lukas [EMAIL PROTECTED] 01/11/07 7:34 PM 
Hello

I want to batch job the calculation of many GLM-models, extract some values and 
store them in a file. Almost everything in the script below works (read file, 
extract values and write them to file) except I fail in indexing the GLM with 
the modelstructure it should run. Running GLM's conventionally is no problem.

 

Conventionally a GLM is calculated as:

--

glm(ZlogHRS ~ ZRi+ZE+ZPROX_MN+ZED+ZAlwd+ZT2+ZW+ZN+Sex+y, family = gaussian, 
data=t.data) 

(just a note: dependent variable is ZlogHRS, while the others are indepent 
variables)

 

Desired way: sequentially run GLM

-

I want R to take the model structure to take from a vector called 
modelstructure and paste it into the GLM like:

glm(modelstructure[i], family = gaussian, data=t.data).

It would considerably ease my workload if there is a solution to the indexing 
problem within a GLM. I appreciate any hint.

Best regards

Lukas

p.s.

my R skills are rather poor

 

START 
R-CODE---

# Read file

t.url - 
C://HR_calculations/2005_2006/HR_SIZE/Kandidatenmodelle_Berechnung/inputfiles/

t.tuti - read.table(paste(t.url, All_animals.txt, sep=),header=T)

 

collect.results - function(x) {

#resets vectors which will be filled

i - 0

AICA - NA;

 

#put models names hierarchically in vector

modelnames - c(1=global, 2=biotic1, 3=biotic2, 4=abiotic) #keep track 
of changes in model names and number

for (i in 1:length(modelnames)) 

#model structure of the four models given for all models to run

#global

modelstructure - c(

ZlogHRS ~ ZRi+ZE+ZPROX_MN+ZED+ZAlwd+ZT2+ZW+ZN+Sex+y,

#biotic1

ZlogHRS ~ ZRi,

#biotic2

ZlogHRS ~ ZPROX_MN,

#abiotic

ZlogHRS ~ ZE)

 

ts.model - glm(modelstructure[i], family = gaussian, data=t.data) 

 

# Extracts some mode results

n[i] - length(resid(ts.model))

AICA[i] - AIC(ts.model)

}

#Writes results to data file

x = data.frame(

modelnames, n, AICA)

write.table(x, paste(t.url, file=Results.txt), sep=\t, quote=F) 

END 
R-CODE---

 

 

 

 
°°° 
Lukas Indermaur, PhD student 
eawag / Swiss Federal Institute of Aquatic Science and Technology 
ECO - Department of Aquatic Ecology
Überlandstrasse 133
CH-8600 Dübendorf
Switzerland
 
Phone: +41 (0) 71 220 38 25
Fax: +41 (0) 44 823 53 15 
Email: [EMAIL PROTECTED]
www.lukasindermaur.ch

__
R-help@stat.math.ethz.ch 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.

__
R-help@stat.math.ethz.ch 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.

Re: [R] batch job GLM calculations

2007-01-11 Thread Prof Brian Ripley 

From ?glm:


 formula: a symbolic description of the model to be fit. The details of
  model specification are given below.

which could be clearer. It needs to be a object of type 'formula'.

I believe as.formula(modelstructure[i]) will do what you want (but your 
posting has come out rather awkwardly laid out in double spacing).


On Thu, 11 Jan 2007, Indermaur Lukas wrote:


Hello

I want to batch job the calculation of many GLM-models, extract some values and 
store them in a file. Almost everything in the script below works (read file, 
extract values and write them to file) except I fail in indexing the GLM with 
the modelstructure it should run. Running GLM's conventionally is no problem.



Conventionally a GLM is calculated as:

--

glm(ZlogHRS ~ ZRi+ZE+ZPROX_MN+ZED+ZAlwd+ZT2+ZW+ZN+Sex+y, family = gaussian, 
data=t.data)

(just a note: dependent variable is ZlogHRS, while the others are indepent 
variables)



Desired way: sequentially run GLM

-

I want R to take the model structure to take from a vector called 
modelstructure and paste it into the GLM like:

glm(modelstructure[i], family = gaussian, data=t.data).

It would considerably ease my workload if there is a solution to the indexing 
problem within a GLM. I appreciate any hint.

Best regards

Lukas

p.s.

my R skills are rather poor



START 
R-CODE---

# Read file

t.url - 
C://HR_calculations/2005_2006/HR_SIZE/Kandidatenmodelle_Berechnung/inputfiles/

t.tuti - read.table(paste(t.url, All_animals.txt, sep=),header=T)



collect.results - function(x) {

#resets vectors which will be filled

i - 0

AICA - NA;



#put models names hierarchically in vector

modelnames - c(1=global, 2=biotic1, 3=biotic2, 4=abiotic) #keep track 
of changes in model names and number

for (i in 1:length(modelnames))

#model structure of the four models given for all models to run

#global

modelstructure - c(

ZlogHRS ~ ZRi+ZE+ZPROX_MN+ZED+ZAlwd+ZT2+ZW+ZN+Sex+y,

#biotic1

ZlogHRS ~ ZRi,

#biotic2

ZlogHRS ~ ZPROX_MN,

#abiotic

ZlogHRS ~ ZE)



ts.model - glm(modelstructure[i], family = gaussian, data=t.data)



# Extracts some mode results

n[i] - length(resid(ts.model))

AICA[i] - AIC(ts.model)

}

#Writes results to data file

x = data.frame(

modelnames, n, AICA)

write.table(x, paste(t.url, file=Results.txt), sep=\t, quote=F)

END 
R-CODE---








°°°
Lukas Indermaur, PhD student
eawag / Swiss Federal Institute of Aquatic Science and Technology
ECO - Department of Aquatic Ecology
Überlandstrasse 133
CH-8600 Dübendorf
Switzerland

Phone: +41 (0) 71 220 38 25
Fax: +41 (0) 44 823 53 15
Email: [EMAIL PROTECTED]
www.lukasindermaur.ch

__
R-help@stat.math.ethz.ch 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.



--
Brian D. Ripley,  [EMAIL PROTECTED]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel:  +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax:  +44 1865 272595__
R-help@stat.math.ethz.ch 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.