8 Dec
2015
8 Dec
'15
8:22 a.m.
Dear list members,
I would like to analyse a multiply imputed data set with zelig,
but I don't know how to do with the last version of the Zelig package.
For instance, the following code, which runs well using a previous version
of the package (4.2.1 for instance), produces an error with the version
5.0.9:
library("Amelia")
data(freetrade)
amelia.out <- amelia(freetrade, m = 15, ts = "year", cs =
"country")
is.list(amelia.out$imputations)
#TRUE
is.data.frame(amelia.out$imputations[[1]])
#TRUE
library("Zelig")
zelig.fit <- zelig(tariff ~ pop + gdp.pc + year + polity, data =
amelia.out$imputations, model = "ls", cite = FALSE)
#Error: data is not a data frame
Could you give me an example to show me how to use the last version
of Zelig?
Thank you very much for your help,
Best,
--
*AUDIGIER Vincent*
Applied Mathematic Department, Agrocampus Ouest
65 rue de Saint-Brieuc, 35042 Rennes Cedex, France
Tel: (+33)2 23 48 54 76
Website: http://vincentaudigier.weebly.com/
8 Dec
8 Dec
9:12 a.m.
Hi Vincent,
We just released an update to Amelia and now the vignette shows how to use
the latest version of Zelig. See Section 4.10 here:
https://cran.r-project.org/web/packages/Amelia/vignettes/amelia.pdf
Or see the Zelig documentation here:
http://docs.zeligproject.org/en/latest/using-Zelig-with-Amelia.html
Cheers,
Matt
~~~~~~~~~~~
Matthew Blackwell
Assistant Professor of Government
Harvard University
url: http://www.mattblackwell.org
On Tue, Dec 8, 2015 at 8:22 AM, Vincent Audigier <
vincent.audigier(a)agrocampus-ouest.fr> wrote:
Dear list members,
I would like to analyse a multiply imputed data set with zelig,
but I don't know how to do with the last version of the Zelig package.
For instance, the following code, which runs well using a previous version
of the package (4.2.1 for instance), produces an error with the version
5.0.9:
library("Amelia")
data(freetrade)
amelia.out <- amelia(freetrade, m = 15, ts = "year", cs =
"country")
is.list(amelia.out$imputations)
#TRUE
is.data.frame(amelia.out$imputations[[1]])
#TRUE
library("Zelig")
zelig.fit <- zelig(tariff ~ pop + gdp.pc + year + polity, data =
amelia.out$imputations, model = "ls", cite = FALSE)
#Error: data is not a data frame
Could you give me an example to show me how to use the last version
of Zelig?
Thank you very much for your help,
Best,
--
*AUDIGIER Vincent*
Applied Mathematic Department, Agrocampus Ouest
65 rue de Saint-Brieuc, 35042 Rennes Cedex, France
Tel: (+33)2 23 48 54 76
Website: http://vincentaudigier.weebly.com/
<https://urldefense.proofpoint.com/v2/url?u=http-3A__vincentaudigier.weebly.com_&d=CwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=EwICq0J5pL8CwgEJz8qkmauGonk0XmiLpxcYOEgk2a0&m=FXpCFO6P5ad6FfRsV0Ok0x6YB5-_Gicd4NdG0FzUAtk&s=hp7cTyqA159HN2feIubmqiH_eza7Th9oANR_anImwi0&e=>
--
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10:01 a.m.
Dear All,
I have looked at this problem with *Zelig* previously, but still cannot
find how to combine the five datasets produced by *AmeliaView*. In
our data it is critical to set bounds for factors, otherwise the imputed
data produces out of range values for standard blood tests. How exactly do
you create the *output object* that is needed to combine the five
datasets that are produced by AmeliaView?
Although page 27 of the *Amelia* user's manual gives the instructions
for setting bounds without using the *AmeliaView* GUI, the syntax seems
cumbersome "* bds <- matrix(c(3, 30, 40), nrow = 1, ncol = 3) "* if this
must be done for each variable. The alternative presented, to allow
unbounded imputation that might produce negative values, that would
then be set to "0" would produce unacceptable results.... such patients
would be dead.
I very much appreciate your efforts with this program. I and my
colleagues at the Wistar Institute of the University of Pennsylvania have
successfully used the older version of Amelia and Zelig for a
manuscript on pediatric treatment response for HIV that has been accepted
pending revisions by PLoS- One, so I hope to be able to continue to use
the program. I even tried to load the older, more user friendly version
of *Zelig* , but it would not work with the latest version of *R*. Any
additional guidance as to how the bounded datasets produced by *AmeliaView*
can be turned into an output object and then combined would be much
appreciated. Perhaps a new updated version of this excellent package
(named "*Hoffa*" ?) might simplify this process.
Skip Barbour
>
--
*There is nothing so fatal to character as half finished tasks.*
David Lloyd George
10:14 a.m.
Hi Skip,
With AmeliaView, you can save your data in a number of formats, but in all
of them you get "m" imputed datasets which you can pass to the relevant
analysis model. That is, Amelia will not combine the imputed datasets into
one dataset because with multiple imputation, you want to combine the final
quantities of interest from each imputed dataset, not the imputed data
itself. If you want to use the output with Zelig in R itself, it's probably
best to set the output file type as "RData" then use the load() function in
R to load that object:
load("myimps.RData")
ameliaObject ## name of the output, includes all m imputed datasets
z.out <- zelig(dvar ~ ivar, data = ameliaObject, model = "ls")
Cheers,
Matt
~~~~~~~~~~~
Matthew Blackwell
Assistant Professor of Government
Harvard University
url: http://www.mattblackwell.org
On Tue, Dec 8, 2015 at 10:01 AM, Skip Barbour <russellbarbour(a)gmail.com>
wrote:
Dear All,
I have looked at this problem with *Zelig* previously, but still
cannot find how to combine the five datasets produced by
*AmeliaView*. In our data it is critical to set bounds for factors,
otherwise the imputed data produces out of range values for standard blood
tests. How exactly do you create the *output object* that is needed to
combine the five datasets that are produced by AmeliaView?
Although page 27 of the *Amelia* user's manual gives the instructions
for setting bounds without using the *AmeliaView* GUI, the syntax seems
cumbersome "* bds <- matrix(c(3, 30, 40), nrow = 1, ncol = 3) "* if this
must be done for each variable. The alternative presented, to allow
unbounded imputation that might produce negative values, that would
then be set to "0" would produce unacceptable results.... such patients
would be dead.
I very much appreciate your efforts with this program. I and my
colleagues at the Wistar Institute of the University of Pennsylvania have
successfully used the older version of Amelia and Zelig for a
manuscript on pediatric treatment response for HIV that has been accepted
pending revisions by PLoS- One, so I hope to be able to continue to use
the program. I even tried to load the older, more user friendly version
of *Zelig* , but it would not work with the latest version of *R*. Any
additional guidance as to how the bounded datasets produced by
*AmeliaView* can be turned into an output object and then combined
would be much appreciated. Perhaps a new updated version of this excellent
package (named "*Hoffa*" ?) might simplify this process.
Skip Barbour
>
--
*There is nothing so fatal to character as half finished tasks.*
David Lloyd George
10:21 a.m.
Matt,
Thanks.. that is what I needed to know. And yes I realize that we are
not combining the datasets into one.I will send you the PloS-One
manuscript acknowledging the Amelia program once the final version is
accepted.
Thank you again for your assistance.
Skip
On Tue, Dec 8, 2015 at 10:14 AM, Matt Blackwell <mblackwell(a)gov.harvard.edu>
wrote:
Hi Skip,
With AmeliaView, you can save your data in a number of formats, but in all
of them you get "m" imputed datasets which you can pass to the relevant
analysis model. That is, Amelia will not combine the imputed datasets into
one dataset because with multiple imputation, you want to combine the final
quantities of interest from each imputed dataset, not the imputed data
itself. If you want to use the output with Zelig in R itself, it's probably
best to set the output file type as "RData" then use the load() function in
R to load that object:
load("myimps.RData")
ameliaObject ## name of the output, includes all m imputed datasets
z.out <- zelig(dvar ~ ivar, data = ameliaObject, model = "ls")
Cheers,
Matt
~~~~~~~~~~~
Matthew Blackwell
Assistant Professor of Government
Harvard University
url: http://www.mattblackwell.org
On Tue, Dec 8, 2015 at 10:01 AM, Skip Barbour <russellbarbour(a)gmail.com>
wrote:
--
*There is nothing so fatal to character as half finished tasks.*
David Lloyd George
Dear All,
I have looked at this problem with *Zelig* previously, but still
cannot find how to combine the five datasets produced by
*AmeliaView*. In our data it is critical to set bounds for factors,
otherwise the imputed data produces out of range values for standard blood
tests. How exactly do you create the *output object* that is needed to
combine the five datasets that are produced by AmeliaView?
Although page 27 of the *Amelia* user's manual gives the instructions
for setting bounds without using the *AmeliaView* GUI, the syntax seems
cumbersome "* bds <- matrix(c(3, 30, 40), nrow = 1, ncol = 3) "* if
this must be done for each variable. The alternative presented, to allow
unbounded imputation that might produce negative values, that would
then be set to "0" would produce unacceptable results.... such patients
would be dead.
I very much appreciate your efforts with this program. I and my
colleagues at the Wistar Institute of the University of Pennsylvania have
successfully used the older version of Amelia and Zelig for a
manuscript on pediatric treatment response for HIV that has been accepted
pending revisions by PLoS- One, so I hope to be able to continue to use
the program. I even tried to load the older, more user friendly version
of *Zelig* , but it would not work with the latest version of *R*. Any
additional guidance as to how the bounded datasets produced by
*AmeliaView* can be turned into an output object and then combined
would be much appreciated. Perhaps a new updated version of this excellent
package (named "*Hoffa*" ?) might simplify this process.
Skip Barbour
>
--
*There is nothing so fatal to character as half finished tasks.*
David Lloyd George
10:42 a.m.
Thank you very much for your help Matt.
Indeed, it works well when the multiply imputed dataset comes from the
amelia function:
library(Rmixmod)
data(titanic);
library(missForest)
set.seed(0)
titanicna<-prodNA(titanic,.2)
summary(titanicna)
Class Age Sex Survived
0 :733 0 : 85 0 : 388 0 :1183
1 :256 1 :1662 1 :1393 1 : 566
2 :225 NA's: 454 NA's: 420 NA's: 452
3 :553
NA's:434
res.amelia<-amelia(titanicna,noms = 1:4)
z5 <- zlogit$new()
z5$zelig(Survived~ Class+Age, data = res.amelia)
z5
Model: Combined Imputations
Estimate Std.Error z value Pr(>|z|)
(Intercept) -0.50632 0.2047 -2.47350 1.338e-02 .
Class1 1.40721 0.1776 7.92321 2.220e-15 ***
Class2 0.66160 0.1602 4.12910 3.642e-05 ***
Class3 -0.00529 0.1374 -0.03852 9.693e-01
Age1 -0.53445 0.1947 -2.74473 6.056e-03 *
---
Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05 '.'
0.1 ' ' 1
For results from individual imputed datasets, use summary(x, subset = i:j)
Next step: Use 'setx' method
However, now I would like to use another function than amelia to perform
MI.
My output is a list of dataframes. Can I use Zelig to achieve this goal?
Thank you very much for your help,
*AUDIGIER Vincent*
Applied Mathematic Department, Agrocampus Ouest
65 rue de Saint-Brieuc, 35042 Rennes Cedex, France
Tel: (+33)2 23 48 54 76
Website: http://vincentaudigier.weebly.com/
Le 08/12/2015 15:12, Matt Blackwell a écrit :
Hi Vincent,
We just released an update to Amelia and now the vignette shows how to
use the latest version of Zelig. See Section 4.10 here:
https://cran.r-project.org/web/packages/Amelia/vignettes/amelia.pdf
Or see the Zelig documentation here:
http://docs.zeligproject.org/en/latest/using-Zelig-with-Amelia.html
Cheers,
Matt
~~~~~~~~~~~
Matthew Blackwell
Assistant Professor of Government
Harvard University
url: http://www.mattblackwell.org
On Tue, Dec 8, 2015 at 8:22 AM, Vincent Audigier
<vincent.audigier(a)agrocampus-ouest.fr
<mailto:vincent.audigier@agrocampus-ouest.fr>> wrote:
Dear list members,
I would like to analyse a multiply imputed data set with zelig,
but I don't know how to do with the last version of the Zelig package.
For instance, the following code, which runs well using a previous
version
of the package (4.2.1 for instance), produces an error with the
version 5.0.9:
library("Amelia")
data(freetrade)
amelia.out <- amelia(freetrade, m = 15, ts = "year", cs =
"country")
is.list(amelia.out$imputations)
#TRUE
is.data.frame(amelia.out$imputations[[1]])
#TRUE
library("Zelig")
zelig.fit <- zelig(tariff ~ pop + gdp.pc + year + polity, data =
amelia.out$imputations, model = "ls", cite = FALSE)
#Error: data is not a data frame
Could you give me an example to show me how to use the last version
of Zelig?
Thank you very much for your help,
Best,
--
*AUDIGIER Vincent*
Applied Mathematic Department, Agrocampus Ouest
65 rue de Saint-Brieuc, 35042 Rennes Cedex, France
Tel: (+33)2 23 48 54 76 <tel:%28%2B33%292%2023%2048%2054%2076>
Website: http://vincentaudigier.weebly.com/
<https://urldefense.proofpoint.com/v2/url?u=http-3A__vincentaudigier.weebly.com_&d=CwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=EwICq0J5pL8CwgEJz8qkmauGonk0XmiLpxcYOEgk2a0&m=FXpCFO6P5ad6FfRsV0Ok0x6YB5-_Gicd4NdG0FzUAtk&s=hp7cTyqA159HN2feIubmqiH_eza7Th9oANR_anImwi0&e=>
--
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[Un]Subscribe/View Archive:
http://lists.gking.harvard.edu/?info=amelia
More info about Amelia: http://gking.harvard.edu/amelia
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10:45 a.m.
Hi Vincent,
I'm actually not sure if Zelig can handle that, but I don't work on it so
I'm probably the wrong person to ask. You may want to inquire on the Zelig
mailing list/Google group.
Cheers,
Matt
On Tue, Dec 8, 2015 at 10:42 AM, audigier <audigier(a)agrocampus-ouest.fr>
wrote:
Thank you very much for your help Matt.
Indeed, it works well when the multiply imputed dataset comes from the
amelia function:
library(Rmixmod)
data(titanic);
library(missForest)
set.seed(0)
titanicna<-prodNA(titanic,.2)
summary(titanicna)
Class Age Sex Survived
0 :733 0 : 85 0 : 388 0 :1183
1 :256 1 :1662 1 :1393 1 : 566
2 :225 NA's: 454 NA's: 420 NA's: 452
3 :553
NA's:434
res.amelia<-amelia(titanicna,noms = 1:4)
z5 <- zlogit$new()
z5$zelig(Survived~ Class+Age, data = res.amelia)
z5
Model: Combined Imputations
Estimate Std.Error z value Pr(>|z|)
(Intercept) -0.50632 0.2047 -2.47350 1.338e-02 .
Class1 1.40721 0.1776 7.92321 2.220e-15 ***
Class2 0.66160 0.1602 4.12910 3.642e-05 ***
Class3 -0.00529 0.1374 -0.03852 9.693e-01
Age1 -0.53445 0.1947 -2.74473 6.056e-03 *
---
Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05
'.' 0.1 ' ' 1
For results from individual imputed datasets, use summary(x, subset = i:j)
Next step: Use 'setx' method
However, now I would like to use another function than amelia to perform
MI.
My output is a list of dataframes. Can I use Zelig to achieve this goal?
Thank you very much for your help,
*AUDIGIER Vincent*
Applied Mathematic Department, Agrocampus Ouest
65 rue de Saint-Brieuc, 35042 Rennes Cedex, France
Tel: (+33)2 23 48 54 76
Website: http://vincentaudigier.weebly.com/
<https://urldefense.proofpoint.com/v2/url?u=http-3A__vincentaudigier.weebly.com_&d=CwMDaQ&c=WO-RGvefibhHBZq3fL85hQ&r=EwICq0J5pL8CwgEJz8qkmauGonk0XmiLpxcYOEgk2a0&m=-vAcQ4-i7N-0s3RoxgXKMkFUertfXtbGk1uP3Q5rrnw&s=C56CMfCFmK_9oX46hLiwSab2-k_MvuFQFwSOIXU_5L0&e=>
Le 08/12/2015 15:12, Matt Blackwell a écrit :
Hi Vincent,
We just released an update to Amelia and now the vignette shows how to use
the latest version of Zelig. See Section 4.10 here:
https://cran.r-project.org/web/packages/Amelia/vignettes/amelia.pdf
<https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_packages_Amelia_vignettes_amelia.pdf&d=CwMDaQ&c=WO-RGvefibhHBZq3fL85hQ&r=EwICq0J5pL8CwgEJz8qkmauGonk0XmiLpxcYOEgk2a0&m=-vAcQ4-i7N-0s3RoxgXKMkFUertfXtbGk1uP3Q5rrnw&s=p6halMunaLh02OIg5g3ilYp9ion6x5VSMSoi6WWW-dk&e=>
Or see the Zelig documentation here:
<https://urldefense.proofpoint.com/v2/url?u=http-3A__docs.zeligproject.org_en_latest_using-2DZelig-2Dwith-2DAmelia.html&d=CwMDaQ&c=WO-RGvefibhHBZq3fL85hQ&r=EwICq0J5pL8CwgEJz8qkmauGonk0XmiLpxcYOEgk2a0&m=-vAcQ4-i7N-0s3RoxgXKMkFUertfXtbGk1uP3Q5rrnw&s=2XxLDHSueEdcsJjYBxkufcO004gAD95fcXaYM_F8kZQ&e=>
http://docs.zeligproject.org/en/latest/using-Zelig-with-Amelia.html
<https://urldefense.proofpoint.com/v2/url?u=http-3A__docs.zeligproject.org_en_latest_using-2DZelig-2Dwith-2DAmelia.html&d=CwMDaQ&c=WO-RGvefibhHBZq3fL85hQ&r=EwICq0J5pL8CwgEJz8qkmauGonk0XmiLpxcYOEgk2a0&m=-vAcQ4-i7N-0s3RoxgXKMkFUertfXtbGk1uP3Q5rrnw&s=2XxLDHSueEdcsJjYBxkufcO004gAD95fcXaYM_F8kZQ&e=>
Cheers,
Matt
~~~~~~~~~~~
Matthew Blackwell
Assistant Professor of Government
Harvard University
url: http://www.mattblackwell.org
<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mattblackwell.org&d=CwMDaQ&c=WO-RGvefibhHBZq3fL85hQ&r=EwICq0J5pL8CwgEJz8qkmauGonk0XmiLpxcYOEgk2a0&m=-vAcQ4-i7N-0s3RoxgXKMkFUertfXtbGk1uP3Q5rrnw&s=D7WJsoQYeyzE-23YpgYAHzT10rjw0TrI2MxTNaUjMJo&e=>
On Tue, Dec 8, 2015 at 8:22 AM, Vincent Audigier <
vincent.audigier(a)agrocampus-ouest.fr> wrote:
Dear list members,
I would like to analyse a multiply imputed data set with zelig,
but I don't know how to do with the last version of the Zelig package.
For instance, the following code, which runs well using a previous version
of the package (4.2.1 for instance), produces an error with the version
5.0.9:
library("Amelia")
data(freetrade)
amelia.out <- amelia(freetrade, m = 15, ts = "year", cs =
"country")
is.list(amelia.out$imputations)
#TRUE
is.data.frame(amelia.out$imputations[[1]])
#TRUE
library("Zelig")
zelig.fit <- zelig(tariff ~ pop + gdp.pc + year + polity, data =
amelia.out$imputations, model = "ls", cite = FALSE)
#Error: data is not a data frame
Could you give me an example to show me how to use the last version
of Zelig?
Thank you very much for your help,
Best,
--
*AUDIGIER Vincent*
Applied Mathematic Department, Agrocampus Ouest
65 rue de Saint-Brieuc, 35042 Rennes Cedex, France
Tel: (+33)2 23 48 54 76 <%28%2B33%292%2023%2048%2054%2076>
Website: http://vincentaudigier.weebly.com/
<https://urldefense.proofpoint.com/v2/url?u=http-3A__vincentaudigier.weebly.com_&d=CwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=EwICq0J5pL8CwgEJz8qkmauGonk0XmiLpxcYOEgk2a0&m=FXpCFO6P5ad6FfRsV0Ok0x6YB5-_Gicd4NdG0FzUAtk&s=hp7cTyqA159HN2feIubmqiH_eza7Th9oANR_anImwi0&e=>
--
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[Un]Subscribe/View Archive: http://lists.gking.harvard.edu/?info=amelia
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6 comments
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Vincent Audigier