Numeric class and sasxport.get

Thanks a lot Frank,

One last question, though. I was tempted to remove all attributes of my 
variables after the sasxport.get call using
foo <- sasxport.get(...)
foo <- as.data.frame(lapply(unclass(foo),as.vector))
Since I never worked with the objects of class 'labeled', I was 
wondering what I will loose by removing this attribute.

*Sebastien Bihorel, PharmD, PhD*
PKPD Scientist
Cognigen Corp
Email: sebastien.bihorel at cognigencorp.com 
<mailto:sebastien.bihorel at cognigencorp.com>
Phone: (716) 633-3463 ext. 323


Frank E Harrell Jr wrote:

Sebastien.Bihorel at cognigencorp.com wrote:

The problem is actually not related to a broken command but a attempt of
operational qualification of R. A few years ago, my company developed a
set of scripts for the 'operational qualification' of Splus. We are
switching to R so I am currently trying to port the scripts to R.
All Splus scripts imported SAS data using the importData function, 
which I
substituted by sasxport.get. One particular script returns the class of
each variable of the imported data frame; the output must match the
expected values: numeric, factor, integer, etc... The R 'translation' 
with
sasxport.get is thus problematic.
If there is no easy tweak of the function, we will probably have to 
remove
this script from our list of 'qualification' scripts.

Although it would be nice

Then my advice is to write your own wrapper function for sasxport.get 
that takes its output, looks for labelled variables, and adds a new 
class of your choosing depending on properties of the variable, making 
sure that you write methods needed for that class (if any).  Then test 
your new function, not sasxport.get explicitly.

Frank

Sebastien Bihorel wrote:

Frank,

It is a non existing issue for me if the variables of class "labelled"
(and only "labelled") can only be numerical variables (integer or
numeric).

Sebastien

'labelled' can apply to any type of vector.  I'm not clear on the
problem this causes you.  Please provide a command that is broken by
this behavior.

Frank

Frank E Harrell Jr wrote:

Sebastien Bihorel wrote:

Dear R-users,

The sasxport.get function (from the Hmisc package) automatically
defines the class of imported variables. I have noticed that the
class of theoretically numeric variables is simply "labelled",
although character variables might end up been defined as "labelled"
"Date" or "labelled" "factor".
Is there a way to tell sasxport.get to define numeric variable as
"labelled" "integer" or "labelled" "numeric"?

Sebastien,

If that would fix a problem you're having we could look into it.
Otherwise I'd tend to leave well enough alone.

Frank

Thank you

Sebastien

-- 
Frank E Harrell Jr   Professor and Chair           School of Medicine
                      Department of Biostatistics   Vanderbilt 
University

Sebastien Bihorel wrote:

Thanks a lot Frank,

One last question, though. I was tempted to remove all attributes of 
my variables after the sasxport.get call using
foo <- sasxport.get(...)
foo <- as.data.frame(lapply(unclass(foo),as.vector))
Since I never worked with the objects of class 'labeled', I was 
wondering what I will loose by removing this attribute.

Not a good idea, for many reasons including dates and other types.

And the labelled type is need if you subset the data, in order to keep 
the labels.

Note that your original issue is related to "class" being "soft" for 
integers and regular numerics:

 x <- 1:3

attributes(x)

NULL

class(x)

[1] "integer"

x <- runif(3)
class(x)

[1] "numeric"

attributes(x)

NULL

Frank

*Sebastien Bihorel, PharmD, PhD*
PKPD Scientist
Cognigen Corp
Email: sebastien.bihorel at cognigencorp.com 
<mailto:sebastien.bihorel at cognigencorp.com>
Phone: (716) 633-3463 ext. 323


Frank E Harrell Jr wrote:

Sebastien.Bihorel at cognigencorp.com wrote:

The problem is actually not related to a broken command but a 
attempt of
operational qualification of R. A few years ago, my company 
developed a
set of scripts for the 'operational qualification' of Splus. We are
switching to R so I am currently trying to port the scripts to R.
All Splus scripts imported SAS data using the importData function, 
which I
substituted by sasxport.get. One particular script returns the 
class of
each variable of the imported data frame; the output must match the
expected values: numeric, factor, integer, etc... The R 
'translation' with
sasxport.get is thus problematic.
If there is no easy tweak of the function, we will probably have to 
remove
this script from our list of 'qualification' scripts.

Although it would be nice

Then my advice is to write your own wrapper function for 
sasxport.get that takes its output, looks for labelled variables, 
and adds a new class of your choosing depending on properties of the 
variable, making sure that you write methods needed for that class 
(if any).  Then test your new function, not sasxport.get explicitly.

Frank

Sebastien Bihorel wrote:

Frank,

It is a non existing issue for me if the variables of class 
"labelled"
(and only "labelled") can only be numerical variables (integer or
numeric).

Sebastien

'labelled' can apply to any type of vector.  I'm not clear on the
problem this causes you.  Please provide a command that is broken by
this behavior.

Frank

Frank E Harrell Jr wrote:

Sebastien Bihorel wrote:

Dear R-users,

The sasxport.get function (from the Hmisc package) automatically
defines the class of imported variables. I have noticed that the
class of theoretically numeric variables is simply "labelled",
although character variables might end up been defined as 
"labelled"
"Date" or "labelled" "factor".
Is there a way to tell sasxport.get to define numeric variable as
"labelled" "integer" or "labelled" "numeric"?

Sebastien,

If that would fix a problem you're having we could look into it.
Otherwise I'd tend to leave well enough alone.

Frank

Thank you

Sebastien

-- 
Frank E Harrell Jr   Professor and Chair           School of Medicine
                      Department of Biostatistics   Vanderbilt 
University

I also realized the flaw after testing the script on various datasets...

Following up on your last note:
1- Is that the reason why the class of integer and regular numeric 
variable is solely "labelled" following sasxport.get?

2- Can class be 'soft' for other 'kind' of variables?

3- Would you anticipate the following wrapper function to generate 
incompatibilities with other R functions?

SASxpt.get <- function(file, force.single = TRUE,
                 method=c('read.xport','dataload','csv'), formats=NULL, 
allow=NULL,
                 out=NULL, keep=NULL, drop=NULL, as.is=0.5, FUN=NULL) {

 foo <- sasxport.get(file=file, force.single=force.single, method=method,
                     formats=formats, allow=allow, out=out, keep=keep,
                     drop=drop, as.is=as.is, FUN=FUN)

 # For each variable of class "labelled" (and only "labelled"), add the 
native class as a second class argument

 sglClassVarInd <- which(lapply(lapply(unclass(foo),class),length)==1)

 for (i in 1:length(sglClassVarInd)){
   x <- foo[,sglClassVarInd[i]]      if (class(x)=="labelled") 
class(foo[,sglClassVarInd[i]]) <- c(class(x), class(unclass(x)))
 }
 return(foo)
}


*Sebastien Bihorel, PharmD, PhD*
PKPD Scientist
Cognigen Corp
Email: sebastien.bihorel at cognigencorp.com 
<mailto:sebastien.bihorel at cognigencorp.com>
Phone: (716) 633-3463 ext. 323


Frank E Harrell Jr wrote:

Sebastien Bihorel wrote:

Thanks a lot Frank,

One last question, though. I was tempted to remove all attributes of 
my variables after the sasxport.get call using
foo <- sasxport.get(...)
foo <- as.data.frame(lapply(unclass(foo),as.vector))
Since I never worked with the objects of class 'labeled', I was 
wondering what I will loose by removing this attribute.

Not a good idea, for many reasons including dates and other types.

And the labelled type is need if you subset the data, in order to keep 
the labels.

Note that your original issue is related to "class" being "soft" for 
integers and regular numerics:

 x <- 1:3

attributes(x)

NULL

class(x)

[1] "integer"

x <- runif(3)
class(x)

[1] "numeric"

attributes(x)

NULL

Frank

*Sebastien Bihorel, PharmD, PhD*
PKPD Scientist
Cognigen Corp
Email: sebastien.bihorel at cognigencorp.com 
<mailto:sebastien.bihorel at cognigencorp.com>
Phone: (716) 633-3463 ext. 323


Frank E Harrell Jr wrote:

Sebastien.Bihorel at cognigencorp.com wrote:

The problem is actually not related to a broken command but a 
attempt of
operational qualification of R. A few years ago, my company 
developed a
set of scripts for the 'operational qualification' of Splus. We are
switching to R so I am currently trying to port the scripts to R.
All Splus scripts imported SAS data using the importData function, 
which I
substituted by sasxport.get. One particular script returns the 
class of
each variable of the imported data frame; the output must match the
expected values: numeric, factor, integer, etc... The R 
'translation' with
sasxport.get is thus problematic.
If there is no easy tweak of the function, we will probably have to 
remove
this script from our list of 'qualification' scripts.

Although it would be nice

Then my advice is to write your own wrapper function for 
sasxport.get that takes its output, looks for labelled variables, 
and adds a new class of your choosing depending on properties of the 
variable, making sure that you write methods needed for that class 
(if any).  Then test your new function, not sasxport.get explicitly.

Frank

Sebastien Bihorel wrote:

Frank,

It is a non existing issue for me if the variables of class 
"labelled"
(and only "labelled") can only be numerical variables (integer or
numeric).

Sebastien

'labelled' can apply to any type of vector.  I'm not clear on the
problem this causes you.  Please provide a command that is broken by
this behavior.

Frank

Frank E Harrell Jr wrote:

Sebastien Bihorel wrote:

Dear R-users,

The sasxport.get function (from the Hmisc package) automatically
defines the class of imported variables. I have noticed that the
class of theoretically numeric variables is simply "labelled",
although character variables might end up been defined as 
"labelled"
"Date" or "labelled" "factor".
Is there a way to tell sasxport.get to define numeric variable as
"labelled" "integer" or "labelled" "numeric"?

Sebastien,

If that would fix a problem you're having we could look into it.
Otherwise I'd tend to leave well enough alone.

Frank

Thank you

Sebastien

-- 
Frank E Harrell Jr   Professor and Chair           School of Medicine
                      Department of Biostatistics   Vanderbilt 
University

Sebastien Bihorel wrote:

I also realized the flaw after testing the script on various datasets...

Following up on your last note:
1- Is that the reason why the class of integer and regular numeric 
variable is solely "labelled" following sasxport.get?

Yes.  R gurus might correct me but just creating a numeric vector 
doesn't create a 'hard' class, add adding your own class attribute 
equal to 'numeric' or 'integer' might cause a problem downstream.

2- Can class be 'soft' for other 'kind' of variables?

Not that I can recall.

3- Would you anticipate the following wrapper function to generate 
incompatibilities with other R functions?

I'm going to beg off on that.  I'm not enough of an expert on the 
impact of adding such classes.

Frank

SASxpt.get <- function(file, force.single = TRUE,
                 method=c('read.xport','dataload','csv'), 
formats=NULL, allow=NULL,
                 out=NULL, keep=NULL, drop=NULL, as.is=0.5, FUN=NULL) {

 foo <- sasxport.get(file=file, force.single=force.single, 
method=method,
                     formats=formats, allow=allow, out=out, keep=keep,
                     drop=drop, as.is=as.is, FUN=FUN)

 # For each variable of class "labelled" (and only "labelled"), add 
the native class as a second class argument

 sglClassVarInd <- which(lapply(lapply(unclass(foo),class),length)==1)

 for (i in 1:length(sglClassVarInd)){
   x <- foo[,sglClassVarInd[i]]      if (class(x)=="labelled") 
class(foo[,sglClassVarInd[i]]) <- c(class(x), class(unclass(x)))
 }
 return(foo)
}


*Sebastien Bihorel, PharmD, PhD*
PKPD Scientist
Cognigen Corp
Email: sebastien.bihorel at cognigencorp.com 
<mailto:sebastien.bihorel at cognigencorp.com>
Phone: (716) 633-3463 ext. 323


Frank E Harrell Jr wrote:

Sebastien Bihorel wrote:

Thanks a lot Frank,

One last question, though. I was tempted to remove all attributes 
of my variables after the sasxport.get call using
foo <- sasxport.get(...)
foo <- as.data.frame(lapply(unclass(foo),as.vector))
Since I never worked with the objects of class 'labeled', I was 
wondering what I will loose by removing this attribute.

Not a good idea, for many reasons including dates and other types.

And the labelled type is need if you subset the data, in order to 
keep the labels.

Note that your original issue is related to "class" being "soft" for 
integers and regular numerics:

 x <- 1:3

attributes(x)

NULL

class(x)

[1] "integer"

x <- runif(3)
class(x)

[1] "numeric"

attributes(x)

NULL

Frank

*Sebastien Bihorel, PharmD, PhD*
PKPD Scientist
Cognigen Corp
Email: sebastien.bihorel at cognigencorp.com 
<mailto:sebastien.bihorel at cognigencorp.com>
Phone: (716) 633-3463 ext. 323


Frank E Harrell Jr wrote:

Sebastien.Bihorel at cognigencorp.com wrote:

The problem is actually not related to a broken command but a 
attempt of
operational qualification of R. A few years ago, my company 
developed a
set of scripts for the 'operational qualification' of Splus. We are
switching to R so I am currently trying to port the scripts to R.
All Splus scripts imported SAS data using the importData 
function, which I
substituted by sasxport.get. One particular script returns the 
class of
each variable of the imported data frame; the output must match the
expected values: numeric, factor, integer, etc... The R 
'translation' with
sasxport.get is thus problematic.
If there is no easy tweak of the function, we will probably have 
to remove
this script from our list of 'qualification' scripts.

Although it would be nice

Then my advice is to write your own wrapper function for 
sasxport.get that takes its output, looks for labelled variables, 
and adds a new class of your choosing depending on properties of 
the variable, making sure that you write methods needed for that 
class (if any).  Then test your new function, not sasxport.get 
explicitly.

Frank

Sebastien Bihorel wrote:

Frank,

It is a non existing issue for me if the variables of class 
"labelled"
(and only "labelled") can only be numerical variables (integer or
numeric).

Sebastien

'labelled' can apply to any type of vector.  I'm not clear on the
problem this causes you.  Please provide a command that is 
broken by
this behavior.

Frank

Frank E Harrell Jr wrote:

Sebastien Bihorel wrote:

Dear R-users,

The sasxport.get function (from the Hmisc package) automatically
defines the class of imported variables. I have noticed that the
class of theoretically numeric variables is simply "labelled",
although character variables might end up been defined as 
"labelled"
"Date" or "labelled" "factor".
Is there a way to tell sasxport.get to define numeric 
variable as
"labelled" "integer" or "labelled" "numeric"?

Sebastien,

If that would fix a problem you're having we could look into it.
Otherwise I'd tend to leave well enough alone.

Frank

Thank you

Sebastien

-- 
Frank E Harrell Jr   Professor and Chair           School of 
Medicine
                      Department of Biostatistics   Vanderbilt 
University

Ok, just so as I get that straight, is the 'labelled' class something 
that you created in your package or a readily available class in base R?

*Sebastien Bihorel, PharmD, PhD*
PKPD Scientist
Cognigen Corp
Email: sebastien.bihorel at cognigencorp.com 
<mailto:sebastien.bihorel at cognigencorp.com>
Phone: (716) 633-3463 ext. 323


Frank E Harrell Jr wrote:

Sebastien Bihorel wrote:

I also realized the flaw after testing the script on various datasets...

Following up on your last note:
1- Is that the reason why the class of integer and regular numeric 
variable is solely "labelled" following sasxport.get?

Yes.  R gurus might correct me but just creating a numeric vector 
doesn't create a 'hard' class, add adding your own class attribute 
equal to 'numeric' or 'integer' might cause a problem downstream.

2- Can class be 'soft' for other 'kind' of variables?

Not that I can recall.

3- Would you anticipate the following wrapper function to generate 
incompatibilities with other R functions?

I'm going to beg off on that.  I'm not enough of an expert on the 
impact of adding such classes.

Frank

SASxpt.get <- function(file, force.single = TRUE,
                 method=c('read.xport','dataload','csv'), 
formats=NULL, allow=NULL,
                 out=NULL, keep=NULL, drop=NULL, as.is=0.5, FUN=NULL) {

 foo <- sasxport.get(file=file, force.single=force.single, 
method=method,
                     formats=formats, allow=allow, out=out, keep=keep,
                     drop=drop, as.is=as.is, FUN=FUN)

 # For each variable of class "labelled" (and only "labelled"), add 
the native class as a second class argument

 sglClassVarInd <- which(lapply(lapply(unclass(foo),class),length)==1)

 for (i in 1:length(sglClassVarInd)){
   x <- foo[,sglClassVarInd[i]]      if (class(x)=="labelled") 
class(foo[,sglClassVarInd[i]]) <- c(class(x), class(unclass(x)))
 }
 return(foo)
}


*Sebastien Bihorel, PharmD, PhD*
PKPD Scientist
Cognigen Corp
Email: sebastien.bihorel at cognigencorp.com 
<mailto:sebastien.bihorel at cognigencorp.com>
Phone: (716) 633-3463 ext. 323


Frank E Harrell Jr wrote:

Sebastien Bihorel wrote:

Thanks a lot Frank,

One last question, though. I was tempted to remove all attributes 
of my variables after the sasxport.get call using
foo <- sasxport.get(...)
foo <- as.data.frame(lapply(unclass(foo),as.vector))
Since I never worked with the objects of class 'labeled', I was 
wondering what I will loose by removing this attribute.

Not a good idea, for many reasons including dates and other types.

And the labelled type is need if you subset the data, in order to 
keep the labels.

Note that your original issue is related to "class" being "soft" for 
integers and regular numerics:

 x <- 1:3

attributes(x)

NULL

class(x)

[1] "integer"

x <- runif(3)
class(x)

[1] "numeric"

attributes(x)

NULL

Frank

*Sebastien Bihorel, PharmD, PhD*
PKPD Scientist
Cognigen Corp
Email: sebastien.bihorel at cognigencorp.com 
<mailto:sebastien.bihorel at cognigencorp.com>
Phone: (716) 633-3463 ext. 323


Frank E Harrell Jr wrote:

Sebastien.Bihorel at cognigencorp.com wrote:

The problem is actually not related to a broken command but a 
attempt of
operational qualification of R. A few years ago, my company 
developed a
set of scripts for the 'operational qualification' of Splus. We are
switching to R so I am currently trying to port the scripts to R.
All Splus scripts imported SAS data using the importData 
function, which I
substituted by sasxport.get. One particular script returns the 
class of
each variable of the imported data frame; the output must match the
expected values: numeric, factor, integer, etc... The R 
'translation' with
sasxport.get is thus problematic.
If there is no easy tweak of the function, we will probably have 
to remove
this script from our list of 'qualification' scripts.

Although it would be nice

Then my advice is to write your own wrapper function for 
sasxport.get that takes its output, looks for labelled variables, 
and adds a new class of your choosing depending on properties of 
the variable, making sure that you write methods needed for that 
class (if any).  Then test your new function, not sasxport.get 
explicitly.

Frank

Sebastien Bihorel wrote:

Frank,

It is a non existing issue for me if the variables of class 
"labelled"
(and only "labelled") can only be numerical variables (integer or
numeric).

Sebastien

'labelled' can apply to any type of vector.  I'm not clear on the
problem this causes you.  Please provide a command that is 
broken by
this behavior.

Frank

Frank E Harrell Jr wrote:

Sebastien Bihorel wrote:

Dear R-users,

The sasxport.get function (from the Hmisc package) automatically
defines the class of imported variables. I have noticed that the
class of theoretically numeric variables is simply "labelled",
although character variables might end up been defined as 
"labelled"
"Date" or "labelled" "factor".
Is there a way to tell sasxport.get to define numeric 
variable as
"labelled" "integer" or "labelled" "numeric"?

Sebastien,

If that would fix a problem you're having we could look into it.
Otherwise I'd tend to leave well enough alone.

Frank

Thank you

Sebastien

-- 
Frank E Harrell Jr   Professor and Chair           School of 
Medicine
                      Department of Biostatistics   Vanderbilt 
University