Issue with formula conversion

A random effect formulation for R package nlme is read in as a string
of characters from an input file:

ranEff <- "pdCompSymm(~1+Age)"

I need to convert 'ranEff' to a formula class. However, as shown below:

as.formula(ranEff)

~1 + Age

the "pdCompSymm" is lost in the conversion. Any solutions? 

On Aug 27, 2014, at 11:19 AM, Gang Chen wrote:

A random effect formulation for R package nlme is read in as a string
of characters from an input file:

ranEff <- "pdCompSymm(~1+Age)"

I need to convert 'ranEff' to a formula class. However, as shown below:

as.formula(ranEff)

~1 + Age

the "pdCompSymm" is lost in the conversion. Any solutions?

as.formula(paste("~",ranEff))
~pdCompSymm(~1 + Age)
--

David Winsemius
Alameda, CA, USA

Thanks for the help! However, I just need to get

pdCompSymm(~1 + Age)

On Aug 27, 2014, at 12:44 PM, Gang Chen wrote:

Thanks for the help! However, I just need to get

pdCompSymm(~1 + Age)

That's not a formula in the R sense of the word. You should do a better job of posting a use case. Perhaps you want an expression?

--
David.

without a tilde (~) at the beginning.

On Wed, Aug 27, 2014 at 3:34 PM, David Winsemius <dwinsemius at comcast.net> wrote:

On Aug 27, 2014, at 11:19 AM, Gang Chen wrote:

A random effect formulation for R package nlme is read in as a string
of characters from an input file:

ranEff <- "pdCompSymm(~1+Age)"

I need to convert 'ranEff' to a formula class. However, as shown below:

as.formula(ranEff)

~1 + Age

the "pdCompSymm" is lost in the conversion. Any solutions?

as.formula(paste("~",ranEff))
~pdCompSymm(~1 + Age)
--

David Winsemius
Alameda, CA, USA

David Winsemius
Alameda, CA, USA

Good point!

Here is an example:

library(nlme)
fm <- lme(yield ~ nitro, data=Oats, random=list(Block=pdComSymm(~Variety-1)))

Now the problem I'm facing is that the following part

pdComSymm(~Variety-1)

is read in as a string of characters from an external source:

ranEff <- 'pdComSymm(~Variety-1)'

The following

(ranEff1 <- as.formula(ranEff))
~Variety - 1

is not what I want. Even though

fm <- lme(yield ~ nitro, data=Oats, random=list(Block=pdCompSymm(ranEff1)))

ranEff <- 'pdCompSymm(~Variety-1)'
tt <- parse(text=ranEff)

fm <- lme(yield ~ nitro, data=Oats, random=list(Block=eval(tt) ))
fm

On Aug 27, 2014, at 1:11 PM, Gang Chen wrote:

Good point!

Here is an example:

library(nlme)
fm <- lme(yield ~ nitro, data=Oats, random=list(Block=pdComSymm(~Variety-1)))

One problem is that youa re misspelling the function name.

Now the problem I'm facing is that the following part

pdComSymm(~Variety-1)

is read in as a string of characters from an external source:

ranEff <- 'pdComSymm(~Variety-1)'

The following

(ranEff1 <- as.formula(ranEff))
~Variety - 1

is not what I want. Even though

fm <- lme(yield ~ nitro, data=Oats, random=list(Block=pdCompSymm(ranEff1)))

ranEff <- 'pdCompSymm(~Variety-1)'
tt <- parse(text=ranEff)

# Returns an unevaluated expression

fm <- lme(yield ~ nitro, data=Oats, random=list(Block=eval(tt) ))
fm

Linear mixed-effects model fit by REML
  Data: Oats
  Log-restricted-likelihood: -296.5209
  Fixed: yield ~ nitro
(Intercept)       nitro
   81.87222    73.66667
snipped rest of output.

--
David

works, I don't know the 'pdCompSymm' part in advance and would like to
make the process automatic.

On Wed, Aug 27, 2014 at 3:49 PM, David Winsemius <dwinsemius at comcast.net> wrote:

On Aug 27, 2014, at 12:44 PM, Gang Chen wrote:

Thanks for the help! However, I just need to get

pdCompSymm(~1 + Age)

That's not a formula in the R sense of the word. You should do a better job of posting a use case. Perhaps you want an expression?

--
David.

without a tilde (~) at the beginning.

On Wed, Aug 27, 2014 at 3:34 PM, David Winsemius <dwinsemius at comcast.net> wrote:

On Aug 27, 2014, at 11:19 AM, Gang Chen wrote:

A random effect formulation for R package nlme is read in as a string
of characters from an input file:

ranEff <- "pdCompSymm(~1+Age)"

I need to convert 'ranEff' to a formula class. However, as shown below:

as.formula(ranEff)

~1 + Age

the "pdCompSymm" is lost in the conversion. Any solutions?

as.formula(paste("~",ranEff))
~pdCompSymm(~1 + Age)
--

David Winsemius
Alameda, CA, USA

David Winsemius
Alameda, CA, USA

David Winsemius
Alameda, CA, USA

get("sum")(1:4)

fortunes::fortune(106)

Good point!

Here is an example:

library(nlme)
fm <- lme(yield ~ nitro, data=Oats, random=list(Block=pdComSymm(~Variety-1)))

Now the problem I'm facing is that the following part

pdComSymm(~Variety-1)

is read in as a string of characters from an external source:

ranEff <- 'pdComSymm(~Variety-1)'

The following

(ranEff1 <- as.formula(ranEff))
~Variety - 1

is not what I want. Even though

fm <- lme(yield ~ nitro, data=Oats, random=list(Block=pdCompSymm(ranEff1)))

works, I don't know the 'pdCompSymm' part in advance and would like to
make the process automatic.

On Wed, Aug 27, 2014 at 3:49 PM, David Winsemius <dwinsemius at comcast.net> wrote:

On Aug 27, 2014, at 12:44 PM, Gang Chen wrote:

Thanks for the help! However, I just need to get

pdCompSymm(~1 + Age)

That's not a formula in the R sense of the word. You should do a better job of posting a use case. Perhaps you want an expression?

--
David.

without a tilde (~) at the beginning.

On Wed, Aug 27, 2014 at 3:34 PM, David Winsemius <dwinsemius at comcast.net> wrote:

On Aug 27, 2014, at 11:19 AM, Gang Chen wrote:

A random effect formulation for R package nlme is read in as a string
of characters from an input file:

ranEff <- "pdCompSymm(~1+Age)"

I need to convert 'ranEff' to a formula class. However, as shown below:

as.formula(ranEff)

~1 + Age

the "pdCompSymm" is lost in the conversion. Any solutions?

as.formula(paste("~",ranEff))
~pdCompSymm(~1 + Age)
--

David Winsemius
Alameda, CA, USA

David Winsemius
Alameda, CA, USA

do you have control over the external source?

if so, then something like

BlockFunction <- "pdComSymm"
ranEff1 <- "~Variety -1"

fm <- lme(yield ~ nitro, data=Oats,
random=list(Block=get(BlockFunction)(ranEff1)))

On Aug 27, 2014, at 1:33 PM, Richard M. Heiberger wrote:

do you have control over the external source?

if so, then something like

BlockFunction <- "pdComSymm"
ranEff1 <- "~Variety -1"

I doubt that would work, since it is not a formula object.

fm <- lme(yield ~ nitro, data=Oats,
random=list(Block=get(BlockFunction)(ranEff1)))

After correcting the misspelling of the function name, I tested this approach:

 BlockFunction <- "pdCompSymm"
 ranEff1 <- as.formula("~Variety -1")
 fm <- lme(yield ~ nitro, data=Oats, random=list(Block=do.call(BlockFunction, list(form=ranEff1) )
  ))
 fm
#----------
Linear mixed-effects model fit by REML
  Data: Oats
  Log-restricted-likelihood: -296.5209
  Fixed: yield ~ nitro
snipped

--
David.

The above is untested.  An example if get() is

get("sum")(1:4)

[1] 10

The main problem with David's solution, which does work, is the use
of the eval(parse()) idiom.  This is usually strongly discouraged.  See, for
example,

fortunes::fortune(106)

If the answer is parse() you should usually rethink the question.
  -- Thomas Lumley
     R-help (February 2005)

On Wed, Aug 27, 2014 at 4:11 PM, Gang Chen <gangchen6 at gmail.com> wrote:

Good point!

Here is an example:

library(nlme)
fm <- lme(yield ~ nitro, data=Oats, random=list(Block=pdComSymm(~Variety-1)))

Now the problem I'm facing is that the following part

pdComSymm(~Variety-1)

is read in as a string of characters from an external source:

ranEff <- 'pdComSymm(~Variety-1)'

The following

(ranEff1 <- as.formula(ranEff))
~Variety - 1

is not what I want. Even though

fm <- lme(yield ~ nitro, data=Oats, random=list(Block=pdCompSymm(ranEff1)))

works, I don't know the 'pdCompSymm' part in advance and would like to
make the process automatic.

On Wed, Aug 27, 2014 at 3:49 PM, David Winsemius <dwinsemius at comcast.net> wrote:

On Aug 27, 2014, at 12:44 PM, Gang Chen wrote:

Thanks for the help! However, I just need to get

pdCompSymm(~1 + Age)

That's not a formula in the R sense of the word. You should do a better job of posting a use case. Perhaps you want an expression?

--
David.

without a tilde (~) at the beginning.

On Wed, Aug 27, 2014 at 3:34 PM, David Winsemius <dwinsemius at comcast.net> wrote:

On Aug 27, 2014, at 11:19 AM, Gang Chen wrote:

A random effect formulation for R package nlme is read in as a string
of characters from an input file:

ranEff <- "pdCompSymm(~1+Age)"

I need to convert 'ranEff' to a formula class. However, as shown below:

as.formula(ranEff)

~1 + Age

the "pdCompSymm" is lost in the conversion. Any solutions?

as.formula(paste("~",ranEff))
~pdCompSymm(~1 + Age)
--

David Winsemius
Alameda, CA, USA

David Winsemius
Alameda, CA, USA

David Winsemius
Alameda, CA, USA