thr3ads.net - R help - [R] Passing formula as parameter to `lm` within `sapply` causes error [BUG?] [May 2019]

If this information is useful, please help other people find it:
Share via:

Jens Heumann

2019-Apr-30 15:24 UTC

[R] Passing formula as parameter to `lm` within `sapply` causes error [BUG?]

Hi,

`lm` won't take formula as a parameter when it is within a `sapply`; see 
example below. Please, could anyone either point me to a syntax error or 
confirm that this might be a bug?

Best,
Jens

[Disclaimer: This is my first post here, following advice of how to 
proceed with possible bugs from here: https://www.r-project.org/bugs.html]


SUMMARY

While `lm` alone accepts formula parameter `FO` well, the same within a 
`sapply` causes an error. When putting everything as parameter but 
formula `FO`, it's still working, though. All parameters work fine 
within a similar `for` loop.


MCVE (see data / R-version at bottom)

 > summary(lm(y ~ x, df1, df1[["z"]] == 1,
df1[["w"]]))$coef[1, ]
   Estimate Std. Error    t value   Pr(>|t|)
  1.6269038  0.9042738  1.7991275  0.3229600
 > summary(lm(FO, data, data[[st]] == st1, data[[ws]]))$coef[1, ]
   Estimate Std. Error    t value   Pr(>|t|)
  1.6269038  0.9042738  1.7991275  0.3229600
 > sapply(unique(df1$z), function(s)
+   summary(lm(y ~ x, df1, df1[["z"]] == s, df1[[ws]]))$coef[1, ])
                 [,1]       [,2]         [,3]
Estimate   1.6269038 -0.1404174 -0.010338774
Std. Error 0.9042738  0.4577001  1.858138516
t value    1.7991275 -0.3067890 -0.005564049
Pr(>|t|)   0.3229600  0.8104951  0.996457853
 > sapply(unique(data[[st]]), function(s)
+   summary(lm(FO, data, data[[st]] == s, data[[ws]]))$coef[1, ])  # !!!
Error in eval(substitute(subset), data, env) : object 's' not found
 > sapply(unique(data[[st]]), function(s)
+   summary(lm(y ~ x, data, data[[st]] == s, data[[ws]]))$coef[1, ])
                 [,1]       [,2]         [,3]
Estimate   1.6269038 -0.1404174 -0.010338774
Std. Error 0.9042738  0.4577001  1.858138516
t value    1.7991275 -0.3067890 -0.005564049
Pr(>|t|)   0.3229600  0.8104951  0.996457853
 > m <- matrix(NA, 4, length(unique(data[[st]])))
 > for (s in unique(data[[st]])) {
+   m[, s] <- summary(lm(FO, data, data[[st]] == s, data[[ws]]))$coef[1, ]
+ }
 > m
           [,1]       [,2]         [,3]
[1,] 1.6269038 -0.1404174 -0.010338774
[2,] 0.9042738  0.4577001  1.858138516
[3,] 1.7991275 -0.3067890 -0.005564049
[4,] 0.3229600  0.8104951  0.996457853

# DATA #################################################################

df1 <- structure(list(x = c(1.37095844714667, -0.564698171396089, 
0.363128411337339,
0.63286260496104, 0.404268323140999, -0.106124516091484, 1.51152199743894,
-0.0946590384130976, 2.01842371387704), y = c(1.30824434809425,
0.740171482827397, 2.64977380403845, -0.755998096151299, 0.125479556323628,
-0.239445852485142, 2.14747239550901, -0.37891195982917, -0.638031707027734
), z = c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L), w = c(0.7, 0.8,
1.2, 0.9, 1.3, 1.2, 0.8, 1, 1)), class = "data.frame", row.names =
c(NA,
-9L))

FO <- y ~ x; data <- df1; st <- "z"; ws <- "w";
st1 <- 1

########################################################################

 > R.version
                _
platform       x86_64-w64-mingw32
arch           x86_64
os             mingw32
system         x86_64, mingw32
status
major          3
minor          6.0
year           2019
month          04
day            26
svn rev        76424
language       R
version.string R version 3.6.0 (2019-04-26)
nickname       Planting of a Tree

#########################################################################

NOTE: Question on SO two days ago 
(https://stackoverflow.com/questions/55893189/passing-formula-as-parameter-to-lm-within-sapply-causes-error-bug-confirmation)
brought many views but neither answer nor bug confirmation.

David Winsemius

2019-Apr-30 21:03 UTC

head link

[R] Passing formula as parameter to `lm` within `sapply` causes error [BUG?]

Try using do.call

? 
David

Sent from my iPhone
> On Apr 30, 2019, at 9:24 AM, Jens Heumann <jens.heumann at
students.unibe.ch> wrote:
> 
> Hi,
> 
> `lm` won't take formula as a parameter when it is within a `sapply`;
see example below. Please, could anyone either point me to a syntax error or
confirm that this might be a bug?
> 
> Best,
> Jens
> 
> [Disclaimer: This is my first post here, following advice of how to proceed
with possible bugs from here: https://www.r-project.org/bugs.html]
> 
> 
> SUMMARY
> 
> While `lm` alone accepts formula parameter `FO` well, the same within a
`sapply` causes an error. When putting everything as parameter but formula `FO`,
it's still working, though. All parameters work fine within a similar `for`
loop.
> 
> 
> MCVE (see data / R-version at bottom)
> 
> > summary(lm(y ~ x, df1, df1[["z"]] == 1,
df1[["w"]]))$coef[1, ]
>  Estimate Std. Error    t value   Pr(>|t|)
> 1.6269038  0.9042738  1.7991275  0.3229600
> > summary(lm(FO, data, data[[st]] == st1, data[[ws]]))$coef[1, ]
>  Estimate Std. Error    t value   Pr(>|t|)
> 1.6269038  0.9042738  1.7991275  0.3229600
> > sapply(unique(df1$z), function(s)
> +   summary(lm(y ~ x, df1, df1[["z"]] == s, df1[[ws]]))$coef[1,
])
>                [,1]       [,2]         [,3]
> Estimate   1.6269038 -0.1404174 -0.010338774
> Std. Error 0.9042738  0.4577001  1.858138516
> t value    1.7991275 -0.3067890 -0.005564049
> Pr(>|t|)   0.3229600  0.8104951  0.996457853
> > sapply(unique(data[[st]]), function(s)
> +   summary(lm(FO, data, data[[st]] == s, data[[ws]]))$coef[1, ])  # !!!
> Error in eval(substitute(subset), data, env) : object 's' not found
> > sapply(unique(data[[st]]), function(s)
> +   summary(lm(y ~ x, data, data[[st]] == s, data[[ws]]))$coef[1, ])
>                [,1]       [,2]         [,3]
> Estimate   1.6269038 -0.1404174 -0.010338774
> Std. Error 0.9042738  0.4577001  1.858138516
> t value    1.7991275 -0.3067890 -0.005564049
> Pr(>|t|)   0.3229600  0.8104951  0.996457853
> > m <- matrix(NA, 4, length(unique(data[[st]])))
> > for (s in unique(data[[st]])) {
> +   m[, s] <- summary(lm(FO, data, data[[st]] == s, data[[ws]]))$coef[1,
]
> + }
> > m
>          [,1]       [,2]         [,3]
> [1,] 1.6269038 -0.1404174 -0.010338774
> [2,] 0.9042738  0.4577001  1.858138516
> [3,] 1.7991275 -0.3067890 -0.005564049
> [4,] 0.3229600  0.8104951  0.996457853
> 
> # DATA #################################################################
> 
> df1 <- structure(list(x = c(1.37095844714667, -0.564698171396089,
0.363128411337339,
> 0.63286260496104, 0.404268323140999, -0.106124516091484, 1.51152199743894,
> -0.0946590384130976, 2.01842371387704), y = c(1.30824434809425,
> 0.740171482827397, 2.64977380403845, -0.755998096151299, 0.125479556323628,
> -0.239445852485142, 2.14747239550901, -0.37891195982917, -0.638031707027734
> ), z = c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L), w = c(0.7, 0.8,
> 1.2, 0.9, 1.3, 1.2, 0.8, 1, 1)), class = "data.frame", row.names
= c(NA,
> -9L))
> 
> FO <- y ~ x; data <- df1; st <- "z"; ws <-
"w"; st1 <- 1
> 
> ########################################################################
> 
> > R.version
>               _
> platform       x86_64-w64-mingw32
> arch           x86_64
> os             mingw32
> system         x86_64, mingw32
> status
> major          3
> minor          6.0
> year           2019
> month          04
> day            26
> svn rev        76424
> language       R
> version.string R version 3.6.0 (2019-04-26)
> nickname       Planting of a Tree
> 
> #########################################################################
> 
> NOTE: Question on SO two days ago
(https://stackoverflow.com/questions/55893189/passing-formula-as-parameter-to-lm-within-sapply-causes-error-bug-confirmation)
brought many views but neither answer nor bug confirmation.
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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 Murdoch

2019-Apr-30 22:32 UTC

head link

[R] Passing formula as parameter to `lm` within `sapply` causes error [BUG?]

On 30/04/2019 11:24 a.m., Jens Heumann wrote:> Hi,
> 
> `lm` won't take formula as a parameter when it is within a `sapply`;
see
> example below. Please, could anyone either point me to a syntax error or
> confirm that this might be a bug?
> 
I haven't looked carefully at your example.  From a quick glance, 
however, I'd suspect that the issue is with the formula.  Formulas have 
attached environments, where they look up variables in them that aren't 
in the data argument to lm().  In your code it's not obvious to me what 
environment would be attached, but I suspect it's the caller of sapply, 
not the environment that sapply creates for a particular value of its 
argument.  I think this because of a rule that is supposed to be 
followed in R:

   Formulas get the environment where they were created attached to 
them.  That would be your global environment.

R is flexible, so functions don't have to follow this rule, but it 
causes lots of confusion when they don't.

Duncan Murdoch


> Best,
> Jens
> 
> [Disclaimer: This is my first post here, following advice of how to
> proceed with possible bugs from here: https://www.r-project.org/bugs.html]
> 
> 
> SUMMARY
> 
> While `lm` alone accepts formula parameter `FO` well, the same within a
> `sapply` causes an error. When putting everything as parameter but
> formula `FO`, it's still working, though. All parameters work fine
> within a similar `for` loop.
> 
> 
> MCVE (see data / R-version at bottom)
> 
>   > summary(lm(y ~ x, df1, df1[["z"]] == 1,
df1[["w"]]))$coef[1, ]
>     Estimate Std. Error    t value   Pr(>|t|)
>    1.6269038  0.9042738  1.7991275  0.3229600
>   > summary(lm(FO, data, data[[st]] == st1, data[[ws]]))$coef[1, ]
>     Estimate Std. Error    t value   Pr(>|t|)
>    1.6269038  0.9042738  1.7991275  0.3229600
>   > sapply(unique(df1$z), function(s)
> +   summary(lm(y ~ x, df1, df1[["z"]] == s, df1[[ws]]))$coef[1,
])
>                   [,1]       [,2]         [,3]
> Estimate   1.6269038 -0.1404174 -0.010338774
> Std. Error 0.9042738  0.4577001  1.858138516
> t value    1.7991275 -0.3067890 -0.005564049
> Pr(>|t|)   0.3229600  0.8104951  0.996457853
>   > sapply(unique(data[[st]]), function(s)
> +   summary(lm(FO, data, data[[st]] == s, data[[ws]]))$coef[1, ])  # !!!
> Error in eval(substitute(subset), data, env) : object 's' not found
>   > sapply(unique(data[[st]]), function(s)
> +   summary(lm(y ~ x, data, data[[st]] == s, data[[ws]]))$coef[1, ])
>                   [,1]       [,2]         [,3]
> Estimate   1.6269038 -0.1404174 -0.010338774
> Std. Error 0.9042738  0.4577001  1.858138516
> t value    1.7991275 -0.3067890 -0.005564049
> Pr(>|t|)   0.3229600  0.8104951  0.996457853
>   > m <- matrix(NA, 4, length(unique(data[[st]])))
>   > for (s in unique(data[[st]])) {
> +   m[, s] <- summary(lm(FO, data, data[[st]] == s, data[[ws]]))$coef[1,
]
> + }
>   > m
>             [,1]       [,2]         [,3]
> [1,] 1.6269038 -0.1404174 -0.010338774
> [2,] 0.9042738  0.4577001  1.858138516
> [3,] 1.7991275 -0.3067890 -0.005564049
> [4,] 0.3229600  0.8104951  0.996457853
> 
> # DATA #################################################################
> 
> df1 <- structure(list(x = c(1.37095844714667, -0.564698171396089,
> 0.363128411337339,
> 0.63286260496104, 0.404268323140999, -0.106124516091484, 1.51152199743894,
> -0.0946590384130976, 2.01842371387704), y = c(1.30824434809425,
> 0.740171482827397, 2.64977380403845, -0.755998096151299, 0.125479556323628,
> -0.239445852485142, 2.14747239550901, -0.37891195982917, -0.638031707027734
> ), z = c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L), w = c(0.7, 0.8,
> 1.2, 0.9, 1.3, 1.2, 0.8, 1, 1)), class = "data.frame", row.names
= c(NA,
> -9L))
> 
> FO <- y ~ x; data <- df1; st <- "z"; ws <-
"w"; st1 <- 1
> 
> ########################################################################
> 
>   > R.version
>                  _
> platform       x86_64-w64-mingw32
> arch           x86_64
> os             mingw32
> system         x86_64, mingw32
> status
> major          3
> minor          6.0
> year           2019
> month          04
> day            26
> svn rev        76424
> language       R
> version.string R version 3.6.0 (2019-04-26)
> nickname       Planting of a Tree
> 
> #########################################################################
> 
> NOTE: Question on SO two days ago
>
(https://stackoverflow.com/questions/55893189/passing-formula-as-parameter-to-lm-within-sapply-causes-error-bug-confirmation)
> brought many views but neither answer nor bug confirmation.
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> 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.
>

Jens Heumann

2019-May-01 05:14 UTC

head link

[R] Passing formula as parameter to `lm` within `sapply` causes error [BUG?]

Thanks a lot for your hint, David. It finally worked doing:

 > sapply(unique(data[[st]]), function(s)
+   summary(do.call("lm", list(FO, data, data[[st]] == s,
+                              data[[ws]])))$coef[1, ])
                 [,1]       [,2]         [,3]
Estimate   1.6269038 -0.1404174 -0.010338774
Std. Error 0.9042738  0.4577001  1.858138516
t value    1.7991275 -0.3067890 -0.005564049
Pr(>|t|)   0.3229600  0.8104951  0.996457853

Best,
Jens

On 30.04.2019 23:03, David Winsemius wrote:> Try using do.call
> 
> ?
> David
> 
> Sent from my iPhone
> 
>> On Apr 30, 2019, at 9:24 AM, Jens Heumann <jens.heumann at
students.unibe.ch> wrote:
>>
>> Hi,
>>
>> `lm` won't take formula as a parameter when it is within a
`sapply`; see example below. Please, could anyone either point me to a syntax
error or confirm that this might be a bug?
>>
>> Best,
>> Jens
>>
>> [Disclaimer: This is my first post here, following advice of how to
proceed with possible bugs from here: https://www.r-project.org/bugs.html]
>>
>>
>> SUMMARY
>>
>> While `lm` alone accepts formula parameter `FO` well, the same within a
`sapply` causes an error. When putting everything as parameter but formula `FO`,
it's still working, though. All parameters work fine within a similar `for`
loop.
>>
>>
>> MCVE (see data / R-version at bottom)
>>
>>> summary(lm(y ~ x, df1, df1[["z"]] == 1,
df1[["w"]]))$coef[1, ]
>>   Estimate Std. Error    t value   Pr(>|t|)
>> 1.6269038  0.9042738  1.7991275  0.3229600
>>> summary(lm(FO, data, data[[st]] == st1, data[[ws]]))$coef[1, ]
>>   Estimate Std. Error    t value   Pr(>|t|)
>> 1.6269038  0.9042738  1.7991275  0.3229600
>>> sapply(unique(df1$z), function(s)
>> +   summary(lm(y ~ x, df1, df1[["z"]] == s,
df1[[ws]]))$coef[1, ])
>>                 [,1]       [,2]         [,3]
>> Estimate   1.6269038 -0.1404174 -0.010338774
>> Std. Error 0.9042738  0.4577001  1.858138516
>> t value    1.7991275 -0.3067890 -0.005564049
>> Pr(>|t|)   0.3229600  0.8104951  0.996457853
>>> sapply(unique(data[[st]]), function(s)
>> +   summary(lm(FO, data, data[[st]] == s, data[[ws]]))$coef[1, ])  #
!!!
>> Error in eval(substitute(subset), data, env) : object 's' not
found
>>> sapply(unique(data[[st]]), function(s)
>> +   summary(lm(y ~ x, data, data[[st]] == s, data[[ws]]))$coef[1, ])
>>                 [,1]       [,2]         [,3]
>> Estimate   1.6269038 -0.1404174 -0.010338774
>> Std. Error 0.9042738  0.4577001  1.858138516
>> t value    1.7991275 -0.3067890 -0.005564049
>> Pr(>|t|)   0.3229600  0.8104951  0.996457853
>>> m <- matrix(NA, 4, length(unique(data[[st]])))
>>> for (s in unique(data[[st]])) {
>> +   m[, s] <- summary(lm(FO, data, data[[st]] == s,
data[[ws]]))$coef[1, ]
>> + }
>>> m
>>           [,1]       [,2]         [,3]
>> [1,] 1.6269038 -0.1404174 -0.010338774
>> [2,] 0.9042738  0.4577001  1.858138516
>> [3,] 1.7991275 -0.3067890 -0.005564049
>> [4,] 0.3229600  0.8104951  0.996457853
>>
>> # DATA
#################################################################
>>
>> df1 <- structure(list(x = c(1.37095844714667, -0.564698171396089,
0.363128411337339,
>> 0.63286260496104, 0.404268323140999, -0.106124516091484,
1.51152199743894,
>> -0.0946590384130976, 2.01842371387704), y = c(1.30824434809425,
>> 0.740171482827397, 2.64977380403845, -0.755998096151299,
0.125479556323628,
>> -0.239445852485142, 2.14747239550901, -0.37891195982917,
-0.638031707027734
>> ), z = c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L), w = c(0.7, 0.8,
>> 1.2, 0.9, 1.3, 1.2, 0.8, 1, 1)), class = "data.frame",
row.names = c(NA,
>> -9L))
>>
>> FO <- y ~ x; data <- df1; st <- "z"; ws <-
"w"; st1 <- 1
>>
>>
########################################################################
>>
>>> R.version
>>                _
>> platform       x86_64-w64-mingw32
>> arch           x86_64
>> os             mingw32
>> system         x86_64, mingw32
>> status
>> major          3
>> minor          6.0
>> year           2019
>> month          04
>> day            26
>> svn rev        76424
>> language       R
>> version.string R version 3.6.0 (2019-04-26)
>> nickname       Planting of a Tree
>>
>>
#########################################################################
>>
>> NOTE: Question on SO two days ago
(https://stackoverflow.com/questions/55893189/passing-formula-as-parameter-to-lm-within-sapply-causes-error-bug-confirmation)
brought many views but neither answer nor bug confirmation.
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> 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 - May 2019 - Passing formula as parameter to `lm` within `sapply` causes error [BUG?]

[R] Passing formula as parameter to `lm` within `sapply` causes error [BUG?]

[R] Passing formula as parameter to `lm` within `sapply` causes error [BUG?]

[R] Passing formula as parameter to `lm` within `sapply` causes error [BUG?]

[R] Passing formula as parameter to `lm` within `sapply` causes error [BUG?]