avoid <<- in specific case

Hi all,

I improved a function drawing horizontal histograms (code below) which uses barplot and works fine.
It does,however, need to assign a function to the global environment to later find the actual location on the vertical axis, and not the number of bars used by barplot.
Hopefully, running the examples below will illustrate that.

As said, it works perfectly fine and does exactly what I want.
The problem arises now that I'm building a package (just for myself, for now) and run into R CMD
check telling me 'no visible binding for '<<-' assignment'.
(wording below)
Similar problem as in http://r.789695.n4.nabble.com/R-CMD-check-tells-me-no-visible-binding-for-global-variable-what-does-it-mean-td1837236.html

My question is:
Is there a way to avoid assigning the function to the global environment with <<- but still have it available? I know it is generally not good practice.

Or ist it OK in a case like this, and is there a way to avoid the notes from the rcmd check (make the function package-compatible)?
Or should I just ignore these notes? (I'm completely new to building packages and cannot judge the importance yet.)

I'd be very thankful for any hints!

Berry

PS: I recently read about barcharts in lattice, but by now I'm already used to my function. (And I learned a lot writing it a couple of years ago).

  
# Function
horiz.hist <- function(Data, breaks="Sturges", col="transparent", las=1,
ylim=range(HBreaks), labelat=pretty(ylim), labels=labelat, border=par("fg"), ... )
   {a <- hist(Data, plot=FALSE, breaks=breaks)
   HBreaks <- a$breaks
   HBreak1 <- a$breaks[1]
   hpos <<- function(Pos) (Pos-HBreak1)*(length(HBreaks)-1)/ diff(range(HBreaks)) # Assign a function to the global environment with values calculated inside the main function.
   barplot(a$counts, space=0, horiz=T, ylim=hpos(ylim), col=col, border=border,...)
   axis(2, at=hpos(labelat), labels=labels, las=las, ...)
   print("use hpos() to address y-coordinates") }

# Data and basic concept
set.seed(8); ExampleData <- rnorm(50,8,5)+5
hist(ExampleData)
horiz.hist(ExampleData, xlab="absolute frequency")
# Caution: the labels at the y-axis are not the real coordinates!
# abline(h=2) will draw above the second bar, not at the label value 2. Use hpos:
abline(h=hpos(11), col=2)

# Further arguments
horiz.hist(ExampleData, xlim=c(-8,20))
horiz.hist(ExampleData, main="the ... argument worked!", col.axis=3)
hist(ExampleData, xlim=c(-10,40)) # with xlim
horiz.hist(ExampleData, ylim=c(-10,40), border="red") # with ylim
horiz.hist(ExampleData, breaks=20, col="orange")
axis(2, hpos(0:10), labels=F, col=2) # another use of hpos()

# One shortcoming: doesn't work with breakpoints provided as a vector with different widths of the bars


Wording from the rcmd check when building a package:
* checking R code for possible problems ... NOTE
horiz.hist: no visible binding for '<<-' assignment to 'hpos'
horiz.hist: no visible global function definition for 'hpos'


  		 	   		
	[[alternative HTML version deleted]]

On 05/10/2012 8:19 AM, Berry Boessenkool wrote:

Hi all,

I improved a function drawing horizontal histograms (code below) which
uses barplot and works fine.
It does,however, need to assign a function to the global environment to
later find the actual location on the vertical axis, and not the number of
bars used by barplot.
Hopefully, running the examples below will illustrate that.

As said, it works perfectly fine and does exactly what I want.
The problem arises now that I'm building a package (just for myself, for
now) and run into R CMD
check telling me 'no visible binding for '<<-' assignment'.
(wording below)
Similar problem as in
http://r.789695.n4.nabble.com/R-CMD-check-tells-me-no-visible-binding-for-global-variable-what-does-it-mean-td1837236.html

My question is:
Is there a way to avoid assigning the function to the global environment
with <<- but still have it available? I know it is generally not good
practice.

You can return the function as the value of your function.   A bonus:  if it
is created within the body of your function, it will have access to all the
local variables there.

You shouldn't write to the global environment, because globalenv belongs to
the user, not to you.  If the user wants your function in the global
environment s/he can just assign the value of your function to a variable
there.

Duncan Murdoch

Or ist it OK in a case like this, and is there a way to avoid the notes
from the rcmd check (make the function package-compatible)?
Or should I just ignore these notes? (I'm completely new to building
packages and cannot judge the importance yet.)

I'd be very thankful for any hints!

Berry

PS: I recently read about barcharts in lattice, but by now I'm already
used to my function. (And I learned a lot writing it a couple of years ago).

  # Function
horiz.hist <- function(Data, breaks="Sturges", col="transparent", las=1,
ylim=range(HBreaks), labelat=pretty(ylim), labels=labelat,
border=par("fg"), ... )
   {a <- hist(Data, plot=FALSE, breaks=breaks)
   HBreaks <- a$breaks
   HBreak1 <- a$breaks[1]
   hpos <<- function(Pos) (Pos-HBreak1)*(length(HBreaks)-1)/
diff(range(HBreaks)) # Assign a function to the global environment with
values calculated inside the main function.
   barplot(a$counts, space=0, horiz=T, ylim=hpos(ylim), col=col,
border=border,...)
   axis(2, at=hpos(labelat), labels=labels, las=las, ...)
   print("use hpos() to address y-coordinates") }

# Data and basic concept
set.seed(8); ExampleData <- rnorm(50,8,5)+5
hist(ExampleData)
horiz.hist(ExampleData, xlab="absolute frequency")
# Caution: the labels at the y-axis are not the real coordinates!
# abline(h=2) will draw above the second bar, not at the label value 2.
Use hpos:
abline(h=hpos(11), col=2)

# Further arguments
horiz.hist(ExampleData, xlim=c(-8,20))
horiz.hist(ExampleData, main="the ... argument worked!", col.axis=3)
hist(ExampleData, xlim=c(-10,40)) # with xlim
horiz.hist(ExampleData, ylim=c(-10,40), border="red") # with ylim
horiz.hist(ExampleData, breaks=20, col="orange")
axis(2, hpos(0:10), labels=F, col=2) # another use of hpos()

# One shortcoming: doesn't work with breakpoints provided as a vector with
different widths of the bars


Wording from the rcmd check when building a package:
* checking R code for possible problems ... NOTE
horiz.hist: no visible binding for '<<-' assignment to 'hpos'
horiz.hist: no visible global function definition for 'hpos'

Hi all,

I improved a function drawing horizontal histograms (code below) which

It does,however, need to assign a function to the global environment to

Hopefully, running the examples below will illustrate that.

As said, it works perfectly fine and does exactly what I want.
The problem arises now that I'm building a package (just for myself, 
for now) and run into R CMD check telling me 'no visible binding for '<<-'

(wording below)
Similar problem as in 
http://r.789695.n4.nabble.com/R-CMD-check-tells-me-no-visible-binding-
for-global-variable-what-does-it-mean-td1837236.html

My question is:
Is there a way to avoid assigning the function to the global environment

Or ist it OK in a case like this, and is there a way to avoid the notes

Or should I just ignore these notes? (I'm completely new to building 
packages and cannot judge the importance yet.)

I'd be very thankful for any hints!

Berry

PS: I recently read about barcharts in lattice, but by now I'm already

  
# Function
horiz.hist <- function(Data, breaks="Sturges", col="transparent", 
las=1, ylim=range(HBreaks), labelat=pretty(ylim), labels=labelat,

   {a <- hist(Data, plot=FALSE, breaks=breaks)
   HBreaks <- a$breaks
   HBreak1 <- a$breaks[1]
   hpos <<- function(Pos) (Pos-HBreak1)*(length(HBreaks)-1)/

   barplot(a$counts, space=0, horiz=T, ylim=hpos(ylim), col=col,

   axis(2, at=hpos(labelat), labels=labels, las=las, ...)
   print("use hpos() to address y-coordinates") }

# Data and basic concept
set.seed(8); ExampleData <- rnorm(50,8,5)+5
hist(ExampleData)
horiz.hist(ExampleData, xlab="absolute frequency") # Caution: the 
labels at the y-axis are not the real coordinates!
# abline(h=2) will draw above the second bar, not at the label value 2.

abline(h=hpos(11), col=2)

# Further arguments
horiz.hist(ExampleData, xlim=c(-8,20)) horiz.hist(ExampleData, 
main="the ... argument worked!", col.axis=3) hist(ExampleData, 
xlim=c(-10,40)) # with xlim horiz.hist(ExampleData, ylim=c(-10,40), 
border="red") # with ylim horiz.hist(ExampleData, breaks=20, 
col="orange") axis(2, hpos(0:10), labels=F, col=2) # another use of 
hpos()

# One shortcoming: doesn't work with breakpoints provided as a vector 
with different widths of the bars


Wording from the rcmd check when building a package:
* checking R code for possible problems ... NOTE
horiz.hist: no visible binding for '<<-' assignment to 'hpos'
horiz.hist: no visible global function definition for 'hpos'


  		 	   		
	[[alternative HTML version deleted]]

I agree with this. But there is (in my opinion) a much more dangerous point:
a<b
If  there is an object  called b in the function, it uses this b. But if you
forgot to inialise b in the function, it looks in the global environment. So
the following happens:
b<<-100
a<-b (if there is no b in the function, it uses b in the global environment.
So a=100
b<9 (writes to b in the local environment)
Now b in the global environment is 100, while b in the function is 9
It would be more logical if a<-b would give an error if b does not exist in
the function (just like pascal does).

-------------------
Frans

-----Oorspronkelijk bericht-----
Van: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
Namens Duncan Murdoch
Verzonden: vrijdag 5 oktober 2012 14:26
Aan: Berry Boessenkool
CC: R Help
Onderwerp: Re: [R] avoid <<- in specific case

On 05/10/2012 8:19 AM, Berry Boessenkool wrote:

Hi all,

I improved a function drawing horizontal histograms (code below) which

uses barplot and works fine.

It does,however, need to assign a function to the global environment to

later find the actual location on the vertical axis, and not the number of
bars used by barplot.

Hopefully, running the examples below will illustrate that.

As said, it works perfectly fine and does exactly what I want.
The problem arises now that I'm building a package (just for myself,
for now) and run into R CMD check telling me 'no visible binding for '<<-'

assignment'.

(wording below)
Similar problem as in
http://r.789695.n4.nabble.com/R-CMD-check-tells-me-no-visible-binding-
for-global-variable-what-does-it-mean-td1837236.html

My question is:
Is there a way to avoid assigning the function to the global environment

with <<- but still have it available? I know it is generally not good
practice.

You can return the function as the value of your function.   A bonus:
if it is created within the body of your function, it will have access to
all the local variables there.

You shouldn't write to the global environment, because globalenv belongs to
the user, not to you.  If the user wants your function in the global
environment s/he can just assign the value of your function to a variable
there.

Duncan Murdoch

Or ist it OK in a case like this, and is there a way to avoid the notes

from the rcmd check (make the function package-compatible)?

Or should I just ignore these notes? (I'm completely new to building
packages and cannot judge the importance yet.)

I'd be very thankful for any hints!

Berry

PS: I recently read about barcharts in lattice, but by now I'm already

used to my function. (And I learned a lot writing it a couple of years ago).

# Function
horiz.hist <- function(Data, breaks="Sturges", col="transparent",
las=1, ylim=range(HBreaks), labelat=pretty(ylim), labels=labelat,

border=par("fg"), ... )

   {a <- hist(Data, plot=FALSE, breaks=breaks)
   HBreaks <- a$breaks
   HBreak1 <- a$breaks[1]
   hpos <<- function(Pos) (Pos-HBreak1)*(length(HBreaks)-1)/

diff(range(HBreaks)) # Assign a function to the global environment with
values calculated inside the main function.

   barplot(a$counts, space=0, horiz=T, ylim=hpos(ylim), col=col,

border=border,...)

   axis(2, at=hpos(labelat), labels=labels, las=las, ...)
   print("use hpos() to address y-coordinates") }

# Data and basic concept
set.seed(8); ExampleData <- rnorm(50,8,5)+5
hist(ExampleData)
horiz.hist(ExampleData, xlab="absolute frequency") # Caution: the
labels at the y-axis are not the real coordinates!
# abline(h=2) will draw above the second bar, not at the label value 2.

Use hpos:

abline(h=hpos(11), col=2)

# Further arguments
horiz.hist(ExampleData, xlim=c(-8,20)) horiz.hist(ExampleData,
main="the ... argument worked!", col.axis=3) hist(ExampleData,
xlim=c(-10,40)) # with xlim horiz.hist(ExampleData, ylim=c(-10,40),
border="red") # with ylim horiz.hist(ExampleData, breaks=20,
col="orange") axis(2, hpos(0:10), labels=F, col=2) # another use of
hpos()

# One shortcoming: doesn't work with breakpoints provided as a vector
with different widths of the bars


Wording from the rcmd check when building a package:
* checking R code for possible problems ... NOTE
horiz.hist: no visible binding for '<<-' assignment to 'hpos'
horiz.hist: no visible global function definition for 'hpos'


  		 	   		
	[[alternative HTML version deleted]]

I agree with this. But there is (in my opinion) a much more dangerous point:
a<b
If  there is an object  called b in the function, it uses this b. But if you
forgot to inialise b in the function, it looks in the global environment. So
the following happens:
b<<-100
a<-b (if there is no b in the function, it uses b in the global environment.
So a=100
b<9 (writes to b in the local environment)
Now b in the global environment is 100, while b in the function is 9
It would be more logical if a<-b would give an error if b does not exist in
the function (just like pascal does).

-------------------
Frans

-----Oorspronkelijk bericht-----
Van: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
Namens Duncan Murdoch
Verzonden: vrijdag 5 oktober 2012 14:26
Aan: Berry Boessenkool
CC: R Help
Onderwerp: Re: [R] avoid <<- in specific case

On 05/10/2012 8:19 AM, Berry Boessenkool wrote:

Hi all,

I improved a function drawing horizontal histograms (code below) which

uses barplot and works fine.

It does,however, need to assign a function to the global environment to

later find the actual location on the vertical axis, and not the number of
bars used by barplot.

Hopefully, running the examples below will illustrate that.

As said, it works perfectly fine and does exactly what I want.
The problem arises now that I'm building a package (just for myself,
for now) and run into R CMD check telling me 'no visible binding for '<<-'

assignment'.

(wording below)
Similar problem as in
http://r.789695.n4.nabble.com/R-CMD-check-tells-me-no-visible-binding-
for-global-variable-what-does-it-mean-td1837236.html

My question is:
Is there a way to avoid assigning the function to the global environment

with <<- but still have it available? I know it is generally not good
practice.

You can return the function as the value of your function.   A bonus:
if it is created within the body of your function, it will have access to
all the local variables there.

You shouldn't write to the global environment, because globalenv belongs to
the user, not to you.  If the user wants your function in the global
environment s/he can just assign the value of your function to a variable
there.

Duncan Murdoch

Or ist it OK in a case like this, and is there a way to avoid the notes

from the rcmd check (make the function package-compatible)?

Or should I just ignore these notes? (I'm completely new to building
packages and cannot judge the importance yet.)

I'd be very thankful for any hints!

Berry

PS: I recently read about barcharts in lattice, but by now I'm already

used to my function. (And I learned a lot writing it a couple of years ago).

# Function
horiz.hist <- function(Data, breaks="Sturges", col="transparent",
las=1, ylim=range(HBreaks), labelat=pretty(ylim), labels=labelat,

border=par("fg"), ... )

   {a <- hist(Data, plot=FALSE, breaks=breaks)
   HBreaks <- a$breaks
   HBreak1 <- a$breaks[1]
   hpos <<- function(Pos) (Pos-HBreak1)*(length(HBreaks)-1)/

diff(range(HBreaks)) # Assign a function to the global environment with
values calculated inside the main function.

   barplot(a$counts, space=0, horiz=T, ylim=hpos(ylim), col=col,

border=border,...)

   axis(2, at=hpos(labelat), labels=labels, las=las, ...)
   print("use hpos() to address y-coordinates") }

# Data and basic concept
set.seed(8); ExampleData <- rnorm(50,8,5)+5
hist(ExampleData)
horiz.hist(ExampleData, xlab="absolute frequency") # Caution: the
labels at the y-axis are not the real coordinates!
# abline(h=2) will draw above the second bar, not at the label value 2.

Use hpos:

abline(h=hpos(11), col=2)

# Further arguments
horiz.hist(ExampleData, xlim=c(-8,20)) horiz.hist(ExampleData,
main="the ... argument worked!", col.axis=3) hist(ExampleData,
xlim=c(-10,40)) # with xlim horiz.hist(ExampleData, ylim=c(-10,40),
border="red") # with ylim horiz.hist(ExampleData, breaks=20,
col="orange") axis(2, hpos(0:10), labels=F, col=2) # another use of
hpos()

# One shortcoming: doesn't work with breakpoints provided as a vector
with different widths of the bars


Wording from the rcmd check when building a package:
* checking R code for possible problems ... NOTE
horiz.hist: no visible binding for '<<-' assignment to 'hpos'
horiz.hist: no visible global function definition for 'hpos'



      [[alternative HTML version deleted]]