Re: [R] assign()ing within apply
Any tips?
DaveT.
-Original Message-
From: Thompson, David (MNR)
Sent: December 9, 2008 04:03 PM
To: 'r-help@r-project.org'
Subject: assign()ing within apply
Hello,
I'm trying to convert a character column in several dataframes
to lower case.
###
#
# Sample data and 'spp' column summaries:
# dput(ban.ovs.1993[sample(row.names(ban.ovs.1993), 20), 1:4])
ban.ovs.93 - structure(list(oplt = c(43L, 43L, 38L, 26L, 35L,
8L, 39L, 1L,
34L, 50L, 10L, 29L, 31L, 24L, 18L, 12L, 27L, 49L, 28L, 51L),
rplt = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_), tree = c(427L, 410L, 639L, 494L, 649L, 166L,
735L, 163L, 120L, 755L, 612L, 174L, 129L, 331L, 269L, 152L,
552L, 227L, 243L, 96L), spp = c(MH, MST, MH, HE,
BE, MH, MH, MH, MH, Or, IW, Or, MH, MH,
BY, MH, MH, BE, MH, MR)), .Names = c(oplt,
rplt, tree, spp), row.names = c(4587L, 4570L, 3947L, 2761L,
3653L, 652L, 4136L, 64L, 3567L, 5318L, 838L, 3091L, 3366L, 2423L,
1775L, 1061L, 2893L, 5161L, 2967L, 5395L), class = data.frame)
# dput(pem.ovs.1994[sample(row.names(pem.ovs.1994), 20), 1:4])
pem.ovs.94 - structure(list(oplt = c(8L, 17L, 36L, 9L, 31L,
11L, 35L, 51L,
51L, 49L, 40L, 1L, 9L, 17L, 4L, 42L, 6L, 3L, 39L, 25L), tree = c(531L,
557L, 546L, 261L, 592L, 134L, 695L, 933L, 945L, 114L, 34L, 54L,
549L, 574L, 193L, 96L, 70L, 4L, 546L, 789L), spp = c(MH, MH,
MH, BF, BF, MH, IW, OR, OR, BF, MH, IW, OR,
MH, SM, BE, BE, BE, OR, OR), oaz = c(38L, 205L,
140L, 277L, 329L, 209L, 222L, 24L, 67L, 187L, 156L, 181L, 174L,
248L, 42L, 279L, 273L, 357L, 160L, 183L)), .Names = c(oplt,
tree, spp, oaz), row.names = c(1204L, 2943L, 5790L, 1616L,
5063L, 2013L, 5691L, 8188L, 8200L, 7822L, 6302L, 54L, 1698L,
2960L, 421L, 6690L, 775L, 245L, 6205L, 4121L), class = data.frame)
# count per spp
invisible(lapply(ls(pat='ovs'), function(y) { cat(y, \n) ;
print(summary.factor(get(y)[,'spp'])) ; cat(\n) } ) )
ban.ovs.93
BE BY HE IW MH MR MST Or
2 1 1 1 11 1 1 2
pem.ovs.94
BE BF IW MH OR SM
3 3 2 6 5 1
#
###
I have tried variants on the following and cannot remember how
to have the result assign()ed back to the original dataframes.
lapply(ls(pat='ovs'), function(y) { assign(paste(y,
[,'spp'], sep=), tolower(get(y)[,'spp'])) } )
I *do* get the expected results:
[[1]]
[1] mh mst mh he be mh mh mh mh
or iw or mh mh by mh mh be mh mr
[[2]]
[1] mh mh mh bf bf mh iw or or bf mh
iw or mh sm be be be or or
, I just can't remember how to get them back into the original
dataframe objects. Suggestions?
Thanx, DaveT.
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
david.john.thomp...@ontario.ca
http://ontario.ca/ofri
*
__
R-help@r-project.org mailing list
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.
Re: [R] assign()ing within apply
Thanks Jorge,
I am aware of the method you suggest, however, it's not quite what I was
asking for.
I was attempting to do this change on 56 dataframes, so I attempted to
do so with a list of all rather than each individually.
Thanks, DaveT.
From: Jorge Ivan Velez [mailto:jorgeivanve...@gmail.com]
Sent: December 12, 2008 11:11 AM
To: Thompson, David (MNR)
Subject: Re: [R] assign()ing within apply
Dear David,
Try this:
ban.ovs.93[,'spp']-tolower(ban.ovs.93[,'spp'])
ban.ovs.93
pem.ovs.94[,'spp']-tolower(pem.ovs.94[,'spp'])
pem.ovs.94
HTH,
Jorge
On Fri, Dec 12, 2008 at 9:51 AM, Thompson, David (MNR)
david.john.thomp...@ontario.ca wrote:
Any tips?
DaveT.
-Original Message-
From: Thompson, David (MNR)
Sent: December 9, 2008 04:03 PM
To: 'r-help@r-project.org'
Subject: assign()ing within apply
Hello,
I'm trying to convert a character column in several
dataframes
to lower case.
###
#
# Sample data and 'spp' column summaries:
# dput(ban.ovs.1993[sample(row.names(ban.ovs.1993),
20), 1:4])
ban.ovs.93 - structure(list(oplt = c(43L, 43L, 38L,
26L, 35L,
8L, 39L, 1L,
34L, 50L, 10L, 29L, 31L, 24L, 18L, 12L, 27L, 49L, 28L,
51L),
rplt = c(NA_integer_, NA_integer_, NA_integer_,
NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_,
NA_integer_), tree = c(427L, 410L, 639L, 494L,
649L, 166L,
735L, 163L, 120L, 755L, 612L, 174L, 129L, 331L,
269L, 152L,
552L, 227L, 243L, 96L), spp = c(MH, MST, MH,
HE,
BE, MH, MH, MH, MH, Or, IW, Or,
MH, MH,
BY, MH, MH, BE, MH, MR)), .Names =
c(oplt,
rplt, tree, spp), row.names = c(4587L, 4570L,
3947L, 2761L,
3653L, 652L, 4136L, 64L, 3567L, 5318L, 838L, 3091L,
3366L, 2423L,
1775L, 1061L, 2893L, 5161L, 2967L, 5395L), class =
data.frame)
# dput(pem.ovs.1994[sample(row.names(pem.ovs.1994),
20), 1:4])
pem.ovs.94 - structure(list(oplt = c(8L, 17L, 36L, 9L,
31L,
11L, 35L, 51L,
51L, 49L, 40L, 1L, 9L, 17L, 4L, 42L, 6L, 3L, 39L, 25L),
tree = c(531L,
557L, 546L, 261L, 592L, 134L, 695L, 933L, 945L, 114L,
34L, 54L,
549L, 574L, 193L, 96L, 70L, 4L, 546L, 789L), spp =
c(MH, MH,
MH, BF, BF, MH, IW, OR, OR, BF, MH,
IW, OR,
MH, SM, BE, BE, BE, OR, OR), oaz = c(38L,
205L,
140L, 277L, 329L, 209L, 222L, 24L, 67L, 187L, 156L,
181L, 174L,
248L, 42L, 279L, 273L, 357L, 160L, 183L)), .Names =
c(oplt,
tree, spp, oaz), row.names = c(1204L, 2943L,
5790L, 1616L,
5063L, 2013L, 5691L, 8188L, 8200L, 7822L, 6302L, 54L,
1698L,
2960L, 421L, 6690L, 775L, 245L, 6205L, 4121L), class =
data.frame)
# count per spp
invisible(lapply(ls(pat='ovs'), function(y) { cat(y,
\n) ;
print(summary.factor(get(y)[,'spp'])) ; cat(\n) } ) )
ban.ovs.93
BE BY HE IW MH MR MST Or
2 1 1 1 11 1 1 2
pem.ovs.94
BE BF IW MH OR SM
3 3 2 6 5 1
#
###
I have tried variants on the following and cannot
remember how
to have the result assign()ed back to the original
dataframes.
lapply(ls(pat='ovs'), function(y) { assign(paste(y,
[,'spp'], sep=), tolower(get(y)[,'spp'])) } )
I *do* get the expected results:
[[1]]
[1] mh mst mh he be mh mh mh
mh
or iw or mh mh by mh mh be
mh mr
[[2]]
[1] mh mh mh bf bf mh iw or or bf
mh
iw or mh sm be be be or or
, I just can't remember how to get them back into the
original
dataframe objects. Suggestions?
Thanx, DaveT.
*
Silviculture Data Analyst
[R] assign()ing within apply
Hello,
I'm trying to convert a character column in several dataframes to lower
case.
###
#
# Sample data and 'spp' column summaries:
# dput(ban.ovs.1993[sample(row.names(ban.ovs.1993), 20), 1:4])
ban.ovs.93 - structure(list(oplt = c(43L, 43L, 38L, 26L, 35L, 8L, 39L,
1L,
34L, 50L, 10L, 29L, 31L, 24L, 18L, 12L, 27L, 49L, 28L, 51L),
rplt = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_), tree = c(427L, 410L, 639L, 494L, 649L, 166L,
735L, 163L, 120L, 755L, 612L, 174L, 129L, 331L, 269L, 152L,
552L, 227L, 243L, 96L), spp = c(MH, MST, MH, HE,
BE, MH, MH, MH, MH, Or, IW, Or, MH, MH,
BY, MH, MH, BE, MH, MR)), .Names = c(oplt,
rplt, tree, spp), row.names = c(4587L, 4570L, 3947L, 2761L,
3653L, 652L, 4136L, 64L, 3567L, 5318L, 838L, 3091L, 3366L, 2423L,
1775L, 1061L, 2893L, 5161L, 2967L, 5395L), class = data.frame)
# dput(pem.ovs.1994[sample(row.names(pem.ovs.1994), 20), 1:4])
pem.ovs.94 - structure(list(oplt = c(8L, 17L, 36L, 9L, 31L, 11L, 35L,
51L,
51L, 49L, 40L, 1L, 9L, 17L, 4L, 42L, 6L, 3L, 39L, 25L), tree = c(531L,
557L, 546L, 261L, 592L, 134L, 695L, 933L, 945L, 114L, 34L, 54L,
549L, 574L, 193L, 96L, 70L, 4L, 546L, 789L), spp = c(MH, MH,
MH, BF, BF, MH, IW, OR, OR, BF, MH, IW, OR,
MH, SM, BE, BE, BE, OR, OR), oaz = c(38L, 205L,
140L, 277L, 329L, 209L, 222L, 24L, 67L, 187L, 156L, 181L, 174L,
248L, 42L, 279L, 273L, 357L, 160L, 183L)), .Names = c(oplt,
tree, spp, oaz), row.names = c(1204L, 2943L, 5790L, 1616L,
5063L, 2013L, 5691L, 8188L, 8200L, 7822L, 6302L, 54L, 1698L,
2960L, 421L, 6690L, 775L, 245L, 6205L, 4121L), class = data.frame)
# count per spp
invisible(lapply(ls(pat='ovs'), function(y) { cat(y, \n) ;
print(summary.factor(get(y)[,'spp'])) ; cat(\n) } ) )
ban.ovs.93
BE BY HE IW MH MR MST Or
2 1 1 1 11 1 1 2
pem.ovs.94
BE BF IW MH OR SM
3 3 2 6 5 1
#
###
I have tried variants on the following and cannot remember how to have
the result assign()ed back to the original dataframes.
lapply(ls(pat='ovs'), function(y) { assign(paste(y, [,'spp'], sep=),
tolower(get(y)[,'spp'])) } )
I *do* get the expected results:
[[1]]
[1] mh mst mh he be mh mh mh mh or iw
or mh mh by mh mh be mh mr
[[2]]
[1] mh mh mh bf bf mh iw or or bf mh iw or
mh sm be be be or or
, I just can't remember how to get them back into the original dataframe
objects. Suggestions?
Thanx, DaveT.
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ontario.ca/ofri
__
R-help@r-project.org mailing list
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.
Re: [R] a bit off topic: data for dragsters?
Roland, I don't know of the specific data you are asking for but the official website of the 'National Hot Rod Assoc' (?) is www.nhra.com. DaveT. * Silviculture Data Analyst Ontario Forest Research Institute Ontario Ministry of Natural Resources [EMAIL PROTECTED] http://ontario.ca/ofri * Dear all, does anyone of you know where to get some simple data from dragster racing (the race where you go for 1/4 mile straight)? Best would be some data where you have two columns with Col 1 Time since start of race in milliseconds and Col 2 Distance traveled. Thank you very much, Roland __ R-help@r-project.org mailing list 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.
Re: [R] Date classes in ggplot2
Is not melt part of reshape package, i.e., require(reshape)? DaveT. -Original Message- From: stephen sefick [mailto:[EMAIL PROTECTED] Sent: October 19, 2008 12:12 PM To: hadley wickham Cc: R Help Subject: Re: [R] Date classes in ggplot2 well I must have either resolve it without knowing it, ot something funny is going on... sorry I didn't run it in a clean R session. Should have. works fine thanks Stephen Sefick On Sun, Oct 19, 2008 at 12:01 PM, hadley wickham [EMAIL PROTECTED] wrote: On Sun, Oct 19, 2008 at 10:49 AM, stephen sefick [EMAIL PROTECTED] wrote: updn.gg - (structure(list(date = structure(c(11808, 11869, 11961, 11992, 12084, 12173, 12265, 12418, 12600, 12631, 12753, 12996, 13057, 13149), class = Date), unrestored = c(1.13789418691602, 0.704948049842955, 0.276777348238899, 0.417586861554189, 0.504870337754768, 0.673201771716216, 0.560704221510771, 0.835737007551542, 1.10773858390693, 0.197070828834836, 0.942350681588179, 0.950447141061461, 0.246637790002705, 0.324035567509960 ), restored = c(1.39981554315924, 0.89196314359498, 0.407816250252697, 0.823496839063978, 1.14429021220358, 1.23971035967413, 0.960868900583432, 0.927685306209829, 1.22072345292821, 0.249842897450642, 1.00879641624694, 0.925372139878243, 0.317259909172362, 0.382677149697482)), .Names = c(date, unrestored, restored), row.names = c(NA, -14L), class = data.frame)) #I would like to do this in ggplot xyplot(unrestored+restored~date, data=updn.gg, type=c(l), auto.key=TRUE) #this is what I have tried and get an error message melt.updn - melt(updn.gg, id.var=date) What error message? It works for me. Hadley -- http://had.co.nz/ -- Stephen Sefick Research Scientist Southeastern Natural Sciences Academy Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list 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.
Re: [R] package Utils Sweave Example Error
(Question/suggestion inline below)
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: October 16, 2008 02:17 PM
To: [EMAIL PROTECTED]
Cc: [EMAIL PROTECTED]
Subject: Re: [R] package Utils Sweave Example Error
On 10/16/2008 12:19 PM, Felipe Carrillo wrote:
This is my sessionInfo() and Sys.getenv(PATH)
library(tools)
testfile - system.file(Sweave, Sweave-test-1.Rnw,
package = utils)
## enforce par(ask=FALSE)
options(device.ask.default=FALSE)
## create a LaTeX file
Sweave(testfile)
Writing to file Sweave-test-1.tex
Processing code chunks ...
1 : print term verbatim
2 : term hide
3 : echo print term verbatim
4 : term verbatim
5 : echo term verbatim
6 : echo term verbatim eps pdf
7 : echo term verbatim eps pdf
You can now run LaTeX on 'Sweave-test-1.tex'
## This can be compiled to PDF by
texi2dvi(Sweave-test-1.tex, pdf=TRUE,quiet=FALSE)
This is pdfTeX, Version 3.1415926-1.40.9 (MiKTeX 2.7)
entering extended mode
(C:/Program Files/R/R-2.7.2/bin/Sweave-test-1.tex
LaTeX2e 2005/12/01
Babel v3.8l and hyphenation patterns for english,
dumylang, nohyphenation, ge
rman, ngerman, german-x-2008-06-18, ngerman-x-2008-06-18,
french, loaded.
(C:\Program Files\MiKTeX 2.7\tex\latex\base\article.cls
Document Class: article 2005/09/16 v1.4f Standard LaTeX
document class
(C:\Program Files\MiKTeX 2.7\tex\latex\base\size10.clo))
(C:\Program Files\MiKTeX 2.7\tex\latex\ltxmisc\a4wide.sty
(C:\Program Files\MiKTeX 2.7\tex\latex\ntgclass\a4.sty))
! Missing \endcsname inserted.
to be read again
\protect
l.11 \begin
{document}
? pdflatex.EXE: Bad file descriptor
This appears to be the problem. I'm not certain, but I would guess if
you look in the C:/Program
Files/R/R-2.7.2/bin/Sweave-test-1.tex file
you'll see a line something like this:
\usepackage{C:/Program Files/R/R-2.7.2/share/texmf/Sweave}
That line (which was added by Sweave) will not work, because
LaTeX does
not understand blanks in file paths. There are a couple of
workarounds:
Does the Windoze convention of using C:/Progra~1/ to represent
C:/Program Files/ not work in these situations?
DaveT.
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ontario.ca/ofri
*
1. Install R in a directory that doesn't contain blanks.
2. Include \usepackage{Sweave} in the Rnw file you're
processing; this
will stop Sweave from adding anything. I believe we set things up so
that MikTeX will find it in the right place (though I don't
normally use
texi2dvi, so I'm not sure).
To test this, you can just go and edit the Sweave-test-1.tex file now,
replacing the long line with the short version.
Duncan Murdoch
texify: pdflatex failed for some reason (see log file).
Error in texi2dvi(Sweave-test-1.tex, pdf = TRUE, quiet = FALSE) :
running 'texi2dvi' on 'Sweave-test-1.tex' failed
sessionInfo()
R version 2.7.2 (2008-08-25)
i386-pc-mingw32
locale:
LC_COLLATE=English_United
States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] tools stats graphics grDevices utils
datasets methods base
Sys.getenv(PATH)
PATH
C:\\Program Files\\MiKTeX
2.7\\miktex\\bin;C:\\GTK\\bin;C:\\WINDOWS\\system32;C:\\WINDOWS
;C:\\WINDOWS\\System32\\Wbem;C:\\Program Files\\SYSTAT
10\\;C:\\Program Files\\SYSTAT 10\\XGRAPH\\;C:\\Program
Files\\Wave Systems Corp\\Dell Preboot Manager\\Access
Client\\v5\\;C:\\Program Files\\ATI
Technologies\\ATI.ACE\\Core-Static;c:\\Program
Files\\Microsoft SQL Server\\90\\Tools\\binn\\
Thank you
Felipe D. Carrillo
Supervisory Fishery Biologist
Department of the Interior
US Fish Wildlife Service
California, USA
--- On Thu, 10/16/08, Duncan Murdoch [EMAIL PROTECTED] wrote:
Try running it as texi2dvi(Sweave-test-1.tex,
pdf=TRUE, quiet=FALSE),
and post the list of error messages.
You should also show us the results of sessionInfo() and
Sys.getenv(PATH), and tell us which version of
LaTeX you have installed.
Duncan Murdoch
__
R-help@r-project.org mailing list
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@r-project.org mailing list
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.
Re: [R] YALAQ - Yet Another LApply Question
Please forgive this repost, it's been a week without a squeak. No
comments?
Original post:
https://stat.ethz.ch/pipermail/r-help/2008-October/176340.html
Hello,
Two lapply questions (system info and sample data below):
1) Why does the first form of command1 add the name of y _after_ the
str() output rather than before as does the second (preferred) form?
# command1 version1
invisible(lapply(ls(pattern='bn'), function(y) cat(y, \n,
str(get(y)), \n) ))
# command1 version2 (preferred output)
invisible(lapply(ls(pattern='bn'), function(y) { cat(y, \n) ;
str(get(y)) ; cat(\n) } ))
2) Why does the same method as command1 version2 above not work with the
summary() command as does the second (preferred) set of commands?
# command2 version1
lapply(ls(pattern='bn'), function(y) { cat(y, \n) ; summary(get(y))
; cat(\n) } )
# command2 version2 (preferred output)
smry.list - lapply(ls(pattern='bn'), function(y) summary(get(y)))
names(smry.list) - ls(pattern='bn')
smry.list
Thanx, DaveT.
###
# system info:
sessionInfo() ; cat(\n) ; Sys.info()[c(1:3,5)]
R version 2.7.2 (2008-08-25)
i386-pc-mingw32
locale:
LC_COLLATE=English_Canada.1252;LC_CTYPE=English_Canada.1252;LC_MONETARY=
English_Canada.1252;LC_NUMERIC=C;LC_TIME=English_Canada.1252
attached base packages:
[1] stats graphics grDevices datasets tcltk utils methods
base
other attached packages:
[1] debug_1.1.0 mvbutils_1.1.1 lattice_0.17-14 plotrix_2.4-7
svSocket_0.9-5 TinnR_1.0.2 R2HTML_1.59 Hmisc_3.4-3
loaded via a namespace (and not attached):
[1] cluster_1.11.11 grid_2.7.2 svMisc_0.9-5tools_2.7.2
sysname release
version machine
Windows XP build 2600,
Service Pack 2x86
# system info:
###
###
# sample data
# dput(ban.nat.1994[sample(row.names(ban.nat.1994), 20),])
bn94 - structure(list(oplt = c(18L, 50L, 11L, 16L, 54L, 35L, 45L, 40L,
15L, 50L, 38L, 45L, 53L, 15L, 1L, 54L, 33L, 13L, 30L, 21L), tree =
c(144L,
824L, 47L, 525L, 291L, 702L, 717L, 615L, 821L, 551L, 750L, 639L,
664L, 813L, 31L, 346L, 689L, 59L, 200L, 658L), bd1 = c(NA, NA,
3.6, 3.1, 4.72, 2.03, 2.88, 1.65, 5.39, 3.04, 2.75, 3.06, 2.81,
2.78, NA, 6.5, 4.62, 4.76, NA, 2.69), bd2 = c(NA, NA, 3.41, 3.06,
4.86, 2.09, 2.78, 1.8, 5.08, 3.26, 2.71, 3.1, 2.87, 2.73, NA,
6.6, 4.53, 4.97, NA, 2.81), bd = c(NA, 4.25, 3.51, 3.08, 4.79,
2.06, 2.83, 1.72, 5.23, 3.15, 2.73, 3.08, 2.84, 2.76, NA, 6.55,
4.58, 4.87, NA, 2.75), ht = c(NA, 20.4, 18.1, 18, 25.8, 13.1,
15.7, 4, 16, 14, 12.7, 8.6, 8.1, 16.2, NA, 52.7, 31.7, 23.7,
NA, 17.6), spr = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_), stat = c(1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L), dam = c(NA, 2L, NA,
NA, NA, NA, NA, 2L, NA, NA, 2L, NA, 1L, NA, NA, NA, 1L, NA, NA,
NA), com = c(, from partial data set, tend = 1, , , ,
, , , , , , , , , , , , , , )), .Names =
c(oplt,
tree, bd1, bd2, bd, ht, spr, stat, dam, com
), row.names = c(1049L, 2845L, 549L, 884L, 3128L, 1887L, 2432L,
2087L, 879L, 2729L, 1990L, 2421L, 3089L, 871L, 3L, 3158L, 1801L,
704L, 1653L, 1215L), class = data.frame)
# dput(ban.nat.1995[sample(row.names(ban.nat.1995), 20),])
bn95 - structure(list(oplt = c(2L, 27L, 54L, 8L, 8L, 51L, 3L, 4L, 20L,
35L, 15L, 22L, 31L, 7L, 4L, 31L, 34L, 6L, 20L, 51L), tree = c(773L,
308L, 331L, 234L, 235L, 170L, 211L, 701L, 745L, 709L, 798L, 350L,
207L, 736L, 718L, 240L, 193L, 266L, 735L, 244L), bd1 = c(8.41,
NA, 6.93, 2.74, 6.06, 2.36, 5.87, 3.53, 2.48, NA, 9, 4.18, 1.74,
3.42, 5.54, 3.74, 3.26, 2.38, 4.42, 3.65), bd2 = c(8.76, NA,
7.17, 2.82, 6.16, 2.33, 6.05, 2.58, 2.5, NA, 9.04, 4.22, 1.68,
3.39, 5.52, 3.68, 3.18, 2.38, 4.47, 3.74), bda = c(8.59, NA,
7.05, 2.78, 6.11, 2.34, 5.96, 3.05, 2.49, NA, 9.02, 4.2, 1.71,
3.41, 5.53, 3.71, 3.22, 2.38, 4.44, 3.7), ht = c(69.2, NA, 55.2,
25.7, 47.8, 17.1, 35.6, 11, 12, NA, 52.5, 33.2, 10.4, 16.2, 32.7,
22.1, 15, 13.6, 24.5, 22.4), spr = c(NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_), stat = c(0L, 1L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L), dam = c(NA, NA, NA, NA, NA, NA, NA, 1L, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA), com = c(, , , , ,
, , , , , , , , , , , , , , )), .Names =
c(oplt,
tree, bd1, bd2, bda, ht, spr, stat, dam, com
), row.names = c(34L, 462L, 724L, 227L, 228L, 673L, 76L, 123L,
368L, 632L, 281L, 391L, 495L, 199L, 140L, 528L, 604L, 191L, 358L,
689L), class =
Re: [R] YALAQ - Yet Another LApply Question
Thank you very much Greg.
Apparently, my learning curve is still well below it's horizontal
asymptote.
And no wonder in the vast universe of the R-project, eh?
Thanx, DaveT.
-Original Message-
From: Greg Snow [mailto:[EMAIL PROTECTED]
Sent: October 15, 2008 01:52 PM
To: Thompson, David (MNR); r-help@r-project.org
Subject: RE: YALAQ - Yet Another LApply Question
For the first question, ?str tells us that the str function
does not return anything, but has a side effect of printing
information to the console. So in version 1 when you call the
cat function it evaluates its arguments and as it evaluates
str(...) the information is printed, then nothing is passed
into cat which then prints the name of the object (after str
has done its printing). In the second version cat finishes
printing the name before str is called so that it is in the
correct order.
You might prefer to use lapply/sapply to create a list with
all the pieces of interest, then just do str on the resulting
list, or look at the TkListView function in the TeachingDemos
package for another way to look at the structure of a list.
For example:
TkListView( sapply( ls(pattern='bn'), function(y) get(y),
simplify=FALSE, USE.NAMES=TRUE ) )
For the 2nd question, the difference is that the summary
function does not print anything, just returns the summary
information. When you type summary at the command line the
parser automatically calls the print method for the summary
object returned, but within functions/loops/apply the summary
object is returned (included in the output of lapply) but not
printed. You need to explicitly print the results of summary.
Hope this helps,
--
Gregory (Greg) L. Snow Ph.D.
Statistical Data Center
Intermountain Healthcare
[EMAIL PROTECTED]
801.408.8111
-Original Message-
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
project.org] On Behalf Of Thompson, David (MNR)
Sent: Wednesday, October 15, 2008 10:19 AM
To: r-help@r-project.org
Subject: Re: [R] YALAQ - Yet Another LApply Question
Please forgive this repost, it's been a week without a squeak. No
comments?
Original post:
https://stat.ethz.ch/pipermail/r-help/2008-October/176340.html
Hello,
Two lapply questions (system info and sample data below):
1) Why does the first form of command1 add the name of y _after_ the
str() output rather than before as does the second (preferred) form?
# command1 version1
invisible(lapply(ls(pattern='bn'), function(y) cat(y, \n,
str(get(y)), \n) ))
# command1 version2 (preferred output)
invisible(lapply(ls(pattern='bn'), function(y) { cat(y, \n) ;
str(get(y)) ; cat(\n) } ))
2) Why does the same method as command1 version2 above not work with
the
summary() command as does the second (preferred) set of commands?
# command2 version1
lapply(ls(pattern='bn'), function(y) { cat(y, \n) ;
summary(get(y))
; cat(\n) } )
# command2 version2 (preferred output)
smry.list - lapply(ls(pattern='bn'), function(y) summary(get(y)))
names(smry.list) - ls(pattern='bn')
smry.list
Thanx, DaveT.
###
# system info:
sessionInfo() ; cat(\n) ; Sys.info()[c(1:3,5)]
R version 2.7.2 (2008-08-25)
i386-pc-mingw32
locale:
LC_COLLATE=English_Canada.1252;LC_CTYPE=English_Canada.1252;LC_MONETARY
=
English_Canada.1252;LC_NUMERIC=C;LC_TIME=English_Canada.1252
attached base packages:
[1] stats graphics grDevices datasets tcltk utils
methods
base
other attached packages:
[1] debug_1.1.0 mvbutils_1.1.1 lattice_0.17-14 plotrix_2.4-7
svSocket_0.9-5 TinnR_1.0.2 R2HTML_1.59 Hmisc_3.4-3
loaded via a namespace (and not attached):
[1] cluster_1.11.11 grid_2.7.2 svMisc_0.9-5tools_2.7.2
sysname release
version machine
Windows XP
build 2600,
Service Pack 2x86
# system info:
###
###
# sample data
# dput(ban.nat.1994[sample(row.names(ban.nat.1994), 20),])
bn94 - structure(list(oplt = c(18L, 50L, 11L, 16L, 54L,
35L, 45L, 40L,
15L, 50L, 38L, 45L, 53L, 15L, 1L, 54L, 33L, 13L, 30L, 21L), tree =
c(144L,
824L, 47L, 525L, 291L, 702L, 717L, 615L, 821L, 551L, 750L, 639L,
664L, 813L, 31L, 346L, 689L, 59L, 200L, 658L), bd1 = c(NA, NA,
3.6, 3.1, 4.72, 2.03, 2.88, 1.65, 5.39, 3.04, 2.75, 3.06, 2.81,
2.78, NA, 6.5, 4.62, 4.76, NA, 2.69), bd2 = c(NA, NA, 3.41, 3.06,
4.86, 2.09, 2.78, 1.8, 5.08, 3.26, 2.71, 3.1, 2.87, 2.73, NA,
6.6, 4.53, 4.97, NA, 2.81), bd = c(NA, 4.25, 3.51, 3.08, 4.79,
2.06, 2.83, 1.72, 5.23, 3.15, 2.73, 3.08, 2.84, 2.76, NA, 6.55,
4.58, 4.87, NA, 2.75), ht = c(NA, 20.4, 18.1, 18, 25.8, 13.1,
15.7, 4, 16, 14, 12.7, 8.6, 8.1, 16.2, NA, 52.7, 31.7, 23.7,
NA, 17.6), spr = c(NA_integer_, NA_integer_, NA_integer_,
NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_
[R] Fatal error: unable to restore saved data in .RData
Hello, I am unable to start an R session by double-clicking on an existing .RData file from the Windoze file explorer. A dialogue appears with the message Fatal error: unable to restore saved data in .RData, and I notice in the R Console the last few lines are: Loading required package: R2HTML NULL error in function () : unused argument(s) (1:43) I tried starting a fresh R session, changing the working directory, saving a new empty workspace, closing R, and restarting with the new (empty) .RData file to the same effect. I tried with the --vanilla option, changing the working directory and loading the existing workspace, and get the error message: Error in function () : unused argument(s) (1:43) And again with the --no-restore-data option, same effect. Suggestions? Thanx, DaveT. ### # system info: sessionInfo() ; cat(\n) ; Sys.info()[c(1:3,5)] R version 2.7.2 (2008-08-25) i386-pc-mingw32 locale: LC_COLLATE=English_Canada.1252;LC_CTYPE=English_Canada.1252;LC_MONETARY= English_Canada.1252;LC_NUMERIC=C;LC_TIME=English_Canada.1252 attached base packages: [1] stats graphics grDevices datasets tcltk utils methods base other attached packages: [1] debug_1.1.0 mvbutils_1.1.1 lattice_0.17-14 plotrix_2.4-7 svSocket_0.9-5 TinnR_1.0.2 R2HTML_1.59 Hmisc_3.4-3 loaded via a namespace (and not attached): [1] cluster_1.11.11 grid_2.7.2 svMisc_0.9-5tools_2.7.2 sysname release version machine Windows XP build 2600, Service Pack 2 x86 # system info: ### * Silviculture Data Analyst Ontario Forest Research Institute Ontario Ministry of Natural Resources [EMAIL PROTECTED] http://ontario.ca/ofri __ R-help@r-project.org mailing list 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.
Re: [R] Fatal error: unable to restore saved data in .RData
Hello,
I may have found the problem, although I don't understand it.
When I commented out the following line in my Rprofile.site file the
problem _seemed_ to disappear.
# ans as shorthand for .Last.value
# makeActiveBinding(ans, function() .Last.value, .GlobalEnv)
I decided to do this after reading the help for bindenv {base} and the
phrase . . . experimental interface . . . JUMPED right out at me.
Again, I don't know if this was _actually_ the cause of my problem but,
I am underway again.
Thanx, DaveT.
-Original Message-
From: Thompson, David (MNR)
Sent: October 10, 2008 10:26 AM
To: 'r-help@r-project.org'
Subject: Fatal error: unable to restore saved data in .RData
Hello,
I am unable to start an R session by double-clicking on an
existing .RData file from the Windoze file explorer.
A dialogue appears with the message
Fatal error: unable to restore saved data in .RData,
and I notice in the R Console the last few lines are:
Loading required package: R2HTML
NULL
error in function () : unused argument(s) (1:43)
I tried starting a fresh R session, changing the working
directory, saving a new empty workspace, closing R, and
restarting with the new (empty) .RData file to the same effect.
I tried with the --vanilla option, changing the working
directory and loading the existing workspace, and get the
error message:
Error in function () : unused argument(s) (1:43)
And again with the --no-restore-data option, same effect.
Suggestions?
Thanx, DaveT.
###
# system info:
sessionInfo() ; cat(\n) ; Sys.info()[c(1:3,5)]
R version 2.7.2 (2008-08-25)
i386-pc-mingw32
locale:
LC_COLLATE=English_Canada.1252;LC_CTYPE=English_Canada.1252;LC_
MONETARY=English_Canada.1252;LC_NUMERIC=C;LC_TIME=English_Canada.1252
attached base packages:
[1] stats graphics grDevices datasets tcltk utils
methods base
other attached packages:
[1] debug_1.1.0 mvbutils_1.1.1 lattice_0.17-14
plotrix_2.4-7 svSocket_0.9-5 TinnR_1.0.2 R2HTML_1.59
Hmisc_3.4-3
loaded via a namespace (and not attached):
[1] cluster_1.11.11 grid_2.7.2 svMisc_0.9-5tools_2.7.2
sysname release
version machine
Windows XP build 2600, Service
Pack 2x86
# system info:
###
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ontario.ca/ofri
*
__
R-help@r-project.org mailing list
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] YALAQ - Yet Another LApply Question
Hello,
Two lapply questions (system info and sample data below):
1) Why does the first form of command1 add the name of y _after_ the
str() output rather than before as does the second (preferred) form?
# command1 version1
invisible(lapply(ls(pattern='bn'), function(y) cat(y, \n,
str(get(y)), \n) ))
# command1 version2 (preferred output)
invisible(lapply(ls(pattern='bn'), function(y) { cat(y, \n) ;
str(get(y)) ; cat(\n) } ))
2) Why does the same method as command1 version2 above not work with the
summary() command as does the second (preferred) set of commands?
# command2 version1
lapply(ls(pattern='bn'), function(y) { cat(y, \n) ; summary(get(y))
; cat(\n) } )
# command2 version2 (preferred output)
smry.list - lapply(ls(pattern='bn'), function(y) summary(get(y)))
names(smry.list) - ls(pattern='bn')
smry.list
Thanx, DaveT.
###
# system info:
sessionInfo() ; cat(\n) ; Sys.info()[c(1:3,5)]
R version 2.7.2 (2008-08-25)
i386-pc-mingw32
locale:
LC_COLLATE=English_Canada.1252;LC_CTYPE=English_Canada.1252;LC_MONETARY=
English_Canada.1252;LC_NUMERIC=C;LC_TIME=English_Canada.1252
attached base packages:
[1] stats graphics grDevices datasets tcltk utils methods
base
other attached packages:
[1] debug_1.1.0 mvbutils_1.1.1 lattice_0.17-14 plotrix_2.4-7
svSocket_0.9-5 TinnR_1.0.2 R2HTML_1.59 Hmisc_3.4-3
loaded via a namespace (and not attached):
[1] cluster_1.11.11 grid_2.7.2 svMisc_0.9-5tools_2.7.2
sysname release
version machine
Windows XP build 2600,
Service Pack 2x86
# system info:
###
###
# sample data
# dput(ban.nat.1994[sample(row.names(ban.nat.1994), 20),])
bn94 - structure(list(oplt = c(18L, 50L, 11L, 16L, 54L, 35L, 45L, 40L,
15L, 50L, 38L, 45L, 53L, 15L, 1L, 54L, 33L, 13L, 30L, 21L), tree =
c(144L,
824L, 47L, 525L, 291L, 702L, 717L, 615L, 821L, 551L, 750L, 639L,
664L, 813L, 31L, 346L, 689L, 59L, 200L, 658L), bd1 = c(NA, NA,
3.6, 3.1, 4.72, 2.03, 2.88, 1.65, 5.39, 3.04, 2.75, 3.06, 2.81,
2.78, NA, 6.5, 4.62, 4.76, NA, 2.69), bd2 = c(NA, NA, 3.41, 3.06,
4.86, 2.09, 2.78, 1.8, 5.08, 3.26, 2.71, 3.1, 2.87, 2.73, NA,
6.6, 4.53, 4.97, NA, 2.81), bd = c(NA, 4.25, 3.51, 3.08, 4.79,
2.06, 2.83, 1.72, 5.23, 3.15, 2.73, 3.08, 2.84, 2.76, NA, 6.55,
4.58, 4.87, NA, 2.75), ht = c(NA, 20.4, 18.1, 18, 25.8, 13.1,
15.7, 4, 16, 14, 12.7, 8.6, 8.1, 16.2, NA, 52.7, 31.7, 23.7,
NA, 17.6), spr = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_), stat = c(1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 1L, 0L), dam = c(NA, 2L, NA,
NA, NA, NA, NA, 2L, NA, NA, 2L, NA, 1L, NA, NA, NA, 1L, NA, NA,
NA), com = c(, from partial data set, tend = 1, , , ,
, , , , , , , , , , , , , , )), .Names =
c(oplt,
tree, bd1, bd2, bd, ht, spr, stat, dam, com
), row.names = c(1049L, 2845L, 549L, 884L, 3128L, 1887L, 2432L,
2087L, 879L, 2729L, 1990L, 2421L, 3089L, 871L, 3L, 3158L, 1801L,
704L, 1653L, 1215L), class = data.frame)
# dput(ban.nat.1995[sample(row.names(ban.nat.1995), 20),])
bn95 - structure(list(oplt = c(2L, 27L, 54L, 8L, 8L, 51L, 3L, 4L, 20L,
35L, 15L, 22L, 31L, 7L, 4L, 31L, 34L, 6L, 20L, 51L), tree = c(773L,
308L, 331L, 234L, 235L, 170L, 211L, 701L, 745L, 709L, 798L, 350L,
207L, 736L, 718L, 240L, 193L, 266L, 735L, 244L), bd1 = c(8.41,
NA, 6.93, 2.74, 6.06, 2.36, 5.87, 3.53, 2.48, NA, 9, 4.18, 1.74,
3.42, 5.54, 3.74, 3.26, 2.38, 4.42, 3.65), bd2 = c(8.76, NA,
7.17, 2.82, 6.16, 2.33, 6.05, 2.58, 2.5, NA, 9.04, 4.22, 1.68,
3.39, 5.52, 3.68, 3.18, 2.38, 4.47, 3.74), bda = c(8.59, NA,
7.05, 2.78, 6.11, 2.34, 5.96, 3.05, 2.49, NA, 9.02, 4.2, 1.71,
3.41, 5.53, 3.71, 3.22, 2.38, 4.44, 3.7), ht = c(69.2, NA, 55.2,
25.7, 47.8, 17.1, 35.6, 11, 12, NA, 52.5, 33.2, 10.4, 16.2, 32.7,
22.1, 15, 13.6, 24.5, 22.4), spr = c(NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
NA_integer_, NA_integer_, NA_integer_), stat = c(0L, 1L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L), dam = c(NA, NA, NA, NA, NA, NA, NA, 1L, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA), com = c(, , , , ,
, , , , , , , , , , , , , , )), .Names =
c(oplt,
tree, bd1, bd2, bda, ht, spr, stat, dam, com
), row.names = c(34L, 462L, 724L, 227L, 228L, 673L, 76L, 123L,
368L, 632L, 281L, 391L, 495L, 199L, 140L, 528L, 604L, 191L, 358L,
689L), class = data.frame)
# dput(ban.nat.1996[sample(row.names(ban.nat.1996), 20),])
bn96 - structure(list(oplt = c(23L, 33L, 22L, 19L, 27L, 3L, 27L, 19L,
48L, 31L,
[R] YAPMQ - Yet Another PlotMath Question
Hello, I'm having trouble finding (remembering) how to pass values into text functions in plots, as demonstrated by: slope - 45 ; plot(1:10) ; text(2, 7, labels = expression(45~degree)) ; text(2, 5, labels = paste(bquote(.(slope)), expression(degree))) Thanx, DaveT. * Silviculture Data Analyst Ontario Forest Research Institute Ontario Ministry of Natural Resources [EMAIL PROTECTED] http://ontario.ca/ofri __ R-help@r-project.org mailing list 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.
Re: [R] YAPMQ - Yet Another PlotMath Question
-Original Message-
From: Peter Dalgaard [mailto:[EMAIL PROTECTED]
Sent: June 19, 2008 04:23 PM
To: Thompson, David (MNR)
Cc: r-help@r-project.org
Subject: Re: [R] YAPMQ - Yet Another PlotMath Question
Thompson, David (MNR) wrote:
Hello,
I'm having trouble finding (remembering) how to pass values into text
functions in plots, as demonstrated by:
slope - 45 ; plot(1:10) ; text(2, 7, labels =
expression(45~degree)) ;
text(2, 5, labels = paste(bquote(.(slope)), expression(degree)))
text(2, 5, labels = bquote(paste(.(slope), degree)))
Notice that paste()ing two expressions does not yield an expression
result. Instead, it deparses both arguments and gives a
character string.
Thank you Peter.
Are all the syntactic elements noted in plotmath{grDevices} available to
bquote()?
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ontario.ca/ofri
__
R-help@r-project.org mailing list
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.
Re: [R] YAPMQ - Yet Another PlotMath Question
-Original Message- From: Katharine Mullen [mailto:[EMAIL PROTECTED] Sent: June 19, 2008 04:26 PM To: Thompson, David (MNR) Cc: r-help@r-project.org Subject: Re: [R] YAPMQ - Yet Another PlotMath Question by example: slope - 45 plot(1:10) text(2, 7, labels = expression(45~degree)) ; text(2, 5, labels = substitute(paste(slope * degree), list(slope=45))) text(2, 3, labels = substitute(paste(lambda * = * mt * (nm)), list(mt = 33))) On Thu, 19 Jun 2008, Thompson, David (MNR) wrote: Hello, I'm having trouble finding (remembering) how to pass values into text functions in plots, as demonstrated by: slope - 45 ; plot(1:10) ; text(2, 7, labels = expression(45~degree)) ; text(2, 5, labels = paste(bquote(.(slope)), expression(degree))) Thank you Katharine. I suspected this would be one of those cats that you could skin nine-ways-from-Sunday. Thanx, DaveT. * Silviculture Data Analyst Ontario Forest Research Institute Ontario Ministry of Natural Resources [EMAIL PROTECTED] http://ontario.ca/ofri __ R-help@r-project.org mailing list 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] echo Rprofile.site on startup
Hello,
I have not been able to find how to have R echo the Rprofile.site
contents to the console on start-up.
Changing the windoze shortcut to include the '--verbose' option does not
show what I am looking for.
I would like to see the options and commands listed, in addition to the
library() loadings, as they are processed. Examples of the type of
options I like and shortcut-commands (aliases) that I collect to shrink
my keystroke count are:
options(digits=2)
options(graphics.record=TRUE)
# show head and tail together
so - function(x, n=20) { print(head(x, n)) ; print(tail(x, n))
}
# shorthand for part of Sys.info() and sessionInfo()
si - function() { Sys.info()[c(1,2,3,5)] ; sessionInfo() }
I would like to view these as processed when I am changing options and
adding aliases so that I may know which parts are successfully/properly
defined.
Does the same process work for all of Rprofile.site, .Rprofile, .First,
.Last (, etc.?) profile files?
Is there a 'best practice' on which of the profile files one should use?
I use only the Rprofile.site since I am the only user on my PC.
Thanx, DaveT.
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ontario.ca/ofri
*
Sys.info()
sysname release
version machine
Windows XP build 2600,
Service Pack 2x86
sessionInfo()
R version 2.7.0 (2008-04-22)
i386-pc-mingw32
locale:
LC_COLLATE=English_Canada.1252;LC_CTYPE=English_Canada.1252;LC_MONETARY=
English_Canada.1252;LC_NUMERIC=C;LC_TIME=English_Canada.1252
attached base packages:
[1] datasets grDevices splines grid graphics stats tcltk
utils methods base
other attached packages:
[1] ggplot2_0.6colorspace_0.95RColorBrewer_1.0-2
MASS_7.2-42proto_0.3-8reshape_0.8.0 car_1.2-8
svSocket_0.9-5
[9] svIO_0.9-5 R2HTML_1.59svMisc_0.9-5
svIDE_0.9-5
loaded via a namespace (and not attached):
[1] tools_2.7.0
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] ggplot questions
Thanx Thierry, Suggestion #1 had no effect. I have been playing with variants on #2 along the way. DaveT. -Original Message- From: ONKELINX, Thierry [mailto:[EMAIL PROTECTED] Sent: June 6, 2008 04:02 AM To: Thompson, David (MNR); hadley wickham Cc: r-help@r-project.org Subject: RE: [R] ggplot questions David, 1. Try scale_x_continuous(lim = c(0, 360)) + scale_y_continuous(lim = c(0, 16)) 2. You could set the colour of the gridlines equal to the backgroup colour with ggopt HTH, Thierry __ R-help@r-project.org mailing list 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.
Re: [R] ggplot questions
OK,
The original ggplot() construct (below) on the following two dataframes
(test1, test2) generate different outputs, which I have attached. The
output that I expect is that shown in test2.png. My expectations are
that I have set the plotting limits with 'scale_x_continuous(lim = c(0,
360)) + scale_y_continuous(lim = c(0, 16))' so, both data sets should
produce the same output except for the 'o' at plot center and the 'N' at
the top. The only difference in the two dataframes are inclusion of
first two rows in test2 with rplt column changed to character:
test2[1:2,]
oplt rplt az dist
10o 00
20N 360 16
Ahhh, wait a second! In composing this message I may have found the
problem.
It appears that including the 'scale_x_continuous()' component twice in
my original version was causing (?) the erratic behaviour. And I have
confirmed that the ordering of the layer, scale* and coord* components
does not affect the output. However, I'm still getting more x-breaks
than requested with radial lines corresponding to 45, 135, 225, 315
degrees (NE, SE, SW, NW). Still open to suggestions on that.
# new version working with both dataframes
ggplot() + coord_polar() +
layer( data = test1, mapping = aes(x = az, y = dist, label = rplt), geom
= text) +
scale_x_continuous(lim = c(0, 360), breaks=c(90, 180, 270, 360),
labels=c('E', 'S', 'W', 'N')) +
scale_y_continuous(lim = c(0, 16), breaks=c(0, 4, 8, 12, 16),
labels=c('centre', '4m', '8m', '12m', '16m'))
##
##
##
# original version NOT WORKING with test1
ggplot() + coord_polar() + scale_x_continuous(lim = c(0, 360)) +
scale_y_continuous(lim = c(0, 16)) +
layer( data = test, mapping = aes(x = az, y = dist, label = rplt), geom
= text) +
scale_x_continuous(breaks=c(90, 180, 270, 360), labels=c('90', '180',
'270', '360'))
# data generating test1.png
test1 -structure(list(oplt = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L
), rplt = 1:10, az = c(57L, 94L, 96L, 152L, 182L, 185L, 227L,
264L, 332L, 354L), dist = c(4.09, 2.8, 7.08, 7.09, 3.28, 7.85,
6.12, 1.97, 7.68, 7.9)), .Names = c(oplt, rplt, az, dist
), row.names = c(NA, 10L), class = data.frame)
# data generating test2.png
test2 - structure(list(oplt = c(0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
rplt = c(o, N, 1, 2, 3, 4, 5, 6, 7, 8,
9, 10), az = c(0, 360, 57, 94, 96, 152, 182, 185, 227,
264, 332, 354), dist = c(0, 16, 4.09, 2.8, 7.08, 7.09, 3.28,
7.85, 6.12, 1.97, 7.68, 7.9)), .Names = c(oplt, rplt,
az, dist), row.names = c(NA, 12L), class = data.frame)
Many, many thanks for your patience and perseverance on this one Hadley,
DaveT.
-Original Message-
From: hadley wickham [mailto:[EMAIL PROTECTED]
Sent: June 6, 2008 02:06 PM
To: Thompson, David (MNR)
Cc: r-help@r-project.org
Subject: Re: [R] ggplot questions
Does the difference have something to do with ggplot() using ranges
derived from the data?
When I modify my original 'test' dataframe with two extra rows as
defined below, I get expected results in both versions.
Order shouldn't matter - and if it's making a difference, that's a
bug. But I'm still not completely sure what you're expecting.
This highlights my next question (warned you ;-) ), I have been
unsuccessful in trying to define fixed plotting ranges to generate a
'template' graphic that I may reuse with successive 'overstory plot'
data sets. I have used '+ xlim(0, 360) + ylim(0, 16)' but,
this seems to
not have any effect on the final plot layout.
Could you please produce a small reproducible example that
demonstrates this? It may well be a bug.
Hadley
--
http://had.co.nz/
attachment: test1.pngattachment: test2.png__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] ggplot questions
Thanx Hadley,
More questions inline.
-Original Message-
From: hadley wickham [mailto:[EMAIL PROTECTED]
Sent: June 5, 2008 01:09 PM
To: Thompson, David (MNR)
Cc: r-help@r-project.org
Subject: Re: [R] ggplot questions
On Wed, Jun 4, 2008 at 2:03 PM, Thompson, David (MNR)
[EMAIL PROTECTED] wrote:
Hello,
A few questions about the following examples:
1. Why do the two plotting versions not produce the same result?
Because version one has two layers, and version two has one?
Does the difference have something to do with ggplot() using ranges
derived from the data?
When I modify my original 'test' dataframe with two extra rows as
defined below, I get expected results in both versions.
This highlights my next question (warned you ;-) ), I have been
unsuccessful in trying to define fixed plotting ranges to generate a
'template' graphic that I may reuse with successive 'overstory plot'
data sets. I have used '+ xlim(0, 360) + ylim(0, 16)' but, this seems to
not have any effect on the final plot layout.
2. Is the 'scale_x_continuous' (or *_y_* or *_*_discrete)
geom the best
way to setup grids (as in visual guide-lines) in polar (or for that
matter, any) coordinate system?
It's one way. Another way is to use geom_hline and geom_vline. (Also
note that scale_x_continuous is a _scale_ not a geom)
OK. So, how do I suppress automatic generation of plot grids so that I
could define my own with geom_hline and geom_vline?
3. Why do these commands appear to generate 3 plot pages each?
Could you provide a bit more detail here please?
Sorry Hadley, I could not reproduce the same behaviour.
I had restarted my computer since then so, maybe, I was just suffering
from the usual leaky-resources-M$-syndrome.
Thanks,
Hadley
--
http://had.co.nz/
# for ease of reference:
# the two original dataframes
test - structure(list(oplt = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L
), rplt = 1:10, az = c(57L, 94L, 96L, 152L, 182L, 185L, 227L,
264L, 332L, 354L), dist = c(4.09, 2.8, 7.08, 7.09, 3.28, 7.85,
6.12, 1.97, 7.68, 7.9)), .Names = c(oplt, rplt, az, dist
), row.names = c(NA, 10L), class = data.frame)
labs - structure(list(oplt = c(0, 0, 0, 0, 0), rplt = structure(c(3L,
1L, 4L, 5L, 2L), .Label = c(E, N, o, S, W), class = factor),
az = c(0, 90, 180, 270, 360), dist = c(0, 16, 16, 16, 16)), .Names =
c(oplt,
rplt, az, dist), row.names = c(NA, -5L), class = data.frame)
# the new dataframe
test2 - structure(list(oplt = c(0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1),
rplt = c(o, N, 1, 2, 3, 4, 5, 6, 7, 8,
9, 10), az = c(0, 360, 57, 94, 96, 152, 182, 185, 227,
264, 332, 354), dist = c(0, 16, 4.09, 2.8, 7.08, 7.09, 3.28,
7.85, 6.12, 1.97, 7.68, 7.9)), .Names = c(oplt, rplt,
az, dist), row.names = c(NA, 12L), class = data.frame)
### plot version 1, setup plot structure first, add 'data' points later
ggplot() + coord_polar() +
layer( data = labs, mapping = aes(x = az, y = dist, label = rplt), geom
= text) +
scale_x_continuous(breaks=c(90, 180, 270, 360)) +
layer( data = test, mapping = aes(x = az, y = dist, label = rplt), geom
= text)
### plot version 2, try the same all in one step
ggplot() + coord_polar() +
layer( data = test, mapping = aes(x = az, y = dist, label = rplt), geom
= text) +
scale_x_continuous(breaks=c(90, 180, 270, 360), labels=c('90', '180',
'270', '360'))
sessionInfo()
R version 2.7.0 (2008-04-22)
i386-pc-mingw32
locale:
LC_COLLATE=English_Canada.1252;LC_CTYPE=English_Canada.1252;LC_MONETARY=
English_Canada.1252;LC_NUMERIC=C;LC_TIME=English_Canada.1252
attached base packages:
[1] datasets grDevices splines grid graphics stats tcltk
utils methods base
other attached packages:
[1] ggplot2_0.6colorspace_0.95RColorBrewer_1.0-2
MASS_7.2-42proto_0.3-8reshape_0.8.0 car_1.2-8
[8] svSocket_0.9-5 svIO_0.9-5 R2HTML_1.59
svMisc_0.9-5 svIDE_0.9-5
Thanx again, DaveT.
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ontario.ca/ofri
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] ggplot questions
Hello,
A few questions about the following examples:
1. Why do the two plotting versions not produce the same result?
2. Is the 'scale_x_continuous' (or *_y_* or *_*_discrete) geom the best
way to setup grids (as in visual guide-lines) in polar (or for that
matter, any) coordinate system?
3. Why do these commands appear to generate 3 plot pages each?
4. Perhaps more questions to follow ;-)
### the data
test - structure(list(oplt = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L
), rplt = 1:10, az = c(57L, 94L, 96L, 152L, 182L, 185L, 227L,
264L, 332L, 354L), dist = c(4.09, 2.8, 7.08, 7.09, 3.28, 7.85,
6.12, 1.97, 7.68, 7.9)), .Names = c(oplt, rplt, az, dist
), row.names = c(NA, 10L), class = data.frame)
labs - structure(list(oplt = c(0, 0, 0, 0, 0), rplt = structure(c(3L,
1L, 4L, 5L, 2L), .Label = c(E, N, o, S, W), class = factor),
az = c(0, 90, 180, 270, 360), dist = c(0, 16, 16, 16, 16)), .Names =
c(oplt,
rplt, az, dist), row.names = c(NA, -5L), class = data.frame)
### plot version 1, setup plot structure first, add 'data' points later
ggplot() + coord_polar() +
layer( data = labs, mapping = aes(x = az, y = dist, label = rplt), geom
= text) +
scale_x_continuous(breaks=c(90, 180, 270, 360)) +
layer( data = test, mapping = aes(x = az, y = dist, label = rplt), geom
= text)
### plot version 2, try the same all in one step
ggplot() + coord_polar() +
layer( data = test, mapping = aes(x = az, y = dist, label = rplt), geom
= text) +
scale_x_continuous(breaks=c(90, 180, 270, 360), labels=c('90', '180',
'270', '360'))
### the scenario
I am generating graphics to show the physical layout of a forestry
research experiment.
There are 54 'cut blocks' (64x64m, 0.4ha) each containing 1 circular
'overstory plot' (16m radius, 0.08ha).
Each 'overstory plot' (oplt) contains 10 circular 'regeneration plots'
(rplt) (0.56m radius, 1m^2 or 1.13m radius, 4m^2), these are the label
data points plotted below, later to have the 1m^2 or 4m^2 rplt outline
added.
Later, each individual tree will be plotted across each oplt in the
views below and each rplt in expanded views.
All locations (rplt centers, tree positions) are recorded as azimuth and
distance from their respective plot centers, hence my inclination to use
polar coordinates.
Thanx, DaveT.
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ontario.ca/ofri
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Thank you
Yes! Again, thank you ALL very, very much. Even simply lurking on the list generates many gems worth collecting. DaveT. From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] I totally agree both of you. This is a super place to mature the R. I learn a lot from this R heaven! Chunhao Quoting Esmail Bonakdarian [EMAIL PROTECTED]: Hear hear! .. I've benefited greatly from reading the postings here and some of the members have been very generous with their knowledge too! Esmail Tubin wrote: In the past few weeks I have had to give myself a crash course in R, in order to accomplish some necessary tasks for my job. During that time, I've found this forum to be helpful time and time again - usually I find the answer to my problem by searching the archives; once or twice I've posted questions and been given near-immediate solutions. I just wanted to thank the forum participants for all of their contributions over the years! __ R-help@r-project.org mailing list 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.
Re: [R] list manipulation
Beautiful! Thanks Jim. DaveT. -Original Message- From: jim holtman [mailto:[EMAIL PROTECTED] Sent: May 6, 2008 07:33 PM To: Thompson, David (MNR) Subject: Re: [R] list manipulation The reason for the NULLs is that is the output of the lapply you are executing. If you don't want to see the value, then use 'invisible' or assign to an object since you are executing this at the command level, the default is to print the value. invisible(lapply(...)) On Tue, May 6, 2008 at 2:35 PM, Thompson, David (MNR) [EMAIL PROTECTED] wrote: Hello, I have a set of one-liners (many thanks to previous responses from this list) that I use to look at newly imported data sets with functions like dim(), names(), str(), etc. within lapply(). Generally, these commands work for me but, I am apparently still missing some aspect of list manipulation. I don't understand why I get a set of NULL list elements at the end of each output as demonstrated below. How can I generate this (and similar) result(s) without all the trailing NULLs? lapply(ls(pattern='bn'), function(x) cat(x, dim(get(x)), \t, names(get(x)), \n)) bn1993 2885 11 oplt rplt rsiz tree bd ht oaz odst raz rdst spr bn1994 3158 7oplt tree bd ht spr stat dam bn1995 734 7 oplt tree bd ht spr stat dam bn1996 293 7 oplt tree bd ht spr stat dam bn1997 264 7 oplt tree bd ht spr stat dam bn1998 768 7 oplt tree bd ht spr stat dam bn1999 654 7 oplt tree bd ht dbh stat dam bn2003 1407 9oplt tree bd94 ht94 ht99 ht02 ht03 stat dam [[1]] NULL [[2]] NULL [[3]] NULL [[4]] NULL [[5]] NULL [[6]] NULL [[7]] NULL [[8]] NULL Thanx, DaveT. * Silviculture Data Analyst Ontario Forest Research Institute Ontario Ministry of Natural Resources [EMAIL PROTECTED] http://ofri.mnr.gov.on.ca __ R-help@r-project.org mailing list 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. -- Jim Holtman Cincinnati, OH +1 513 646 9390 What is the problem you are trying to solve? __ R-help@r-project.org mailing list 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] list manipulation
Hello, I have a set of one-liners (many thanks to previous responses from this list) that I use to look at newly imported data sets with functions like dim(), names(), str(), etc. within lapply(). Generally, these commands work for me but, I am apparently still missing some aspect of list manipulation. I don't understand why I get a set of NULL list elements at the end of each output as demonstrated below. How can I generate this (and similar) result(s) without all the trailing NULLs? lapply(ls(pattern='bn'), function(x) cat(x, dim(get(x)), \t, names(get(x)), \n)) bn1993 2885 11 oplt rplt rsiz tree bd ht oaz odst raz rdst spr bn1994 3158 7oplt tree bd ht spr stat dam bn1995 734 7 oplt tree bd ht spr stat dam bn1996 293 7 oplt tree bd ht spr stat dam bn1997 264 7 oplt tree bd ht spr stat dam bn1998 768 7 oplt tree bd ht spr stat dam bn1999 654 7 oplt tree bd ht dbh stat dam bn2003 1407 9oplt tree bd94 ht94 ht99 ht02 ht03 stat dam [[1]] NULL [[2]] NULL [[3]] NULL [[4]] NULL [[5]] NULL [[6]] NULL [[7]] NULL [[8]] NULL Thanx, DaveT. * Silviculture Data Analyst Ontario Forest Research Institute Ontario Ministry of Natural Resources [EMAIL PROTECTED] http://ofri.mnr.gov.on.ca __ R-help@r-project.org mailing list 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.
Re: [R] list manipulation
Thanks Mark, Your suggestion led me to this: !is.null(lapply(ls(pattern='bn'), function(y) cat(y, dim(get(y)), \t, names(get(y)), \n))) bn1993 2885 11 oplt rplt rsiz tree bd ht oaz odst raz rdst spr bn1994 3158 7oplt tree bd ht spr stat dam bn1995 734 7 oplt tree bd ht spr stat dam bn1996 293 7 oplt tree bd ht spr stat dam bn1997 264 7 oplt tree bd ht spr stat dam bn1998 768 7 oplt tree bd ht spr stat dam bn1999 654 7 oplt tree bd ht dbh stat dam bn2003 1407 9oplt tree bd94 ht94 ht99 ht02 ht03 stat dam [1] TRUE Which is far cleaner and more compact (which was probably what I was _actually_ looking for) than what I had started with. Thanx, DaveT. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: May 6, 2008 02:47 PM To: Thompson, David (MNR) Subject: RE: [R] list manipulation Hi: i would guess that you are sending objects into the lapply that dim and names don't work on so you get NULL in those cases. you can probably figure out what's happening by doing ls(pattern='bn') and seeing what gets returned ? There could be some other reason but that's my best guess. if you don't care why and you just want to get rid of them you can do initialoutput-lapply( that stuff) finaloutput-initialoutput[!sapply(initialoutput,is.null] print(finaloutput) i'm no R expert by any stretch but, if you want to get better at R , the best way is to live on this list if possible and watch the questions and solutions. for me, it beats any book out there. good luck and let me know if anything above is unclear or doesn't work. On Tue, May 6, 2008 at 2:35 PM, Thompson, David (MNR) wrote: Hello, I have a set of one-liners (many thanks to previous responses from this list) that I use to look at newly imported data sets with functions like dim(), names(), str(), etc. within lapply(). Generally, these commands work for me but, I am apparently still missing some aspect of list manipulation. I don't understand why I get a set of NULL list elements at the end of each output as demonstrated below. How can I generate this (and similar) result(s) without all the trailing NULLs? lapply(ls(pattern='bn'), function(x) cat(x, dim(get(x)), \t, names(get(x)), \n)) bn1993 2885 11 oplt rplt rsiz tree bd ht oaz odst raz rdst spr bn1994 3158 7oplt tree bd ht spr stat dam bn1995 734 7 oplt tree bd ht spr stat dam bn1996 293 7 oplt tree bd ht spr stat dam bn1997 264 7 oplt tree bd ht spr stat dam bn1998 768 7 oplt tree bd ht spr stat dam bn1999 654 7 oplt tree bd ht dbh stat dam bn2003 1407 9oplt tree bd94 ht94 ht99 ht02 ht03 stat dam [[1]] NULL [[2]] NULL [[3]] NULL [[4]] NULL [[5]] NULL [[6]] NULL [[7]] NULL [[8]] NULL Thanx, DaveT. * Silviculture Data Analyst Ontario Forest Research Institute Ontario Ministry of Natural Resources [EMAIL PROTECTED] http://ofri.mnr.gov.on.ca __ R-help@r-project.org mailing list 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@r-project.org mailing list 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] Recovering SPlus GraphSheets
Hello, Is it possible with R to recover the contents of SPlus GraphSheets (*.sgr) without access to SPlus? Also, some of the .sgr files may have multiple pages. Thanx, DaveT. * Silviculture Data Analyst Ontario Forest Research Institute Ontario Ministry of Natural Resources [EMAIL PROTECTED] http://ofri.mnr.gov.on.ca __ R-help@r-project.org mailing list 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] Changing default plot behaviour
Hello, How would I make the default behaviour of my plots produce output such as the following (i.e. tick marks inside on all axes, labels only on two (arbitrary?) sides) without needing the five additional commands each time? plot(1:10, axes=FALSE) axis(1, tcl=0.5) axis(2, tcl=0.5) axis(3, tcl=0.5, labels=FALSE) axis(4, tcl=0.5, labels=FALSE) box() Thanx, DaveT. * Silviculture Data Analyst Ontario Forest Research Institute Ontario Ministry of Natural Resources [EMAIL PROTECTED] http://ofri.mnr.gov.on.ca __ R-help@r-project.org mailing list 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.
Re: [R] Changing default plot behaviour
Thank you all for your help.
I successfully used Richard's suggestion (much like John's) and
continued with my work, neglecting to respond to the list.
Sorry about that.
Thanx again, DaveT.
-Original Message-
From: John Kane [mailto:[EMAIL PROTECTED]
Sent: April 9, 2008 03:16 PM
To: Thompson, David (MNR); r-help@r-project.org
Subject: Re: [R] Changing default plot behaviour
This may be a bit simple minded but why not change
those commmands into a single function something like
this and run it rather than the actual plot command?
myfunction - function(a) {
plot(a, axes=FALSE)
axis(1, tcl=0.5)
axis(2, tcl=0.5)
axis(3, tcl=0.5, labels=FALSE)
axis(4, tcl=0.5, labels=FALSE)
box()
}
--- Thompson, David (MNR)
[EMAIL PROTECTED] wrote:
Hello,
How would I make the default behaviour of my plots
produce output such
as the following (i.e. tick marks inside on all
axes, labels only on two
(arbitrary?) sides) without needing the five
additional commands each
time?
plot(1:10, axes=FALSE)
axis(1, tcl=0.5)
axis(2, tcl=0.5)
axis(3, tcl=0.5, labels=FALSE)
axis(4, tcl=0.5, labels=FALSE)
box()
Thanx, DaveT.
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ofri.mnr.gov.on.ca
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained,
reproducible code.
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Re: [R] Finding Interaction and main effects contrasts for two-way ANOVA
Dale,
Other than the first SAS contrast, does the following demonstrate what
your asking for?
summary(twoway)
material temp voltage
1:12 50:12 Min. : 20
2:12 65:12 1st Qu.: 70
3:12 80:12 Median :108
Mean :106
3rd Qu.:142
Max. :188
contrasts(twoway$material)
2 3
1 0 0
2 1 0
3 0 1
contrasts(twoway$temp)
65 80
50 0 0
65 1 0
80 0 1
fit - aov(voltage ~ material*temp, data=twoway)
summary.aov(fit)
Df Sum Sq Mean Sq F value Pr(F)
material 2 1068453427.91 0.0020 **
temp 2 39119 19559 28.97 1.9e-07 ***
material:temp 4 961424033.56 0.0186 *
Residuals 27 18231 675
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# setting (partial) contrasts
contrasts(twoway$material) - c(1,-1,0) # ignoring the second
available df
contrasts(twoway$temp) - c(0,1,-1) # ignoring the second available df
contrasts(twoway$material)
[,1] [,2]
11 -0.41
2 -1 -0.41
30 0.82
contrasts(twoway$temp)
[,1] [,2]
500 -0.82
651 0.41
80 -1 0.41
summary.aov(fit, split=list(material=list('m1-m2'=1), temp=list('t50 -
t80'=1)))
Df Sum Sq Mean Sq F value Pr(F)
material 2 1068453427.91 0.00198 **
material: m1-m2 1 380038005.63 0.02506 *
temp 2 39119 19559 28.97 1.9e-07 ***
temp: t50 - t80 1 11310 11310 16.75 0.00035 ***
material:temp 4 961424033.56 0.01861 *
material:temp: m1-m2.t50 - t80 1 497049707.36 0.01146 *
Residuals27 18231 675
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# other examples of setting contrasts
# compare m1 vs m2 and m2 vs m3
contrasts(twoway$material) - matrix(c(1,-1,0,1,1,-2), nrow=3)
contrasts(twoway$material)
[,1] [,2]
110
2 -11
30 -1
# compare m1 vs m2 and m1+m2 vs m3
contrasts(twoway$material) - matrix(c(1,-1,0,1,1,-2), nrow=3)
contrasts(twoway$material)
[,1] [,2]
111
2 -11
30 -2
I'm not sure if 'summary.aov' is the only lm-family summary method with
the split argument.
DaveT.
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ofri.mnr.gov.on.ca
*
-Original Message-
From: Steele [mailto:[EMAIL PROTECTED]
Sent: March 6, 2008 09:08 PM
To: [EMAIL PROTECTED]
Subject: [R] Finding Interaction and main effects contrasts
for two-way ANOVA
I've tried without success to calculate interaction and main effects
contrasts using R. I've found the functions C(), contrasts(),
se.contrasts() and fit.contrasts() in package gmodels. Given the url
for a small dataset and the two-way anova model below, I'd like to
reproduce the results from appended SAS code. Thanks. --Dale.
## the dataset (from Montgomery)
twoway - read.table(http://dsteele.veryspeedy.net/sta501/twoway.txt;,
col.names=c('material', 'temp','voltage'),colClasses=c('factor',
'factor', 'numeric'))
## the model
fit - aov(voltage ~ material*temp, data=twoway)
/* SAS code */
proc glm data=twoway;
class material temp;
model voltage = material temp material*temp;
contrast '21-22-31+32' material*temp 0 0 0 1 -1 0 -1 1 0;
estimate '21-22-31+32' material*temp 0 0 0 1 -1 0 -1 1 0;
contrast 'material1-material2' material 1 -1 0;
estimate 'material1-material2' material 1 -1 0;
contrast 'temp50 - temp80' temp 1 0 -1;
estimate 'temp50 - temp80' temp 1 0 -1;
run;
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[R] Summary: Reorder data frame columns by negating list of names
Thank you all,
All responses worked and focused on the use of combining the desired
column names (or numbers in Barry's solution) with variations of
'match(x, table)' and 'x %in% table' to generate the remaining column
names (numbers).
xxx - data.frame(matrix(1:40, ncol=8))
names(xxx) - letters[1:8]
# Common to all
ind - c('b', 'd', 'h')
xxx[, c(ind, yyy)] # where c(ind, yyy) was:
# Jim Holtman
c(ind, setdiff(names(xxx), ind))
[1] b d h a c e f g
# Dimitris Rizopoulos
c(ind, names(xxx)[!names(xxx) %in% ind])
[1] b d h a c e f g
# Barry Rowlingson
c(match(ind, names(xxx)), (1:dim(xxx)[2])[-match(ind, names(xxx))])
[1] 2 4 8 1 3 5 6 7
Thanks again, DaveT.
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ofri.mnr.gov.on.ca
*
- Original Message -
From: Thompson, David (MNR) [EMAIL PROTECTED]
To: r-help@r-project.org
Sent: Tuesday, February 12, 2008 6:19 PM
Subject: [R] Reorder data frame columns by negating list of names
Hello,
I would like to reorder columns in a data frame by their names as
demonstrated below:
Take this data frame:
xxx - data.frame(matrix(1:40, ncol=8))
names(xxx) - letters[1:8]
xxx
a b c d e f g h
1 1 6 11 16 21 26 31 36
2 2 7 12 17 22 27 32 37
3 3 8 13 18 23 28 33 38
4 4 9 14 19 24 29 34 39
5 5 10 15 20 25 30 35 40
and reorder the columns like this:
xxx[,c( c('b', 'd', 'h'), c('a', 'c', 'e', 'f', 'g') )]
b d h a c e f g
1 6 16 36 1 11 21 26 31
2 7 17 37 2 12 22 27 32
3 8 18 38 3 13 23 28 33
4 9 19 39 4 14 24 29 34
5 10 20 40 5 15 25 30 35
where I only have to name the columns that I'm interested in moving
to
the first few positions, something like:
xxx[,c( c('b', 'd', 'h'), -c('b', 'd', 'h') )]
Error in -c(b, d, h) : invalid argument to unary operator
Suggestions? and Thank you, DaveT.
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ofri.mnr.gov.on.ca
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[R] Reorder data frame columns by negating list of names
Hello,
I would like to reorder columns in a data frame by their names as
demonstrated below:
Take this data frame:
xxx - data.frame(matrix(1:40, ncol=8))
names(xxx) - letters[1:8]
xxx
a b c d e f g h
1 1 6 11 16 21 26 31 36
2 2 7 12 17 22 27 32 37
3 3 8 13 18 23 28 33 38
4 4 9 14 19 24 29 34 39
5 5 10 15 20 25 30 35 40
and reorder the columns like this:
xxx[,c( c('b', 'd', 'h'), c('a', 'c', 'e', 'f', 'g') )]
b d h a c e f g
1 6 16 36 1 11 21 26 31
2 7 17 37 2 12 22 27 32
3 8 18 38 3 13 23 28 33
4 9 19 39 4 14 24 29 34
5 10 20 40 5 15 25 30 35
where I only have to name the columns that I'm interested in moving to
the first few positions, something like:
xxx[,c( c('b', 'd', 'h'), -c('b', 'd', 'h') )]
Error in -c(b, d, h) : invalid argument to unary operator
Suggestions? and Thank you, DaveT.
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ofri.mnr.gov.on.ca
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Can I index a dataframe with a reference from/to a second dataframe?
Hello, I am unable to figure out how to code a new column in a data frame based on an existing column that matches a column in a reference data frame, in a relational-db fashion. I would like this to maintain a minimum set of reference tables that may be reused over several similar datasets. Specifically, I have two data frames as listed below, 'Bos' and 'tree.' For each case in 'Bos' I want to look up the matching 'spp' code in 'tree' and insert the associated 'type' code into a new 'type' column in 'Bos' as in: # add type and keep factors from reference list Bos$type - tree[as.character(tree$spp)==as.character(Bos$spp), 'type'] Bos$keep - tree[tree$spp==Bos$spp, 'keep'] And I know I have seen this before but, can't remember where. I have filtered through many of the threads referencing 'as.numeric(levels(Bos$spp))[as.integer(Bos$spp)]' handling of factors, any kind of sql reference I could think of, anything 'ODBC'-ish but, I think this may be an indexing issue. I am trying to compare elements of two different sized (list) objects (different type objects even?) and not cycling through Bos$spp to find matches in tree$spp as expected, . . . , has this an apply solution? My data frames: dput(head(Bos, 30)) structure(list(oplt = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), rplt = c(3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), tree = c(32, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129), spp = structure(c(10L, 10L, 12L, 14L, 10L, 10L, 14L, 10L, 15L, 10L, 9L, 3L, 10L, 10L, 12L, 10L, 13L, 12L, 12L, 10L, 12L, 10L, 10L, 8L, 5L, 2L, 10L, 2L, 12L, 10L), .Label = c(AW, BD, BE, BF, BW, BY, CB, HE, IW, MH, MR, OR, PO, SW, SA), class = factor), dbh = c(12.1, 10.1, 63.3, 9, 7.1, 12.1, 13.9, 6.3, 6.1, 7.9, 5.1, 9.8, 7.1, 18.7, 44.2, 28.7, 19.8, 28, 46.6, 9, 61.6, 3.3, 9.1, 8.7, 5.8, 3.1, 11.1, 12.3, 28, 8.6), cc = structure(c(2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L), .Label = c(dom, sup), class = factor), ba = c(114.990145103020, 80.1184666481737, 3147.0040469356, 63.6172512351933, 39.5919214168654, 114.990145103020, 151.746779150021, 31.1724531052447, 29.2246656600190, 49.0166993776348, 20.4282062299676, 75.429639612691, 39.5919214168654, 274.645883758454, 1534.38526793979, 646.924613208844, 307.907495978336, 615.7521601036, 1705.53923570736, 63.6172512351933, 2980.24045490142, 8.55298599939821, 65.0388219109427, 59.4467869875528, 26.4207942166902, 7.54767635024948, 96.7689077121996, 118.8228881404, 615.7521601036, 58.0880481648753 )), .Names = c(oplt, rplt, tree, spp, dbh, cc, ba), row.names = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 ), class = data.frame) dput(tree) structure(list(spp = structure(1:33, .Label = c(AB, AS, AW, BD, BE, BF, BW, BY, CA, CB, CC, CE, DL, DP, EA, HE, IW, LC, MH, MM, MR, OR, PO, PR, PV, PW, RS, SA, SB, SM, SW, VC, VL), class = factor), spp.orig = structure(c(1L, 3L, 4L, 5L, 6L, 7L, 8L, 9L, 12L, 10L, 13L, 11L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 21L, 22L, 23L, 24L, 25L, 26L, 27L, 28L, 31L, 29L, 30L, 32L, 33L, 34L ), .Label = c(AB, AMEHUM, AMESPP, AW, BD, BE, BF, BW, BY, CB, CE, CORALT, CORCOR, DIELON, DIRPAL, EA, HE, IW, LONCAN, MH, MM, MR, OR, PO, PR, PRUVIR, PW, RIBSPP, SB, SM, SORAME, SW, VIBACE, VIBALN), class = factor), OPL = structure(c(15L, 7L, 14L, 29L, 13L, 2L, 9L, 8L, 10L, 23L, 1L, 28L, 11L, 12L, 31L, 30L, 17L, 16L, 5L, 6L, 4L, 25L, 22L, 20L, 24L, 21L, 26L, 27L, 19L, 3L, 18L, 32L, 33L), .Label = c(HCORCAN, WABIBAL, WACEPEN, WACERUB, WACESAS, WACESPI, WAMESPP, WBETALL, WBETPAP, WCORALT, WDIELON, WDIRPAL, WFAGGRA, WFRAAME, WFRANIG, WLONCAN, WOSTVIR, WPICGLA, WPICMAR, WPINRES, WPINSTR, WPOPTRE, WPRUSER, WPRUVIV, WQUERUB, WRIBAME, WSORAME, WTHUOCC, WTILAME, WTSUCAN, WULMAME, WVIBACE, WVIBLAO), class = factor), form = c(1.1, 1.2, 1.1, 1.1, 1.1, 1.1, 1.1, 1.1, 1.2, 1.1, 2, 1.1, 1.2, 1.2, 1.1, 1.1, 1.1, 1.2, 1.1, 1.2, 1.1, 1.1, 1.1, 1.1, 1.2, 1.1, 1.2, 1.1, 1.1, 1.2, 1.1, 1.2, 1.2), Type = structure(c(2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c(H, W), class = factor), keep = structure(c(1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L), .Label = c(no, yes), class = factor), Sname = structure(c(15L, 6L, 14L, 29L, 13L, 1L, 8L, 7L, 9L, 23L, 10L, 28L, 11L, 12L, 31L, 30L, 17L, 16L, 4L, 5L, 3L, 25L, 22L, 20L, 24L, 21L, 26L, 27L, 19L, 2L,
Re: [R] Converting plots to ggplot2
Hello Hadley,
Thank you (and Domenico) for your help. I'm almost there.
For convenience, I'll restate the question.
With the following data:
a - seq(0, 360, 5)*pi/180 ; a
ac - sin(a + (45*pi/180)) + 1 ; ac
s - seq(5, 45, 10)*pi/180 ; s
asc - lapply(s, function(x) x*cos(ac) + x*sin(ac)) ; asc
I can generate my desired plot by traditional methods with:
plot(a, ac, type='l', xaxt = n, xlab='azimuth', ylab='index')
axis(1, at=seq(0,6,1), labels=round(seq(0,6,1)*180/pi),0)
abline(v=c(45*pi/180, 225*pi/180)) ; par(new=TRUE)
lapply(asc, function(x) {plot(a, x, type='l', xaxt = n,
yaxt = n, xlab='', ylab='', ylim=c(0, 2)) ; par(new=TRUE)})
With ggplot2 and your suggestions I can generate the same with:
p - qplot(a, ac, geom='line') + geom_line(aes(x=a, y=asc[[1]])) +
geom_line(aes(x=a, y=asc[[2]])) + geom_line(aes(x=a, y=asc[[3]])) +
geom_line(aes(x=a, y=asc[[4]])) + geom_line(aes(x=a, y=asc[[5]])) +
scale_x_continuous(name=azimuth) +
scale_y_continuous(name=index))
But these attempts to recreate the x-axis labels both generate the
following error:
p + scale_x_continuous(labels=round(seq(0,6,1)*180/pi,0))
p + scale_x_continuous(breaks=seq(0,6,1),
labels=round(seq(0,6,1)*180/pi,0))
Error in get(new, env = ScaleContinuous, inherits =
TRUE)(ScaleContinuous, :
unused argument(s) (labels = c(0, 57, 115, 172, 229, 286, 344))
And these attempts to draw reference lines both generate the following
error:
p + geom_vline(45*pi/180) + geom_vline(225*pi/180)
p + geom_vline(0.79) + geom_vline(3.9)
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 73, 1
What am I missing?
Thanx, DaveT.
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ofri.mnr.gov.on.ca
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[R] Converting plots to ggplot2
Hello Hadley,
I am trying to reproduce the following with ggplot:
a - seq(0, 360, 5)*pi/180 ; a
ac - sin(a + (45*pi/180)) + 1 ; ac
plot(a, ac, type='b', xaxt = n)
axis(1, at=seq(0,6,1), labels=round(seq(0,6,1)*180/pi),1)
abline(v=c(45*pi/180, 225*pi/180))
I can get the basic plot:
p - qplot(a, ac, geom=c('point', 'line')) ; p
but cannot seem to add the vertical reference lines:
# representing NE and SW compass points
p + geom_vline(intercept=45*pi/180)
p + geom_vline(intercept=225*pi/180)
nor find a reference to manipulating the axes labels
(still searching the news archives though).
Also, I would like to add additional curves to the same
plot with the sequence 'asc' generated by:
s - seq(5, 45, 10)*pi/180 ; s
asc - lapply(s, function(x) x*cos(ac) + x*sin(ac)) ; asc
Suggestions? Thanx, DaveT.
sessionInfo()
R version 2.6.1 (2007-11-26)
i386-pc-mingw32
locale:
LC_COLLATE=English_Canada.1252;LC_CTYPE=English_Canada.1252;
LC_MONETARY=English_Canada.1252;LC_NUMERIC=C;
LC_TIME=English_Canada.1252
attached base packages:
[1] datasets tcltk utils stats graphics grDevices splines
grid
[9] methods base
other attached packages:
[1] svGUI_0.9-5svViews_0.9-5 svIO_0.9-5
svMisc_0.9-5
[5] R2HTML_1.58ggplot2_0.5.2 RColorBrewer_0.2-3
MASS_7.2-34
[9] proto_0.3-7reshape_0.7.4
loaded via a namespace (and not attached):
[1] lattice_0.14-17
Sys.info()[c(1:3,5)]
sysname release
Windows NT 5.1
version machine
(build 2600) Service Pack 2 x86
*
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[EMAIL PROTECTED]
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[R] Solution: Available environment variables
Thank you Duncan (additional comments below),
-Original Message-
From: Duncan Murdoch [mailto:[EMAIL PROTECTED]
Sent: December 20, 2007 02:36 PM
To: Thompson, David (MNR)
Cc: r-help@r-project.org
Subject: Re: [R] Available environment variables
On 20/12/2007 2:13 PM, Thompson, David (MNR) wrote:
Hello,
I am trying to set my environment to streamline the downloading /
updating of packages. I have been through R-intro.html (10.8
Customizing-the-environment), R-FAQ (5.2 How can add-on packages be
installed?), rw-FAQ, and help pages for Sys.setenv {base},
download.packages {utils}, etc.,.
I am looking for something similar to the download.packages destdir
argument on a global environment level, e.g., destdir - 'C:/Program
Files/_dave/stats/R/library/_download' in Rprofile.site. Any
suggestions?
You could create your own function:
download.packages - function(pkgs, destdir='C:/Program
Files/_dave/stats/R/library/_download', ...)
utils::download.packages(pkgs, destdir, ...)
Also, in a more general context, is there a way of listing all
available
(or common, or default, or standard, . . .) environment variables?
Sys.getenv() will return a list of the ones that are currently defined.
I would like to know if there is an existing convention for any
arbitrary
process that I may try to do without reinventing the wheel. This same
question could apply to options() other than those included with a
standard installation.
I don't know what you mean about an arbitrary process.
For options(), you could save the names that you consider standard
(e.g.
by starting an empty session and entering standardoptions -
names(options()), then at a later time do
newoptions - names(options())
newoptions[ !(newoptions %in% standardoptions) ]
There's no easy way to know the options that would mean something in
the
current context but are not currently defined.
Duncan Murdoch
Creating a local copy of the function with alternate argument defaults
works perfectly. I have done that in the past, don't know why I didn't
think of it this time. Thank you.
Saving initial- and post-session options (or their names) also nicely
addresses part of my concern. Thank you.
I am familiar with Sys.getenv() and was asking about potential
environment variables that are NOT currently defined. However, while
trying to rephrase my question, having reread the Startup {base} help
and related documentation, could not clearly refine the issue in my own
mind so, I am now content with the situation.
I think that I may be confusing the intended use of environment files
and profile files as noted in the details section of the Startup {base}
documentation. Part of my concern is to find a way of safeguarding
against my own errors and typos that may 'break the system' or having
something installed later (the arbitrary process part) breaking my
current setup. Also, I may be thinking of the startup process as
something 'different' from the interactive R session processing, which I
am beginning to see it is not.
Thanks again, DaveT.
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ofri.mnr.gov.on.ca
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Re: [R] str() options
Beautiful!
Exactly what I was looking for.
Thank you, Gabor
-Original Message-
From: Gabor Grothendieck [mailto:[EMAIL PROTECTED]
Sent: November 27, 2007 05:02 PM
To: Thompson, David (MNR)
Subject: Re: [R] str() options
On Nov 27, 2007 1:55 PM, Thompson, David (MNR)
[EMAIL PROTECTED] wrote:
Hello,
Is there a way to have str() and ls.str() return all factor levels?
str is an S3 generic so you can define your own str.factor. Here
we show the usual str and then show it again after we have
added our own str.factor:
str(iris)
'data.frame': 150 obs. of 5 variables:
$ Sepal.Length: num 5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
$ Sepal.Width : num 3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
$ Petal.Length: num 1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
$ Petal.Width : num 0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
$ Species : Factor w/ 3 levels setosa,versicolor,..: 1 1 1 1
1 1 1 1 1 1 ...
str.factor - function(object, ...) {
+ cat(factor w/, nlevels(object), levels, levels(object), \n)
+ }
str(iris)
'data.frame': 150 obs. of 5 variables:
$ Sepal.Length: num 5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
$ Sepal.Width : num 3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
$ Petal.Length: num 1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
$ Petal.Width : num 0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
$ Species :factor w/ 3 levels setosa versicolor virginica
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ofri.mnr.gov.on.ca
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[R] Summary: Process multiple columns of data.frame
Thank you Jim Holtman and Mark Leeds for your help.
Original question:
How do I do the following more concisely?
Bout[is.na(Bout$bd.n), 'bd.n'] - 0
Bout[is.na(Bout$ht.n), 'ht.n'] - 0
Bout[is.na(Bout$dbh.n), 'dbh.n'] - 0
. . .
Solution:
for (i in c('bd.n', 'ht.n', 'dbh.n')) Bout[is.na(Bout[[i]]), i] - 0
Toy example:
df.0 - as.data.frame( cbind(
+ c1=c(NA, NA, 10, NA, 15, 11, 12, 14, 14, 11),
+ c2=c(13, NA, 16, 16, NA, 12, 14, 19, 18, NA),
+ c3=c(NA, NA, 11, 19, 17, NA, 11, 16, 20, 13),
+ c4=c(20, NA, 15, 11, NA, 15, NA, 13, 14, 15),
+ c5=c(14, NA, 13, 16, 17, 17, 16, NA, 15, NA),
+ c6=c(NA, NA, 13, 11, NA, 16, 15, 12, NA, 20)) )
df.1 - df.0
for (i in c('c2', 'c3', 'c4')) df.1[is.na(df.1[[i]]), i] - 0
df.0
c1 c2 c3 c4 c5 c6
1 NA 13 NA 20 14 NA
2 NA NA NA NA NA NA
3 10 16 11 15 13 13
4 NA 16 19 11 16 11
5 15 NA 17 NA 17 NA
6 11 12 NA 15 17 16
7 12 14 11 NA 16 15
8 14 19 16 13 NA 12
9 14 18 20 14 15 NA
10 11 NA 13 15 NA 20
df.1
c1 c2 c3 c4 c5 c6
1 NA 13 0 20 14 NA
2 NA 0 0 0 NA NA
3 10 16 11 15 13 13
4 NA 16 19 11 16 11
5 15 0 17 0 17 NA
6 11 12 0 15 17 16
7 12 14 11 0 16 15
8 14 19 16 13 NA 12
9 14 18 20 14 15 NA
10 11 0 13 15 NA 20
Thank you, DaveT.
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ofri.mnr.gov.on.ca
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Re: [R] Process multiple columns of data.frame
I did specify only the three columns of interest
c('bd.n','ht.n','dbh.n')
as the second (column) index, and I did superficially check the results
which turned out as I had hoped. Only the three columns listed were
changed and existing values _in_ those columns were retained.
So, I appear to be on my way again.
Thanx again, DaveT.
*
-Original Message-
From: jim holtman [mailto:[EMAIL PROTECTED]
Sent: November 20, 2007 04:21 PM
To: Thompson, David (MNR)
Cc: r-help@r-project.org
Subject: Re: [R] Process multiple columns of data.frame
The problem with that solution is that if any of the columns in a row
has an NA in it, then all the columns of that row will be set to zero.
Is the what you want, or do you only want the specific entries set to
0?
On Nov 20, 2007 4:07 PM, Thompson, David (MNR)
[EMAIL PROTECTED] wrote:
Jim,
What I'm getting at is my lack of understanding when manipulating
data frame indices. I have tried something like your matrix example
with variants of: Bout[
is.na(Bout[,c('bd.n','ht.n','dbh.n')]), ] - 0
only to receive the following error message:
Error in `[-.data.frame`(`*tmp*`, is.na(Bout[, c(bd.n, ht.n,
dbh.n)]), :
non-existent rows not allowed
My questions were not focussed on the assignment value but,
on the selection of multiple columns (of a single type) to process.
Which is what I meant by concisely.
And, lo and behold, in my attempts to reframe my questions I
(finally)
came upon a solution:
Bout[is.na(Bout$bd.n) | is.na(Bout$ht.n) | is.na(Bout$dbh.n),
c('bd.n','ht.n','dbh.n')] - 0
Thank you for your time, DaveT.
*
-Original Message-
From: jim holtman [mailto:[EMAIL PROTECTED]
Sent: November 20, 2007 02:25 PM
To: Thompson, David (MNR)
Cc: r-help@r-project.org
Subject: Re: [R] Process multiple columns of data.frame
It really depends on what you want to set the values that
contain NAs
to for the various type of the columns. Do you always want numerics
=0, characters =, and factors =whatever? Do you want to
do this for
all the columns in a dataframe? If you want to it for all
the columns
in a matrix, it is easy, since all are the same type, and you are
setting them to zero (e.g., yourMatrix[is.na(yourMatrix)] - 0).
You can always write a function that can take in the names of the
columns and then depending on their types set the corresponding
values. So it depends on what you mean by concisely and how often
you want to do it.
On Nov 20, 2007 12:27 PM, Thompson, David (MNR)
[EMAIL PROTECTED] wrote:
Hello,
How do I do the following more concisely?
Bout[is.na(Bout$bd.n), 'bd.n'] - 0
Bout[is.na(Bout$ht.n), 'ht.n'] - 0
Bout[is.na(Bout$dbh.n), 'dbh.n'] - 0
Would the form of such a command be different
between numeric, character and factor columns?
. . . between data.frames and matrices?
Thanx, DaveT.
*
Silviculture Data Analyst
Ontario Forest Research Institute
Ontario Ministry of Natural Resources
[EMAIL PROTECTED]
http://ofri.mnr.gov.on.ca
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
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