date:20160827

Re: [R] parsing a complex file

2016-08-27 Thread jim holtman

It is not clear as to how you want to parse the file.  You need to at least
provide an example of what you expect from the output.  You mention " the
detail which begins with 2 at byte location 1 to another file"; I don't see
the '2' at byte location 1.


Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.

On Sat, Aug 27, 2016 at 4:56 PM, Glenn Schultz  wrote:

> All,
>
> I have a complex file I would like to parse in R a sample is described
> below
>
> The header is 1:200 and the detail is 1 to 200.  I have written code to
> parse the file so far.  As follows:
>
> numchar <- nchar(x = data, type = "chars")
> start <- c(seq(1, numchar, 398))
> end <- c(seq(398, numchar, 398))
> quartile <- NULL
> final <- str_sub(data, start[1:length(start)], end[1:length(end)])
> quartile <- append(quartile, final)
> write(quartile, Result)
> data2 <- readLines(Result)
>
> The function gets me to data2.  All is well so far. However, I need to
> send the header which begins with 1 at byte location 1 to a file and the
> detail which begins with 2 at byte location 1 to another file.  When I look
> at data2 in RStudio  I see the following.  The file is 185 meg, I have the
> lines but I am stuck as to the next step.  Any ideas are appreciated.
>
> Glenn
>
>
> dput of the data
>
> "1176552 CL20031031367RBV319920901
>
>
>  217655208875{08875{08875{08875{08875{08875{22D22D22D22D22D2
> 2D13C13C13C13C13C13C604000{604000{604000{
> 604000{604000{604000{36{36{36{36{36{36{
> 08500{08500{08500{08500{08500{08500{1254240 CL20031031371KLV120020201
>
>
>  225424007484{07250{07375{07500{07625{08625{33F06H33H33I34{
> 34A02A01I02{02{02A03B0001121957C123500{92{
> 000128{0001741000{0003849000{35I30{36{36{36{36{
> 07000{07000{07000{07000{07000{07000{1254253 CL20031031371KMA620020301
>
>
>  225425306715{06250{06500{06750{06875{07000{33C23G33C33I34{
> 34A02{01I02{02{02A02C946646A35{85{
> 000103{0001205000{000130{35H30{36{36{36{36{
> 06000{06000{06000{06000{06000{06000{1259455 CL20031031371RE4420020501
>
>
>  225945507045{06750{06875{07000{07250{07375{34{28B34A34B34B3
> 4C01H01G01H01H01H02C93E36{765000{
> 995000{0001384000{0002184000{35I30{36{36{36{36{
> 06500{06500{06500{06500{06500{06500{1261060 CI20031031371S5V219940101
>
>
>  226106006637{06500{06500{06625{06750{06875{05B00C04H05I06B0
> 6B11H11G11G11H11H11I0001169090I65{95{
> 000125{0001328000{000190{18{18{18{18{18{18{
> 06000{06000{06000{06000{06000{06000{1335271 CI20031031375HMU519960101
>
>
>  233527107500{07500{07500{07500{07500{07500{08B06B08E08F08F0
> 8F09D09D09D09D09E09E717375{464000{55{
> 77{0001085500{0001085500{18{18{18{18{18{18{
> 07000{07000{07000{07000{07000{07000{1440840 CL20031031380HV9519981101
>
>
>  244084006707{06500{06625{06750{06875{06875{27D03C28C29H30{
> 30A06{05I06{06{06{06A615172I25{6
> 21000{673000{75{791000{36{36{36{36{36{36{
> 06000{06000{06000{06000{06000{06000{1521993 CI20031031384E3A62101
>
>
>  252199306937{06875{06875{06875{07000{07000{12H02H12H13{13D1
> 3E04E04E04E04E04F04F0001129428F70{955000{0001000
> 000{0002087000{0002087000{18{18{18{18{18{18{06500{06500{
> 06500{06500{06500{06500{1538080 CL20031031384YXH42501
>
>
>  253808008875{08875{08875{08875{08875{08875{31I31I31I31I31I3
> 1I04A04A04A04A04A04A0001419300{0001419300{0001419300{
> 0001419300{0001419300{0001419300{36{36{36{36{36{36{
> 07000{07000{07000{07000{07000{07000{1659123 CI20031031390XG8720020801
>
>
>  265912306909{06750{06750{06875{07000{07125{16E15I16C16E16F1
> 6F01E01D01D01E01E01G998541G162000{792000{
> 0001156500{000160{000199{18{18{18{18{18{18{
> 06000{06000{06000{06000{06000{06000{"
>
>
> dput data2
> c("1176552 CL20031031367RBV319920901 217655208875{08875{08875{08875
> {08875{08875{22D22D22D22D22D22D13C13C13C13C13C13C604000{
> 604000{604000{604000{604000{604000{36{36{36{36{36{36{
> 08500{08500{08500{08500{08500{08500{", "1254240 CL20031031371KLV120020201
> 225424007484{07250{07375{07500{07625{08625{33F06H33H33I34{
> 34A02A01I02{02{02A03B0001121957C123500{92{
> 000128{0001741000{0003849000{35I30{36{36{36{36{
> 07000{07000{07000{07000{07000{07000{", "1254253 CL20031031371KMA620020301
> 225425306715{06250{06500{06750{06875{07000{33C23G33C33I34{
> 34A02{01I02{02{02A02C946646A35{85{
> 000103{0001205000{000130{35H30{36{36{36{36{
> 06000{06000{06000{06000{06000{06000{", "1259455 CL20031031371RE4420020501
> 225945507045{06750{06875{07000{07250{07375{34{28B34A34B34B34
> C01H01G01H01H01H02C93E36{765000{995000{0001384000{
> 0002184000{35I30{36{36{36{36{06500{06500{06500{06500{06500{06500{",
> "1261060 CI20031031371S5V219940101

[R] parsing a complex file

2016-08-27 Thread Glenn Schultz


All,

I have a complex file I would like to parse in R a sample is described below

The header is 1:200 and the detail is 1 to 200.  I have written code to parse 
the file so far.  As follows:

numchar <- nchar(x = data, type = "chars")
start <- c(seq(1, numchar, 398))
end <- c(seq(398, numchar, 398))
quartile <- NULL
final <- str_sub(data, start[1:length(start)], end[1:length(end)])
quartile <- append(quartile, final)
write(quartile, Result)
data2 <- readLines(Result)

The function gets me to data2.  All is well so far. However, I need to send the 
header which begins with 1 at byte location 1 to a file and the detail which 
begins with 2 at byte location 1 to another file.  When I look at data2 in 
RStudio  I see the following.  The file is 185 meg, I have the lines but I am 
stuck as to the next step.  Any ideas are appreciated.

Glenn


dput of the data

"1176552 CL20031031367RBV319920901                                                   
                                                                                          
                         
217655208875{08875{08875{08875{08875{08875{22D22D22D22D22D22D13C13C13C13C13C13C604000{604000{604000{604000{604000{604000{36{36{36{36{36{36{08500{08500{08500{08500{08500{08500{1254240
 CL20031031371KLV120020201                                                                
                                                                                          
            
225424007484{07250{07375{07500{07625{08625{33F06H33H33I34{34A02A01I02{02{02A03B0001121957C123500{92{000128{0001741000{0003849000{35I30{36{36{36{36{07000{07000{07000{07000{07000{07000{1254253
 CL20031031371KMA620020301                                                                
                                                                                          
            
225425306715{06250{06500{06750{06875{07000{33C23G33C33I34{34A02{01I02{02{02A02C946646A35{85{000103{0001205000{000130{35H30{36{36{36{36{06000{06000{06000{06000{06000{06000{1259455
 CL20031031371RE4420020501                                                                
                                                                                          
            
225945507045{06750{06875{07000{07250{07375{34{28B34A34B34B34C01H01G01H01H01H02C93E36{765000{995000{0001384000{0002184000{35I30{36{36{36{36{06500{06500{06500{06500{06500{06500{1261060
 CI20031031371S5V219940101                                                                
                                                                                          
            
226106006637{06500{06500{06625{06750{06875{05B00C04H05I06B06B11H11G11G11H11H11I0001169090I65{95{000125{0001328000{000190{18{18{18{18{18{18{06000{06000{06000{06000{06000{06000{1335271
 CI20031031375HMU519960101                                                                
                                                                                          
            
233527107500{07500{07500{07500{07500{07500{08B06B08E08F08F08F09D09D09D09D09E09E717375{464000{55{77{0001085500{0001085500{18{18{18{18{18{18{07000{07000{07000{07000{07000{07000{1440840
 CL20031031380HV9519981101                                                                
                                                                                          
            
244084006707{06500{06625{06750{06875{06875{27D03C28C29H30{30A06{05I06{06{06{06A615172I25{621000{673000{75{791000{36{36{36{36{36{36{06000{06000{06000{06000{06000{06000{1521993
 CI20031031384E3A62101                                                                
                                                                                          
            
252199306937{06875{06875{06875{07000{07000{12H02H12H13{13D13E04E04E04E04E04F04F0001129428F70{955000{000100{0002087000{0002087000{18{18{18{18{18{18{06500{06500{06500{06500{06500{06500{1538080
 CL20031031384YXH42501                                                                
                                                                                          
            
253808008875{08875{08875{08875{08875{08875{31I31I31I31I31I31I04A04A04A04A04A04A0001419300{0001419300{0001419300{0001419300{0001419300{0001419300{36{36{36{36{36{36{07000{07000{07000{07000{07000{07000{1659123
 CI20031031390XG8720020801                                                                
                                                                                          
            
265912306909{06750{06750{06875{07000{07125{16E15I16C16E16F16F01E01D01D01E01E01G998541G162000{792000{0001156500{000160{000199{18{18{18{18{18{18{06000{06000{06000{06000{06000{06000{"


dput data2
c("1176552 CL20031031367RBV319920901

Re: [R] Labelling interaction axes of a nomogram using rms

2016-08-27 Thread Leonardo Guizzetti

Hi David,

As suggested, here is some example code adapted from the example of the
nomogram() from the rms package.  You'll notice that variable labels are
not being applied to main effects or interaction terms.

Leonardo

rm(list = ls())
# Import libraries
require(Hmisc)
require(rms)

set.seed(12345)
n <- 1000 # define sample size
age <- rnorm(n, 0, 10)
sbp <- rnorm(n, 120, 15)
sex <- factor(sample(c(0,1), n, TRUE), levels=c(0,1),
labels=c('female','male'))
# Specify population model for log odds that Y=1
L <- 0.5*(sex=="male") + 0.01*age + 0.12*sbp + 0.02*sbp*age + rnorm(n, 0,
10)
# Simulate binary y to have Prob(y=1) = 1/[1+exp(-L)]
y <- ifelse(runif(n) < plogis(L), 1, 0)

# Create a dataframe and apply nice labels to each variable.
mydata <- data.frame(age, sbp, sex, y)
var.labels <- c(age = "Patient Age - 50 years",
sbp = "Systolic blood pressure",
sex = "Sex",
y = "Outcome")
label(mydata) = lapply(names(var.labels),
   function(x) label(mydata[,x]) <- var.labels[x])
label(mydata) # show the labels.

# Fit a model
ddist <- datadist(mydata)
options(datadist="ddist")
f <- rms::lrm(y ~ age*sbp + sex)
f
f$coefficients

# Create a nomogram.
nom <- nomogram(f, fun=plogis, lp=F, nint=10, maxscale=100,
interact = list( sbp=c(100,140,180) ),
fun.at=c(.01,.05,seq(.1,.9,by=.1),.95,.99),
funlabel="Risk of Death", vnames="labels")
plot(nom)

# end
options(datadist=NULL)

On Fri, Aug 26, 2016 at 10:35 PM, David Winsemius 
wrote:

>
> > On Aug 26, 2016, at 11:53 AM, Leonardo Guizzetti <
> leonardo.guizze...@gmail.com> wrote:
> >
> > Good afternoon,
> >
> > I have tried searching and have hit a wall with my own trial and error. I
> > have been able to use "nice" labels for non-interacted variables by
> setting
> > them using Newlabels(), but I am unable to do so for the interaction
> terms
> > following a fit.
> >
> > Can you please offer a suggestion?
>
> My suggestion is that you post a minimal example.
>
> --
> David.
> >
> > Kind regards,
> > Leonardo
> >
> >   [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>
> David Winsemius
> Alameda, CA, USA
>
>

[[alternative HTML version deleted]]

__
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Importint stata file and using value labels

2016-08-27 Thread Robert Baer

There has been some good advice not to lose the labels, but perhaps this 
gets you where you seem determined to go?


?read.dta

read.dta(file, convert.dates = TRUE, convert.factors = TRUE,
 missing.type = FALSE,
 convert.underscore = FALSE, warn.missing.labels = TRUE)

or

library(readstata13)

?read.dta13

read.dta13(file, convert.factors = TRUE, generate.factors = FALSE,
  encoding = NULL, fromEncoding = NULL, convert.underscore = FALSE,
  missing.type = FALSE, convert.dates = TRUE, replace.strl = FALSE,
  add.rownames = FALSE, nonint.factors = FALSE)

Perhaps the convert. factors setting at FALSE?


On 08/27/2016 10:55 AM, Michael Friendly wrote:

On 8/26/2016 11:05 AM, Juan Ceccarelli Arias wrote:

Yep. Im a bit stalled.
I can't find the option to import only the values and drop the value 
labels

from the dta file.
Im quite sure R can do that. Then i'd only used the values and i'd 
rely on

my memory.
It isn't a bad alternative.



Hint: use str() to see the class of what you've read.
Then try as.data.frame() on the resulting object read from the .dta file.




__
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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] Leaflet package error while adding Polygons

2016-08-27 Thread Duncan Murdoch


On 26/08/2016 9:20 PM, Jaya Krishnan wrote:

Hi,

I'm trying to use leaflet for web-mapping. While trying to add polygons, I
get this error

Error in `*tmp*`$x : $ operator is invalid for atomic vectors
Any help is appreciated.


You need to post what you did if you want help.  Avoiding HTML is also a 
recommendation of the posting guide (see the footer for the URL).


Duncan Murdoch


Thanks,

Jaya



[[alternative HTML version deleted]]

__
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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 -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

[R] Leaflet package error while adding Polygons

2016-08-27 Thread Jaya Krishnan

Hi,

I'm trying to use leaflet for web-mapping. While trying to add polygons, I
get this error

Error in `*tmp*`$x : $ operator is invalid for atomic vectors
Any help is appreciated.
Thanks,

Jaya



[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Importint stata file and using value labels

2016-08-27 Thread Michael Friendly


On 8/26/2016 11:05 AM, Juan Ceccarelli Arias wrote:

Yep. Im a bit stalled.
I can't find the option to import only the values and drop the value labels
from the dta file.
Im quite sure R can do that. Then i'd only used the values and i'd rely on
my memory.
It isn't a bad alternative.



Hint: use str() to see the class of what you've read.
Then try as.data.frame() on the resulting object read from the .dta file.


--
Michael Friendly Email: friendly AT yorku DOT ca
Professor, Psychology Dept. & Chair, Quantitative Methods
York University  Voice: 416 736-2100 x66249 Fax: 416 736-5814
4700 Keele StreetWeb:   http://www.datavis.ca
Toronto, ONT  M3J 1P3 CANADA

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R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Hickman models with two binary dependent variables in R

2016-08-27 Thread Faradj Koliev

Dear Arne, 

Many thanks for this, 

It actually worked with heckit() command as well, do I need to use selection()? 

Also, I would be really grateful if you can suggest a package that would allow 
for estimation of heckman models with two ordered variables (0-1-2). Can 
sampleSelection handle this? 

Warm regards, 
Faradj 

> 27 aug. 2016 kl. 10:39 skrev Arne Henningsen :
> 
> See also:
> 
> http://r-forge.r-project.org/forum/forum.php?thread_id=31866_id=844_id=256
> 
> 
> 
> On 26 August 2016 at 16:11, PIKAL Petr  wrote:
>> Hi
>> 
>> See in line
>> 
>>> -Original Message-
>>> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Faradj
>>> Koliev
>>> Sent: Thursday, August 25, 2016 12:32 PM
>>> To: r-help@r-project.org
>>> Subject: [R] Hickman models with two binary dependent variables in R
>>> 
>>> Hi everyone,
>>> 
>>> How do I run Heckman models in R with two binary dependent variables?
>>> 
>>> sampleSelection package in R works with standard heckman models ( binary
>>> DV for the selection equation and continuous DV for the outcome equation).
>>> In my case dependent variables are both binary (actually ordered but I 
>>> didn’t
>>> find anything on that)
>> 
>> From help page
>> 
>> The endogenous variable of the argument 'selection' must have exactly two 
>> levels (e.g. 'FALSE' and 'TRUE', or '0' and '1'). By default the levels are 
>> sorted in increasing order ('FALSE' is before 'TRUE', and '0' is before 
>> '1'). This also applies for the binary outcome equation. For 
>> continuous-oucome cases, the dependent variable(s) should be numeric.
>> 
>> seems to me that both equatio0ns can have binary values.
>> 
>> 
>>> 
>>> So using sampleSelection package one could do this by running:
>>> 
>>> SelectionEquation <- binaryDV1 ~ x1+x2+x3+x4
>>> 
>>> OutcomeEquation <-  binaryDV2~o7+x1+x4+x5
>>> 
>>> HeckmanModel <- heckit(SelectionEquation,OutcomeEquation,
>>> data=mydata, method="2step")
>>> 
>>> 
>>> The problem is that heckit() doesn’t work here. I think in STATA one could
>> 
>> What does it mean. Be more specific.
>> 
>> And provide some data (preferably by dput).
>> Or at least result of str(yourdata) to show that they are appropriate to the 
>> function.
>> And do not post in HTML.
>> 
>> Cheers
>> Petr
>> 
>>> use heckprob command for this. Anyone who knows more than me?
>>> 
>>> Thanks!
>>> 
>>> 
>>> 
>>> 
>>> 
>>>  [[alternative HTML version deleted]]
>>> 
>>> __
>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/posting-
>>> guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>> 
>> 
>> Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou 
>> určeny pouze jeho adresátům.
>> Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně 
>> jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze 
>> svého systému.
>> Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email 
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Re: [R] Hickman models with two binary dependent variables in R

2016-08-27 Thread Arne Henningsen

See also:

http://r-forge.r-project.org/forum/forum.php?thread_id=31866_id=844_id=256



On 26 August 2016 at 16:11, PIKAL Petr  wrote:
> Hi
>
> See in line
>
>> -Original Message-
>> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Faradj
>> Koliev
>> Sent: Thursday, August 25, 2016 12:32 PM
>> To: r-help@r-project.org
>> Subject: [R] Hickman models with two binary dependent variables in R
>>
>> Hi everyone,
>>
>> How do I run Heckman models in R with two binary dependent variables?
>>
>> sampleSelection package in R works with standard heckman models ( binary
>> DV for the selection equation and continuous DV for the outcome equation).
>> In my case dependent variables are both binary (actually ordered but I didn’t
>> find anything on that)
>
> From help page
>
> The endogenous variable of the argument 'selection' must have exactly two 
> levels (e.g. 'FALSE' and 'TRUE', or '0' and '1'). By default the levels are 
> sorted in increasing order ('FALSE' is before 'TRUE', and '0' is before '1'). 
> This also applies for the binary outcome equation. For continuous-oucome 
> cases, the dependent variable(s) should be numeric.
>
> seems to me that both equatio0ns can have binary values.
>
>
>>
>> So using sampleSelection package one could do this by running:
>>
>> SelectionEquation <- binaryDV1 ~ x1+x2+x3+x4
>>
>> OutcomeEquation <-  binaryDV2~o7+x1+x4+x5
>>
>> HeckmanModel <- heckit(SelectionEquation,OutcomeEquation,
>> data=mydata, method="2step")
>>
>>
>> The problem is that heckit() doesn’t work here. I think in STATA one could
>
> What does it mean. Be more specific.
>
> And provide some data (preferably by dput).
> Or at least result of str(yourdata) to show that they are appropriate to the 
> function.
> And do not post in HTML.
>
> Cheers
> Petr
>
>> use heckprob command for this. Anyone who knows more than me?
>>
>> Thanks!
>>
>>
>>
>>
>>
>>   [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-
>> guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> 
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> jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat.
> Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či 
> zpožděním přenosu e-mailu.
>
> V případě, že je tento e-mail součástí obchodního jednání:
> - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, 
> a to z jakéhokoliv důvodu i bez uvedení důvodu.
> - a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; 
> Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany 
> příjemce s dodatkem či odchylkou.
> - trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným 
> dosažením shody na všech jejích náležitostech.
> - odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost 
> žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně 
> pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu 
> případně osobě, kterou adresát zastupuje, předloženy nebo jejich existence je 
> adresátovi či osobě jím zastoupené známá.
>
> This e-mail and any documents attached to it may be confidential and are 
> intended only for its intended recipients.
> If you received this e-mail by mistake, please immediately inform its sender. 
> Delete the contents of this e-mail with all attachments and its copies from 
> your system.
> If you are not the intended recipient of this e-mail, you are not authorized 
> to use, disseminate, copy or disclose this e-mail in any manner.
> The sender of this e-mail shall not be liable for any possible damage caused 
> by modifications of the e-mail or by delay with transfer of the email.
>
> In case that this e-mail forms part of business dealings:
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