Re: [R] speed up a function

Santiago Guallar Mon, 15 Jul 2013 07:33:19 -0700

Dear Petr,

Sorry for the delay. I've been out.
Unfortunately, your code doesn't work either even when usingÂ fromLast = T.
Thank you for your help and your time.


Santi



>________________________________
> From: PIKAL Petr <petr.pi...@precheza.cz>
>To: Santiago Guallar <sgual...@yahoo.com> 
>Cc: r-help <r-help@r-project.org> 
>Sent: Wednesday, July 10, 2013 8:35 AM
>Subject: RE: [R] spped up a function
> 
>
>
> 
>Hi Santiago
>Â 
>Keep conversation in list. Others can have better ideas.
>Â 
>I am still messing the reasoning
>Â 
>Merge seems to me the solution but I am lost in your resoning what to keep and 
>what to discard from resulting object.
>Â 
>After merge I have this
>Â 
>result <- structure(list(Ring = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L,
>1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
>1L), .Label = c("6106933", "6134701", "6140497", "6140719", "6140756",
>"6140855", "6143070", "6143090", "6143093", "6175711", "6175726",
>"6175730", "6175769", "6175776", "6175784", "6188609", "6188705",
>"6195159", "6195171", "6198153", "6198154", "6198156", "6198157",
>"6198172"), class = "factor"), jul = c(15135, 15135, 15135, 15135,
>15135, 15135, 15135, 15135, 15135, 15135, 15135, 15135, 15135,
>15135, 15135, 15135, 15135, 15135, 15135, 15135, 15135, 15135,
>15135, 15135), timepos = structure(c(1307680575, 1307680740,
>1307681040, 1307681340, 1307681640, 1307681940, 1307682240, 1307682540,
>1307682780, 1307683080, 1307683380, 1307683680, 1307683980, 1307684280,
>1307684397, 1307684424, 1307684484, 1307684490, 1307684580, 1307684880,
>1307685180, 1307685243, 1307685321, 1307685336), class = c("POSIXct",
>"POSIXt"), tzone = "GMT"), act = c(3822L, NA, NA, NA, NA, NA,
>NA, NA, NA, NA, NA, NA, NA, NA, 27L, 60L, 6L, 753L, NA, NA, NA,
>78L, 15L, 18L), wd = c("dry", NA, NA, NA, NA, NA, NA, NA, NA,
>NA, NA, NA, NA, NA, "wet", "dry", "wet", "dry", NA, NA, NA, "wet",
>"dry", "wet")), .Names = c("Ring", "jul", "timepos", "act", "wd"
>), row.names = c(NA, -24L), class = "data.frame")
>Â 
>> result
>Â Â Â Â Â  RingÂ Â  julÂ Â Â Â Â Â Â Â Â Â Â Â  timeposÂ  actÂ Â  wd
>1Â  6106933 15135 2011-06-10 04:36:15 3822Â  dry
>2Â  6106933 15135 2011-06-10 04:39:00Â Â  NA <NA>
>3Â  6106933 15135 2011-06-10 04:44:00Â Â  NA <NA>
>4Â  6106933 15135 2011-06-10 04:49:00Â Â  NA <NA>
>5Â  6106933 15135 2011-06-10 04:54:00Â Â  NA <NA>
>6Â  6106933 15135 2011-06-10 04:59:00Â Â  NA <NA>
>7Â  6106933 15135 2011-06-10 05:04:00Â Â  NA <NA>
>8Â  6106933 15135 2011-06-10 05:09:00Â Â  NA <NA>
>9Â  6106933 15135 2011-06-10 05:13:00Â Â  NA <NA>
>10 6106933 15135 2011-06-10 05:18:00Â Â  NA <NA>
>11 6106933 15135 2011-06-10 05:23:00Â Â  NA <NA>
>12 6106933 15135 2011-06-10 05:28:00Â Â  NA <NA>
>13 6106933 15135 2011-06-10 05:33:00Â Â  NA <NA>
>14 6106933 15135 2011-06-10 05:38:00Â Â  NA <NA>
>15 6106933 15135 2011-06-10 05:39:57Â Â  27Â  wet
>16 6106933 15135 2011-06-10 05:40:24Â Â  60Â  dry
>17 6106933 15135 2011-06-10 05:41:24Â Â Â  6Â  wet
>18 6106933 15135 2011-06-10 05:41:30Â  753Â  dry
>19 6106933 15135 2011-06-10 05:43:00Â Â  NA <NA>
>20 6106933 15135 2011-06-10 05:48:00Â Â  NA <NA>
>21 6106933 15135 2011-06-10 05:53:00Â Â  NA <NA>
>22 6106933 15135 2011-06-10 05:54:03Â Â  78Â  wet
>23 6106933 15135 2011-06-10 05:55:21Â Â  15 Â dry
>24 6106933 15135 2011-06-10 05:55:36Â Â  18Â  wet
>Â 
>I understand you want to keep only time values from GPL data.frame. OK this 
>can be done in the last step. But I am a bit lost in the logic for discarding 
>lines 15-18. Anyway, this can be what you want
>Â 
>library(zoo)
>result$wd<-na.locf(result$wd)
>final<-result[is.na(result$act),]
>> final
>Â Â Â Â Â  RingÂ Â  julÂ Â Â Â Â Â Â Â Â Â Â Â  timepos actÂ  wd
>2Â  6106933 15135 2011-06-10 04:39:00Â  NA dry
>3Â  6106933 15135 2011-06-10 04:44:00Â  NA dry
>4Â  6106933 15135 2011-06-10 04:49:00Â  NA dry
>5Â  6106933 15135 2011-06-10 04:54:00Â  NA dry
>6Â  6106933 15135 2011-06-10 04:59:00Â  NA dry
>7Â  6106933 15135 2011-06-10 05:04:00Â  NA dry
>8Â  6106933 15135 2011-06-10 05:09:00Â  NA dry
>9Â  6106933 15135 2011-06-10 05:13:00Â  NA dry
>10 6106933 15135 2011-06-10 05:18:00Â  NA dry
>11 6106933 15135 2011-06-10 05:23:00Â  NA dry
>12 6106933 15135 2011-06-10 05:28:00Â  NA dry
>13 6106933 15135 2011-06-10 05:33:00Â  NA dry
>14 6106933 15135 2011-06-10 05:38:00Â  NA dry
>19 6106933 15135 2011-06-10 05:43:00Â  NA dry
>20 6106933 15135 2011-06-10 05:48:00Â  NA dry
>21 6106933 15135 2011-06-10 05:53:00Â  NA dry
>> Â 
>Â 
>Regards
>Petr
>Â 
>From:Santiago Guallar [mailto:sgual...@yahoo.com] 
>Sent: Tuesday, July 09, 2013 10:02 PM
>To: PIKAL Petr
>Subject: Re: [R] spped up a function
>Â 
>Dear Petr,
>Â 
>I wanted the two data sets merged in such a way that the values of the 'wd' 
>vector (from the intervals t of 'xact') are assigned to the corresponding 
>intervals of 'GPS'. If there is more than one value (i.e if there is more than 
>one interval of 'xact' for the corresponding interval of 'GPS'), then take the 
>maximum (i.e. the value of the interval of 'xact' closest to the corresponding 
>interval of 'GPS'). This is why the output of the particular sequence of the 
>result I copied in the previous messageÂ contains only 'dry'.
>Â 
>Santi
>Â 
>Â 
>From:PIKAL Petr <petr.pi...@precheza.cz>
>>To: Santiago Guallar <sgual...@yahoo.com>; r-help <r-help@r-project.org> 
>>Sent: Tuesday, July 9, 2013 11:19 AM
>>Subject: RE: [R] spped up a function
>>Â 
>>Hi Santiago
>>Â 
>>I am a bit confused how is your result organised, why there are only 
>>âdryâ value regardless of timepos values.
>>Â 
>>It is not necessary to attach files resulting from dput. Just copy it to your 
>>mail and anybody can copy it directly to R
>>Â 
>>Ring is factor in xact but numeric in GPS
>>> str(xact)
>>'data.frame':Â Â  8 obs. ofÂ  5 variables:
>>$ RingÂ Â  : Factor w/ 24 levels "6106933","6134701",..: 1 1 1 1 1 1 1 1
>>$ julÂ Â Â  : numÂ  15135 15135 15135 15135 15135 ...
>>$ timepos: POSIXct, format: "2011-06-10 04:36:15" "2011-06-10 05:39:57" ...
>>$ actÂ Â Â  : intÂ  3822 27 60 6 753 78 15 18
>>$ wdÂ Â Â Â  : chrÂ  "dry" "wet" "dry" "wet" ...
>>> str(GPS)
>>'data.frame':Â Â  16 obs. ofÂ  3 variables:
>>$ RingÂ Â  : intÂ  6106933 6106933 6106933 6106933 6106933 6106933 6106933 
>>6106933 6106933 6106933 ...
>>$ jul Â Â Â : numÂ  15135 15135 15135 15135 15135 ...
>>$ timepos: POSIXct, format: "2011-06-10 04:39:00" "2011-06-10 04:44:00" ...
>>Â 
>>So I first changed it to factor in both.
>>Â 
>>GPS$Ring<-factor(GPS$Ring)
>>Â 
>>after that I merged both files
>>Â 
>>result<-merge(xact, GPS, all=T)
>>Â 
>>and here is result
>>Â 
>>dput(result)
>>structure(list(Ring = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 
>>1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
>>1L), .Label = c("6106933", "6134701", "6140497", "6140719", "6140756", 
>>"6140855", "6143070", "6143090", "6143093", "6175711", "6175726", 
>>"6175730", "6175769", "6175776", "6175784", "6188609", "6188705", 
>>"6195159", "6195171", "6198153", "6198154", "6198156", "6198157", 
>>"6198172"), class = "factor"), jul = c(15135, 15135, 15135, 15135, 
>>15135, 15135, 15135, 15135, 15135, 15135, 15135, 15135, 15135, 
>>15135, 15135, 15135, 15135, 15135, 15135, 15135, 15135, 15135, 
>>15135, 15135), timepos = structure(c(1307680575, 1307680740, 
>>1307681040, 1307681340, 1307681640, 1307681940, 1307682240, 1307682540, 
>>1307682780, 1307683080, 1307683380, 1307683680, 1307683980, 1307684280, 
>>1307684397, 1307684424, 1307684484, 1307684490, 1307684580, 1307684880, 
>>1307685180, 1307685243, 1307685321, 1307685336), class = c("POSIXct", 
>>"POSIXt"), tzone = "GMT"), act = c(3822L, NA, NA, NA, NA, NA, 
>>NA, NA, NA, NA, NA, NA, NA, NA, 27L, 60L, 6L, 753L, NA, NA, NA, 
>>78L, 15L, 18L), wd = c("dry", NA, NA, NA, NA, NA, NA, NA, NA, 
>>NA, NA, NA, NA, NA, "wet", "dry", "wet", "dry", NA, NA, NA, "wet", 
>>"dry", "wet")), .Names = c("Ring", "jul", "timepos", "act", "wd"
>>), row.names = c(NA, -24L), class = "data.frame")
>>Â 
>>there are empty values in act and wd column. You can fill it eg. by 
>>âna.locfâ function from âzooâ package.
>>Â 
>>> result$wd
>>[1] "dry" NAÂ Â Â  NAÂ Â Â  NAÂ Â Â  NAÂ Â Â  NAÂ Â Â  NAÂ Â Â  NAÂ Â Â  NAÂ 
>>Â Â  NAÂ Â Â  NAÂ Â Â  NAÂ Â  
>>[13] NAÂ Â Â  NAÂ Â Â  "wet" "dry" "wet" "dry" NAÂ Â Â  NAÂ Â Â  NAÂ Â Â  
>>"wet" "dry" "wet"
>>> na.locf(result$wd)
>>[1] "dry" "dry" "dry" "dry" "dry" "dry" "dry" "dry" "dry" "dry" "dry" "dry"
>>[13] "dry" "dry" "wet" "dry" "wet" "dry" "dry" "dry" "dry" "wet" "dry" "wet"
>>> Â 
>>Â 
>>Is this what you want?
>>Â 
>>Regards
>>Petr
>>Â 
>>Â 
>>From:Santiago Guallar [mailto:sgual...@yahoo.com] 
>>Sent: Tuesday, July 09, 2013 8:53 AM
>>To: PIKAL Petr; r-help
>>Subject: Re: [R] spped up a function
>>Â 
>>Hi Petr, yes the function basically consists on merging two time series with 
>>different time intervals: one regular 'GPS' and one irregular 'xact' (the 
>>latter containing the binomial variable 'wd' that I want to add to 'GPS'.
>>Apparently my attachments did not go through. Here you have the dputs you 
>>requested plus the desired result based on them:
>>Â 
>>head(xact)
>>RingÂ Â Â Â  jul Â  timeposÂ Â Â Â Â  Â  actÂ Â  wd
>>6106933 15135 2011-06-10 04:36:15 Â 3822 dry
>>6106933 15135 2011-06-10 05:39:57 Â  Â 27 wet
>>6106933 15135 2011-06-10 05:40:24 Â  Â 60 dry
>>6106933 15135 2011-06-10 05:41:24 Â  Â  6 wet
>>6106933 15135 2011-06-10 05:41:30 Â  753 dry
>>6106933 15135 2011-06-10 05:54:03 Â  Â 78 wet
>>6106933 15135 2011-06-10 05:55:21 Â  Â 15 dry
>>6106933 15135 2011-06-10 05:55:36 Â  Â 18 wet
>>Â 
>>head(GPS1, 16) and desired result (added column wd)Â 
>>Â  Â  Â  Ring Â  jul Â  Â  Â  Â  Â  Â  timeposwd
>>5 Â 6106933 15135 2011-06-10 04:39:00dry
>>6 Â 6106933 15135 2011-06-10 04:44:00dry
>>7 Â 6106933 15135 2011-06-10 04:49:00dry
>>8 Â 6106933 15135 2011-06-10 04:54:00dry
>>9 Â 6106933 15135 2011-06-10 04:59:00dry
>>10 6106933 15135 2011-06-10 05:04:00dry
>>11 6106933 15135 2011-06-10 05:09:00dry
>>12 6106933 15135 2011-06-10 05:13:00dry
>>13 6106933 15135 2011-06-10 05:18:00dry
>>14 6106933 15135 2011-06-10 05:23:00dry
>>15 6106933 15135 2011-06-10 05:28:00dry
>>16 6106933 15135 2011-06-10 05:33:00dry
>>17 6106933 15135 2011-06-10 05:38:00dry
>>18 6106933 15135 2011-06-10 05:43:00dry
>>19 6106933 15135 2011-06-10 05:48:00dry
>>20 6106933 15135 2011-06-10 05:53:00dry
>>Â 
>>Santi
>>
>>________________________________
>> 
>>From:PIKAL Petr <petr.pi...@precheza.cz>
>>To: Santiago Guallar <sgual...@yahoo.com>; r-help <r-help@r-project.org> 
>>Sent: Monday, July 8, 2013 11:34 AM
>>Subject: RE: [R] spped up a function
>>
>>Hi
>>
>>It seems to me, that you basically want merge, but I can miss the point. Try 
>>post
>>
>>dput(head(xact))
>>dput(head(GPS))
>>
>>and what shall be desired result based on those 2 datasets.
>>
>>Regards
>>Petr
>>
>>
>>> -----Original Message-----
>>> From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
>>> project.org] On Behalf Of Santiago Guallar
>>> Sent: Tuesday, July 02, 2013 7:47 PM
>>> To: r-help
>>> Subject: [R] spped up a function
>>> 
>>> Hi,
>>> 
>>> I have written a function to assign the values of a certain variable
>>> 'wd' from a dataset to another dataset. Both contain data from the
>>> sameÂ time period but differ in the length of their time intervals:
>>> 'GPS' has regular 10-minute intervals whereas 'xact' has irregular
>>> intervals. I attached simplified text versions from write.table. You
>>> can also get a dput of 'xact' in this address:
>>> http://www.megafileupload.com/en/file/431569/xact-dput.html).
>>> The original objects are large and the function takes almost one hour
>>> to finish.
>>> Here's the function:
>>> 
>>> fxG= function(xact, GPS){
>>> l <- rep( 'A', nrow(GPS) )
>>> v <- unique(GPS$Ring) # the process is carried out for several
>>> individuals identified by 'Ring'
>>> for(k in 1:length(v) ){
>>> I = v[k]
>>> df <- xact[xact$Ring == I,]
>>> for(i in 1:nrow(GPS)){
>>> if(GPS[i,]$Ring== I){# the code runs along the whole data.frame for
>>> each i; it'd save time to make it stop with the last record of each i
>>> instead u <- df$timepos <= GPS[i,]$timepos # fill vector l for each
>>> interval t from xact <= each interval from GPS (take the max if there's
>>> > 1 interval) l[i] <- df[max( which(u == TRUE) ),]$wd } } } return(l)}
>>> 
>>> vwd <- fxG(xact, GPS)
>>> 
>>> 
>>> My question is: how can I speed up (optimize) this function?
>>> 
>>> Thank you for your help
>>Â 
>
>
        [[alternative HTML version deleted]]

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Re: [R] speed up a function

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