[R] Problems with time formats when importing data using readHTMLTable
David Winsemius
dwinsemius at comcast.net
Tue Jul 11 16:15:43 CEST 2017
> On Jul 11, 2017, at 6:25 AM, Cristina Silva <csilva at ipma.pt> wrote:
>
> Dear Jeff,
>
> I am sorry, I didn't notice that it was not plain text. I hope that it is now in the correct format. I explain the problem again, now with more detais.
> I am collecting the track positions of our research vessel from www.marinetraffic.com. In the page, the data appear in a table:
>
> Timestamp Source Speed (kn) Latitude (°) Longitude (°) Course (°) Show on Map
> 2017-07-11 10:57 (UTC) Terr-AIS 8.6 37.36228 -9.176811 200
> 2017-07-11 10:54 (UTC) Terr-AIS 8.4 37.36875 -9.174048 200
> 2017-07-11 09:50 (UTC) Terr-AIS 8 37.51499 -9.184502 149
> 2017-07-11 09:08 (UTC) Terr-AIS 7.7 37.60513 -9.228263 169
> 2017-07-11 09:05 (UTC) Terr-AIS 8 37.61168 -9.229627 167
> 2017-07-11 09:03 (UTC) Terr-AIS 6.9 37.61626 -9.230456 132
> 2017-07-11 08:59 (UTC) Terr-AIS 3.4 37.61758 -9.237928 101
> 2017-07-11 08:57 (UTC) Terr-AIS 3.6 37.61808 -9.240235 116
> 2017-07-11 08:47 (UTC) Terr-AIS 3.3 37.62267 -9.249762 112
> 2017-07-11 08:44 (UTC) Terr-AIS 3.2 37.6241 -9.25348 115
> 2017-07-11 08:40 (UTC) Terr-AIS 3.3 37.62557 -9.257295 112
> 2017-07-11 08:32 (UTC) Terr-AIS 3.4 37.62903 -9.266028 111
> 2017-07-11 08:28 (UTC) Terr-AIS 3.3 37.63051 -9.269725 114
> 2017-07-11 08:25 (UTC) Terr-AIS 3.3 37.63207 -9.273642 120
> 2017-07-11 08:20 (UTC) Terr-AIS 3.6 37.63395 -9.278254 118
> 2017-07-11 08:16 (UTC) Terr-AIS 3.3 37.63586 -9.282853 116
> 2017-07-11 08:08 (UTC) Terr-AIS 3.2 37.6392 -9.291157 118
> 2017-07-11 07:38 (UTC) Sat-AIS
> 2017-07-11 06:58 (UTC) Terr-AIS 3 37.68459 -9.321658 159
> 2017-07-11 06:53 (UTC) Terr-AIS 3.3 37.68881 -9.324172 150
>
> To get this table I had to copy manually from the webpage, paste in a text file, delete information on figures, links, etc. and then import to R. This works well, I read the csv file and have no problems with date formats. But instead of 20 records, I have to import e.g. 500 records, i.e. 10 pages of 50 records each, or more. I want to import these data in a more automated and quick procedure. I have done this before with no problems, but probably the webpage changed some permissions.
>
> Here is the script used to get the data directly from the webpage into R, for a sample of 20 records (10 per page):
>
> library(XML)
> x <- list()
> for (i in 1:2)
> {
> x[i]<- readHTMLTable(paste('http://www.marinetraffic.com/en/ais/index/positions/all/shipid:318358/mmsi:263601000/shipname:NORUEGA/per_page:10/page:', i, sep=''))
> }
>
> ais <- do.call('rbind', x)
> ais <- ais[,-7]
>
> and I got the following table:
>
>> ais
> Timestamp Source Speed (kn) Latitude (°) Longitude (°) Course (°)
> 1 149977066014997706604 minutes ago Terr-AIS 8.6 37.36228 -9.176811 200
There's undoubtedly a way to extract the time info from this HTML code (but I'm not the one to provide that solution.) This is the first entry in the webpage source when viewed right now:
<td>
<time class="toggle_time utc_time hide-me formatTime" data-overrideAbbreviation="empty" data-time="1499780737" data-timezone="0"><span>1499780737</span></time><time class="toggle_time my_time hide-me formatTime" data-overrideAbbreviation="MyT" data-time="1499780737" data-timezone="MyT"><span>1499780737</span></time><time class="toggle_time dif_time hide"><span>6 minutes ago</span></time> </td>
So the POSIX-style time is givne twice (with no separator and then an offset in minutes is calculated. If I were given the records as you have them now I would extract the leading 10 digits and convert to POSIXct
as.POSIXct(as.numeric(gsub("(^.{10}).+","", Timestamp)), origin="1970-01-01")
as.POSIXct(as.numeric(gsub("(^.{10}).+","\\1", ais$Timestamp)), origin="1970-01-01")
[1] "2017-07-11 07:09:57 PDT" "2017-07-11 06:45:37 PDT" "2017-07-11 06:40:34 PDT" "2017-07-11 06:34:46 PDT" "2017-07-11 06:32:26 PDT"
[6] "2017-07-11 06:29:34 PDT" "2017-07-11 06:26:37 PDT" "2017-07-11 06:20:24 PDT" "2017-07-11 06:17:18 PDT" "2017-07-11 06:12:37 PDT"
[11] "2017-07-11 06:08:24 PDT" "2017-07-11 06:05:04 PDT" "2017-07-11 06:03:27 PDT" "2017-07-11 05:59:37 PDT" "2017-07-11 05:54:37 PDT"
[16] "2017-07-11 05:50:48 PDT" "2017-07-11 05:44:53 PDT" "2017-07-11 05:29:17 PDT" "2017-07-11 05:26:44 PDT" "2017-07-11 04:30:08 PDT"
-- David.
> 2 149977048714997704876 minutes ago Terr-AIS 8.4 37.36875 -9.174048 200
> 3 149976661414997666141 hour, 11 minutes ago Terr-AIS 8.0 37.51499 -9.184502 149
> 4 149976410714997641071 hour, 53 minutes ago Terr-AIS 7.7 37.60513 -9.228263 169
> 5 149976392714997639271 hour, 56 minutes ago Terr-AIS 8.0 37.61168 -9.229627 167
> 6 149976378014997637801 hour, 58 minutes ago Terr-AIS 6.9 37.61626 -9.230456 132
> 7 149976354014997635402 hours, 2 minutes ago Terr-AIS 3.4 37.61758 -9.237928 101
> 8 149976342014997634202 hours, 4 minutes ago Terr-AIS 3.6 37.61808 -9.240235 116
> 9 149976286114997628612 hours, 14 minutes ago Terr-AIS 3.3 37.62267 -9.249762 112
> 10 149976264714997626472 hours, 17 minutes ago Terr-AIS 3.2 37.6241 -9.25348 115
> 11 149976243014997624302 hours, 21 minutes ago Terr-AIS 3.3 37.62557 -9.257295 112
> 12 149976193714997619372 hours, 29 minutes ago Terr-AIS 3.4 37.62903 -9.266028 111
> 13 149976172814997617282 hours, 32 minutes ago Terr-AIS 3.3 37.63051 -9.269725 114
> 14 149976150714997615072 hours, 36 minutes ago Terr-AIS 3.3 37.63207 -9.273642 120
> 15 149976124714997612472 hours, 40 minutes ago Terr-AIS 3.6 37.63395 -9.278254 118
> 16 149976098714997609872 hours, 45 minutes ago Terr-AIS 3.3 37.63586 -9.282853 116
> 17 149976051014997605102 hours, 53 minutes ago Terr-AIS 3.2 37.6392 -9.291157 118
> 18 149975870414997587043 hours, 23 minutes ago Sat-AIS Add to SAT Fleet for undelayed data <NA> <NA> <NA>
> 19 149975631414997563144 hours, 3 minutes ago Terr-AIS 3.0 37.68459 -9.321658 159
> 20 149975598814997559884 hours, 8 minutes ago Terr-AIS 3.3 37.68881 -9.324172 150
>
> The records correspond exactly to the first table. I have tried to change the colClasses to character, but the results are always the same. My question is: how to change the Timestamp to a POSIXlt POSIXct format, either in the importing phase or within R?
>
> I hope that the question is clear now.
>
> Cristina
>
>
> On Mon, 10 Jul 2017 09:18:05 -0700, Jeff Newmiller wrote:
>> Not reproducible. [1][2][3] If our answers don't seem to apply to
>> your situation, it will likely be because you did not explain your
>> question clearly.
>>
>> Not plain text. This is a plain text mailing list, and the best-case
>> scenario when you let your email program send HTML is that what you
>> saw is not what we see (worst case is your email is scrambled on our
>> end).
>>
>> Have you read the documentation for the function you are using? In
>> particular, what about the colClasses argument? If you don't let
>> readHTMLTable guess what the format is (have it read in as character
>> data) then you have a fighting chance to get it right yourself, e.g.
>>
>> as.POSIXct( "2017-07-10 14:04 (UTC)", format="%Y-%m-%d %H:%M (UTC)",
>> tz="UTC" )
>>
>> -----
>>
>> [1]
>> http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
>>
>> [2] http://adv-r.had.co.nz/Reproducibility.html
>>
>> [3] https://cran.r-project.org/web/packages/reprex/index.html
>> --
>> Sent from my phone. Please excuse my brevity.
>>
>> On July 10, 2017 8:31:30 AM PDT, Cristina Silva <csilva at ipma.pt> wrote:
>>> Hi,
>>>
>>> I am extracting positions data from the marine traffic website. The
>>> table has a "Timestamp" column which, in the browser, appears with the
>>> format yyyy-mm-dd HH:MM (UTC), e.g. 2017-07-10 14:04 (UTC).
>>>
>>> When I import the table, the same date "2017-07-10 14:04 (UTC)" appears
>>>
>>> as "1499696500149969650021 minutes ago", This is the more recent date
>>> and time. Older records, as e.g. "2017-07-09 17:02 (UTC)" appear as
>>> e.g.
>>> "1499619726149961972621 hours, 59 minutes ago".
>>>
>>> I don't know how to convert these data to the time formats used in R
>>> (POSIXct).
>>>
>>> The script is very simple and worked before:
>>>
>>> library(XML)
>>> x <- readHTMLTable('url')
>>>
>>> where the 'url' is the link to the website with the specification of
>>> the
>>> vessel.
>>>
>>> I appreciate any help.
>>>
>>> Cristina
>>>
>>> --
>>> Cristina Silva
>>> Divisão de Modelação e Gestão de Recursos Pesqueiros
>>> Av. Dr. Alfredo Magalhães Ramalho
>>> 1495-165 Lisboa
>>> @: csilva at ipma.pt <mailto:csilva at ipma.pt>
>>> #: +351 213027096 <phoneto:+351213027096>
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>
> --
> Cristina Silva
> Divisão de Modelação e Gestão de Recursos Pesqueiros
> Avenida de Brasília
> 1449-006 Lisboa
> @: csilva at ipma.pt
> #: +351 213027096
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA
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