[R] R related tools - GUI
Neotropical bat risk assessments
neotrop|c@|@b@t@ @end|ng |rom gm@||@com
Sat Jun 29 12:28:42 CEST 2024
For years I used Deducer (Package Deducer) developed by Ian Fellows.
This is still available and partially remains mostly functional. He was
working on a new GUI years ago but appears no longer to be in the
pipeline I think replaced by R-Studio.
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> Today's Topics:
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> 1. Re: Positron as a tool (=?UTF-8?B?RMOpbmVzIFTDs3Ro?=)
> 2. Re: Positron as a tool (avi.e.gross using gmail.com)
> 3. Re: Positron as a tool (Stephen H. Dawson, DSL)
> 4. Re: Converting .grib to excel file (javad bayat)
> 5. Referencing Sys.Date to a different time zone (Dennis Fisher)
> 6. Re: Referencing Sys.Date to a different time zone (Ivan Krylov)
> 7. Re: [Tagged] Re: Referencing Sys.Date to a different time
> zone (Jeff Newmiller)
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 28 Jun 2024 13:03:17 +0200
> From: =?UTF-8?B?RMOpbmVzIFTDs3Ro?= <toth.denes using kogentum.hu>
> To: avi.e.gross using gmail.com, r-help using r-project.org
> Subject: Re: [R] Positron as a tool
> Message-ID: <bb49d4dc-f775-1a65-e138-ad09ab222b7b using kogentum.hu>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> Hi Avi,
>
> I am not sure that the R-help mailing list is a suitable channel for
> advertising R-related tools... But given you mentioned Positron
> (https://github.com/posit-dev/positron), which is based on VSCode, it is
> worth calling out that a free, open-source, community-maintained, very
> feature rich R extension
> (https://code.visualstudio.com/docs/languages/r) already exists in VS
> Code for years.
>
> Regards,
> Denes
>
>
> On 6/28/24 07:10, avi.e.gross using gmail.com wrote:
>> This is just an FYI based on a news item I saw tonight.
>>
>> There have been discussions on what editors or environments people can use
>> when working with R and I personally have mostly been using versions of
>> RSTUDIO and lately for both R and python. As often noted, RSTUDIO is a
>> product of a company, currently still largely free and they have some tweaks
>> that can cause issues.
>>
>> The news article mentions a future project as described below, if anyone is
>> interested, that may be a nice alternative similar (and based on) what some
>> use for programming in multiple languages. Again, I am noty suggesting
>> anyone use it, albeit I plan on trying it out when it is a bit further
>> along.
>>
>> The current name seems to be Positron, to sort of go with the new name of
>> the company behind RSTUDIO, which is now Posit. Nothing to do with Asimov's
>> Positronic Brains, LOL!
>>
>> Here is a reference if anyone is interested.
>>
>> https://www.infoworld.com/article/3715702/maker-of-rstudio-launches-new-r-an
>> d-python-ide.html
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help using 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.
>>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 28 Jun 2024 11:41:04 -0400
> From: <avi.e.gross using gmail.com>
> To: =?UTF-8?Q?'D=C3=A9nes_T=C3=B3th'?= <toth.denes using kogentum.hu>,
> <r-help using r-project.org>
> Subject: Re: [R] Positron as a tool
> Message-ID: <002c01dac971$95d6ca20$c1845e60$@gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Just to be clear, Denis, I am not in any way associated with anybody or anything and just read about it on a news feed not from POSIT directly.
>
> I am aware it is based on existing functionality and have used possibly similar editors for other languages. I did try possibly one touted by Microsoft years ago (perhaps what you are referring to) but felt no need to keep using it at the time. What I am interested in is hearing from others who have opinions, perhaps after having tried it.
>
> And there is a trend I have noted where some development environments have been moving towards multiple language support including at times integration between languages. RSTUDI, itself, has been supporting a number of languages besides R and that is one reason it changed names for the company. What they are offering now, and I am not clear what they are adding or changing, looks like an attempt to evolve along such lines.
>
> Python versions typically have shipped with a fairly rudimentary IDLE program you can use as a sort of editor. Plenty of other add-ons are available independently. As noted, RSTUDIO now is such an add-on for python too.
>
> R, as far as I know, has not taken that route and you get just the language alone and the community is free to use anything else they want. RSTUDIO is one of many but arguably, quite a few here have used it. Many versions are currently FREE and some paid versions may have more functionality. I am wondering if this new product is going to change things such as fee structures or even eventually replace ...
>
>
> -----Original Message-----
> From: Dénes Tóth <toth.denes using kogentum.hu>
> Sent: Friday, June 28, 2024 7:03 AM
> To: avi.e.gross using gmail.com; r-help using r-project.org
> Subject: Re: [R] Positron as a tool
>
> Hi Avi,
>
> I am not sure that the R-help mailing list is a suitable channel for
> advertising R-related tools... But given you mentioned Positron
> (https://github.com/posit-dev/positron), which is based on VSCode, it is
> worth calling out that a free, open-source, community-maintained, very
> feature rich R extension
> (https://code.visualstudio.com/docs/languages/r) already exists in VS
> Code for years.
>
> Regards,
> Denes
>
>
> On 6/28/24 07:10, avi.e.gross using gmail.com wrote:
>> This is just an FYI based on a news item I saw tonight.
>>
>> There have been discussions on what editors or environments people can use
>> when working with R and I personally have mostly been using versions of
>> RSTUDIO and lately for both R and python. As often noted, RSTUDIO is a
>> product of a company, currently still largely free and they have some tweaks
>> that can cause issues.
>>
>> The news article mentions a future project as described below, if anyone is
>> interested, that may be a nice alternative similar (and based on) what some
>> use for programming in multiple languages. Again, I am noty suggesting
>> anyone use it, albeit I plan on trying it out when it is a bit further
>> along.
>>
>> The current name seems to be Positron, to sort of go with the new name of
>> the company behind RSTUDIO, which is now Posit. Nothing to do with Asimov's
>> Positronic Brains, LOL!
>>
>> Here is a reference if anyone is interested.
>>
>> https://www.infoworld.com/article/3715702/maker-of-rstudio-launches-new-r-an
>> d-python-ide.html
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help using 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.
>>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Fri, 28 Jun 2024 11:56:47 -0400
> From: "Stephen H. Dawson, DSL" <service using shdawson.com>
> To: avi.e.gross using gmail.com, =?UTF-8?B?J0TDqW5lcyBUw7N0aCc=?=
> <toth.denes using kogentum.hu>, r-help using r-project.org
> Subject: Re: [R] Positron as a tool
> Message-ID: <9ba1bf10-7230-6b8d-03bb-dd3576db72f6 using shdawson.com>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> The gap I see is in the database engine monitoring.
>
> MySQL has discontinued development of Workbench. Percona Monitoring and
> Management seems nice, but not as integrated in IDE as I would prefer.
>
> A Positron tool proposed by the vendor is positioned as a data science
> tool. The ability to know if any R work is killing the DB by overloading
> it is still a missing piece of the IDE picture without running multiple
> code monitoring sections in watch windows.
>
>
> *Stephen Dawson, DSL*
> /Executive Strategy Consultant/
> Business & Technology
> +1 (865) 804-3454
> http://www.shdawson.com
>
>
> On 6/28/24 11:41, avi.e.gross using gmail.com wrote:
>> Just to be clear, Denis, I am not in any way associated with anybody or anything and just read about it on a news feed not from POSIT directly.
>>
>> I am aware it is based on existing functionality and have used possibly similar editors for other languages. I did try possibly one touted by Microsoft years ago (perhaps what you are referring to) but felt no need to keep using it at the time. What I am interested in is hearing from others who have opinions, perhaps after having tried it.
>>
>> And there is a trend I have noted where some development environments have been moving towards multiple language support including at times integration between languages. RSTUDI, itself, has been supporting a number of languages besides R and that is one reason it changed names for the company. What they are offering now, and I am not clear what they are adding or changing, looks like an attempt to evolve along such lines.
>>
>> Python versions typically have shipped with a fairly rudimentary IDLE program you can use as a sort of editor. Plenty of other add-ons are available independently. As noted, RSTUDIO now is such an add-on for python too.
>>
>> R, as far as I know, has not taken that route and you get just the language alone and the community is free to use anything else they want. RSTUDIO is one of many but arguably, quite a few here have used it. Many versions are currently FREE and some paid versions may have more functionality. I am wondering if this new product is going to change things such as fee structures or even eventually replace ...
>>
>>
>> -----Original Message-----
>> From: Dénes Tóth <toth.denes using kogentum.hu>
>> Sent: Friday, June 28, 2024 7:03 AM
>> To: avi.e.gross using gmail.com; r-help using r-project.org
>> Subject: Re: [R] Positron as a tool
>>
>> Hi Avi,
>>
>> I am not sure that the R-help mailing list is a suitable channel for
>> advertising R-related tools... But given you mentioned Positron
>> (https://github.com/posit-dev/positron), which is based on VSCode, it is
>> worth calling out that a free, open-source, community-maintained, very
>> feature rich R extension
>> (https://code.visualstudio.com/docs/languages/r) already exists in VS
>> Code for years.
>>
>> Regards,
>> Denes
>>
>>
>> On 6/28/24 07:10, avi.e.gross using gmail.com wrote:
>>> This is just an FYI based on a news item I saw tonight.
>>>
>>> There have been discussions on what editors or environments people can use
>>> when working with R and I personally have mostly been using versions of
>>> RSTUDIO and lately for both R and python. As often noted, RSTUDIO is a
>>> product of a company, currently still largely free and they have some tweaks
>>> that can cause issues.
>>>
>>> The news article mentions a future project as described below, if anyone is
>>> interested, that may be a nice alternative similar (and based on) what some
>>> use for programming in multiple languages. Again, I am noty suggesting
>>> anyone use it, albeit I plan on trying it out when it is a bit further
>>> along.
>>>
>>> The current name seems to be Positron, to sort of go with the new name of
>>> the company behind RSTUDIO, which is now Posit. Nothing to do with Asimov's
>>> Positronic Brains, LOL!
>>>
>>> Here is a reference if anyone is interested.
>>>
>>> https://www.infoworld.com/article/3715702/maker-of-rstudio-launches-new-r-an
>>> d-python-ide.html
>>>
>>>
>>>
>>> [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-help using 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-help using 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.
>
>
>
> ------------------------------
>
> Message: 4
> Date: Fri, 28 Jun 2024 18:59:17 +0330
> From: javad bayat <j.bayat194 using gmail.com>
> To: "Richard O'Keefe" <raoknz using gmail.com>
> Cc: R-help <R-help using r-project.org>
> Subject: Re: [R] Converting .grib to excel file
> Message-ID:
> <CANTxAm+36CqGAH1O6=piex=4X1sPdTD0i7SqT_ywZDNGWsrvgQ using mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Richard,
> I could not extract the data at all.
> But what I found is that, the data stored in the grib file converted into
> raster layer, and as I had 6 met parameters for a complete year (6 × 365 ×
> 24) the raster layer has 52,560 layer. The first layer belongs to the first
> parameter for the first hour and second layer to the second parameters for
> the first hour..... .
> And again the seven layer belongs to the first parameter for the second
> hour and the layer number 8 belongs to the second param. for the second
> hour.... and this cycle is repeated until the layer number 52,560.
> I think writing a function to extract these data can be helpful. For
> example writing a function to extract the data number 1 and 7 and 13 and
> ... store in the first column and data number 2,8,14, .... stor in the
> second column and doing this for other parameters to complete the table and
> eventually create a column for Date.
> Can you help me to write a function.
> Sincerely
>
> On Wed, 26 Jun 2024, 12:44 Richard O'Keefe, <raoknz using gmail.com> wrote:
>
>> Whoops, sorry, you *did* answer "what went wrong".
>>> param_names <- c("param1", "param2", "param3", "param4", "param5",
>> "param6")
>>> extracted_data <- extract(raster_data, param_names, df = TRUE)
>> #Error in (function (classes, fdef, mtable) :
>> #unable to find an inherited method for function ‘extract’ for
>> signature ‘"SpatRaster", "character"’
>>
>> OK. The problem is that the extract() function didn't know what to do.
>> What does the documentation for 'extract' say?
>> The error message seems to say that it is not defined for first argument
>> being
>> a SpatRaster and second argument being of type character.
>>
>> (By the way, I'm having trouble updating the terra package in Ubuntu 22.04.
>> That's why I'm not trying any of this out.)
>>
>> Here's what ?extract starts with:
>>
>> Extract values from a SpatRaster for a set of locations. The
>> locations can be a SpatVector (points, lines, polygons), a
>> data.frame or matrix with (x, y) or (longitude, latitude - in that
>> order!) coordinates, or a vector with cell numbers.
>>
>> It does NOT say that the set of locations can be a vector of strings.
>>
>>
>> On Wed, 26 Jun 2024 at 20:05, Richard O'Keefe <raoknz using gmail.com> wrote:
>>> I'm now inclined to go with 'search for "convert GRIB to CSV".
>>> https://confluence.ecmwf.int/display/CKB/How+to+convert+GRIB+to+CSV
>>> is the first line. I know that's not an R solution, but using software
>>> specifically developed for encoding, decoding, extracting, &c GRIB file
>> by the
>>> European Centre for Medium-Range Weather Forecasts and actively
>>> maintained, with an example page showing how to do it, sounds like a
>>> good approach.
>>>
>>> One of the major things about R is that from the very beginnings of S
>>> it was intended to be used with other tools. We have R communicating
>>> with Python and Tcl and dear knows what. Getting a specialised tool
>>> to do its thing is very much part of the R "way".
>>> Or there's gribr https://rdrr.io/github/nawendt/gribr/man/gribr.html
>>> which wraps ecCodes in R.
>>>
>>> I still don't understand what "doesn't work" means. Which step goes
>>> wrong and how does it misbehave?
>>>
>>>
>>> On Wed, 26 Jun 2024 at 06:02, javad bayat <j.bayat194 using gmail.com> wrote:
>>>> Richard,
>>>> Many thanks for your email.
>>>> I had attached the grib file to the original email to R help team but
>> it seems you did not receive it.
>>>> Unfortunately, I do not know how to reduce the volume or extract some
>> of the grib file data to send it for you. The file has the volume of 6
>> Megabyte.
>>>> I can send it by email.
>>>> The file has 6 met parameters and Date (day/month/year hour:minute).
>>>> I want the exported file as excel contains 7 columns (Date + 6 met
>> parameters).
>>>>
>>>> On Tue, 25 Jun 2024, 15:54 Richard O'Keefe, <raoknz using gmail.com> wrote:
>>>>> Your message referred to an attached file but there was no attachment,
>>>>> I have no account at that service, so could not download a sample for
>>>>> myself. Does the licence for the data even allow you to send some of
>>>>> it in a message? Which parameters are you extracting? When you say
>>>>> "it didn't work", what actually happened? Which step went wrong and
>> how?
>>>>>
>>>>> On Tue, 25 Jun 2024 at 20:33, javad bayat <j.bayat194 using gmail.com>
>> wrote:
>>>>>> Dear all;
>>>>>> I have downloaded meteorology data from "
>>>>>>
>> https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-single-levels?tab=form
>> "
>>>>>> as .grib format. It has hourly data of a complete year (every hour
>> of every
>>>>>> day of 12 months) and has 6 meteorology parameters. The file has
>> been
>>>>>> attached.
>>>>>> I am trying to convert it to an excel file that puts every
>> parameter in a
>>>>>> separated column. For instance, the first col represents Date, 2nd
>>>>>> represents Temperature and so on.
>>>>>> Is there any way to do it?
>>>>>> I used these codes but did not work:
>>>>>> # install.packages("rNOMADS")
>>>>>>
>>>>>> library(rNOMADS)
>>>>>>
>>>>>> # Read GRIB data
>>>>>> grib_data <- ReadGrib("C:/Users/admin/Downloads/Met.grib")
>>>>>>
>>>>>> # Convert to a data frame
>>>>>> grib_df <- as.data.frame(grib_data)
>>>>>>
>>>>>> # Write the data frame to a CSV file
>>>>>> write.csv(grib_df, file = "output.csv")
>>>>>>
>>>>>>
>>>>>> I would be more than happy if anyone could help me.
>>>>>> Sincerely
>>>>>>
>>>>>> --
>>>>>> Best Regards
>>>>>> Javad Bayat
>>>>>> M.Sc. Environment Engineering
>>>>>> Alternative Mail: bayat194 using yahoo.com
>>>>>> ______________________________________________
>>>>>> R-help using 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.
> [[alternative HTML version deleted]]
>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Fri, 28 Jun 2024 18:52:26 +0200
> From: Dennis Fisher <fisher using plessthan.com>
> To: r-help <r-help using r-project.org>
> Subject: [R] Referencing Sys.Date to a different time zone
> Message-ID: <D5E8AEC5-7673-4D8E-B4CE-BE373682D597 using plessthan.com>
> Content-Type: text/plain; charset="utf-8"
>
> R 4.3.1
> OS X
>
> Colleagues
>
> Hopefully this question elicits a simple answer.
>
> I am in Europe at present. When I issue the command:
> Sys.Date()
> I would like to be able to obtain the value for Pacific time (which differ for the first 9 hours of the day),
> I would like the process to be automatic, regardless of where in the world I am located.
>
> Dennis
>
> Dennis Fisher MD
> P < (The "P Less Than" Company)
> Phone / Fax: 1-866-PLessThan (1-866-753-7784)
> www.PLessThan.com <http://www.plessthan.com/>
>
>
>
>
>
> [[alternative HTML version deleted]]
>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Fri, 28 Jun 2024 20:16:20 +0300
> From: Ivan Krylov <ikrylov using disroot.org>
> To: Dennis Fisher <fisher using plessthan.com>
> Cc: r-help <r-help using r-project.org>
> Subject: Re: [R] Referencing Sys.Date to a different time zone
> Message-ID: <20240628201620.67ffd964 using arachnoid>
> Content-Type: text/plain; charset="utf-8"
>
> В Fri, 28 Jun 2024 18:52:26 +0200
> Dennis Fisher <fisher using plessthan.com> пишет:
>
>> When I issue the command:
>> Sys.Date()
>> I would like to be able to obtain the value for Pacific time (which
>> differ for the first 9 hours of the day)
> By the time the value of Sys.Date() is created, it's too late to
> discern between Europe and Pacific time. The Date class is intended to
> store the integer number of days since 1970-01-01:
>
> unclass(Sys.Date())
> # [1] 19902
>
> Only by preserving the time we can get a timezone-dependent date:
>
> format(Sys.time(), '%Y-%m-%d') # uses the current time zone
> # [1] "2024-06-28"
> format(Sys.time(), '%Y-%m-%d', tz = 'Asia/Vladivostok')
> # [1] "2024-06-29"
>
--
Bruce W. Miller, PhD.
Neotropical bat acoustic assessments, ID keys and Fact Sheets
Research Fellow - Wildlife Conservation Society - Ret.
Research Associate, American Museum of Natural History
Freely mentoring the next generation of bat biologists and conservationists since 1995
If we lose the bats, we may lose much of the tropical vegetation and the lungs of the planet
Using acoustic sampling to identify and map species distributions
and pioneering acoustic tools for ecology and conservation of bats for >28 years.
https://www.researchgate.net/profile/Bruce-Miller-5
Key projects include providing free interactive identification keys and call fact sheets for the vocal signatures of New World Bats
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