Re: [R] Associate a .R file with the RGui
On 11/5/22 09:58, Amarjit Chandhial via R-help wrote:
Hi Jeff,
Please see my original question.
You were told that RGui is not an editor.
Are you implying that your initial message contained an implicit request
for instructions on how to get R code in an .R file to be opened
automagically when double-clicked or to have "open in "
appear when right-clicked? (I didn't see that clearly expressed.)
If you want something else to happen with a file that has a .R extension
when double-clicked or right-clicked in a GUI file manager, then you
need to configure your OS to do whatever else it is that you expect.
This is not really an R question. It's an OS question. There are many
editors that can also bring up R consoles when the right key combo is
pressed. They do require some study for their specific actions, but this
is not really the place to get guidance on the fine details.
--
David.
Thanks,
Amarjiit
On 5 Nov 2022, at 15:03, Jeff Newmiller wrote:
RGui is not an editor. It is a console (aka REPL,
https://en.wikipedia.org/wiki/Read%E2%80%93eval%E2%80%93print_loop).
When using RGui, it is up to you to edit your R file in an external editor like Notepad++
and copy paste code snippets or use source("yourfile.R") as desired.
On November 5, 2022 6:47:54 AM PDT, Amarjit Chandhial via R-help
wrote:
Hi Andrew/Petr,
Thanks for the replies.
In R Console if I run:
R.home("bin")
I get the following
"C:/PROGRA~1/R/R-42~1.2/bin/x64"
which is where
Rgui.exe is (within the x64 folder there are 13 files in total: 8 . exe
and 5 .dll).
In file Explorer if I right-click on a .R file -> Open With -> R for
Windows GUI Front-End
RGui (64-bit) opens but the .R file does not appear in the editor.
Amarjit
-- Original Message --
From: "Andrew Simmons"
To: "Amarjit Chandhial"
Cc: "R-help Mailing List"
Sent: Friday, 4 Nov, 2022 At 09:08
Subject: Re: [R] Associate a .R file with the RGui
In an R session, run this:
writeLines(normalizePath(R.home("bin")))
Right click your .R file > Open with > Choose another app > Check the
box "Always use this app to open .R files" > Look for another app on
this PC
Paste the directory found above, then select "Rgui.exe"
On Fri, Nov 4, 2022, 04:49 Amarjit Chandhial via R-help
mailto:r-help@r-project.org> > wrote:
Hi,
My OS is Windows 11 Pro 64-Bit, I have R 4.2.2 and RStudio installed.
If I double-click on a .R file in File Explorer the OS gives me the
option of opening the .R in RStudio, or Look for an app in the
Microsoft
Store, or More Apps. Similarly with a right-click.
I would like to associate a .R file with the RGui, not RStudio, thus
when I double-click on a .R file in File Explorer the .R file opens in
the R Editor in RGui.
On my PC R 4.2.2 is located in "C:/Program Files/R/R-4.2.2/etc"
Please can someone provide step-by-step instructions on how to
associate?
thanks,
Amarjit
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--
Sent from my phone. Please excuse my brevity.
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Re: [R] Is this *always* the intended R^2 value for no intercept in lm?
FAQ 7.41
and
https://stackoverflow.com/questions/57415793/r-squared-in-lm-for-zero-intercept-model
(among numerous others that could no doubt be found with a bit of
searching).
In short, the "null models" against which you are comparing the fitted
model are different with and without an intercept.
--Bert
On Sat, Nov 5, 2022 at 11:52 AM Thierry Zell wrote:
> I am puzzled by the computation of R^2 with intercept omitted that is
> already illustrated by the following example taken from help("lm")
>
> ## Annette Dobson (1990) "An Introduction to Generalized Linear Models".
> ## Page 9: Plant Weight Data.
> ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
> trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
> group <- gl(2, 10, 20, labels = c("Ctl","Trt"))
> weight <- c(ctl, trt)
> lm.D9 <- lm(weight ~ group)
> lm.D90 <- lm(weight ~ group - 1) # omitting intercept
>
> The calculations for the R^2 for both models are consistent with the
> help("summary.lm") description:
> "y* is the mean of y[i] if there is an intercept and zero otherwise."
> Which causes a dramatic difference in the resulting R^2 values.
>
> r2.D9 <- summary(lm.D9)$r.squared
> r2.D90 <- summary(lm.D90)$r.squared
>
> all.equal(r2.D9, 0.0730775989903856) #TRUE
> all.equal(r2.D90, 0.981783272435264) #TRUE
>
> This is counter-intuitive to say the least since the two models have
> identical predictions and both models could be described more
> accurately as two intercepts rather than zero. I see three
> possibilities:
>
> 1. This is the intended result, in which case no fix is required, but
> I’d be curious to understand the argument better.
> 2. This is an unfortunate outcome but not worth fixing as the user can
> easily compute the correct R^2. In this case, I'd suggest that this
> unintuitive behavior should be explicitly called out in the
> documentation.
> 3. This is a bug worth fixing.
>
> I look forward to hearing the community’s opinion on this.
> Thanks in advance!
>
> __
> 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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Re: [R] rio: list of extensions for supported formats
Cat was being helpful. On Sat, 5 Nov 2022 at 15:39, John Kane wrote: > o idea but there is a list here > https://thomasleeper.com/rio/articles/rio.html > > On Sat, 5 Nov 2022 at 04:04, Sigbert Klinke > wrote: > >> Hi, >> >> is there a function in the package rio to get the file extensions listed >> in the vignette under supported formats? >> >> Thanks Sigbert >> >> __ >> 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. >> > > > -- > John Kane > Kingston ON Canada > -- John Kane Kingston ON Canada [[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] rio: list of extensions for supported formats
o idea but there is a list here https://thomasleeper.com/rio/articles/rio.html On Sat, 5 Nov 2022 at 04:04, Sigbert Klinke wrote: > Hi, > > is there a function in the package rio to get the file extensions listed > in the vignette under supported formats? > > Thanks Sigbert > > __ > 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. > -- John Kane Kingston ON Canada [[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.
[R] Is this *always* the intended R^2 value for no intercept in lm?
I am puzzled by the computation of R^2 with intercept omitted that is
already illustrated by the following example taken from help("lm")
## Annette Dobson (1990) "An Introduction to Generalized Linear Models".
## Page 9: Plant Weight Data.
ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
group <- gl(2, 10, 20, labels = c("Ctl","Trt"))
weight <- c(ctl, trt)
lm.D9 <- lm(weight ~ group)
lm.D90 <- lm(weight ~ group - 1) # omitting intercept
The calculations for the R^2 for both models are consistent with the
help("summary.lm") description:
"y* is the mean of y[i] if there is an intercept and zero otherwise."
Which causes a dramatic difference in the resulting R^2 values.
r2.D9 <- summary(lm.D9)$r.squared
r2.D90 <- summary(lm.D90)$r.squared
all.equal(r2.D9, 0.0730775989903856) #TRUE
all.equal(r2.D90, 0.981783272435264) #TRUE
This is counter-intuitive to say the least since the two models have
identical predictions and both models could be described more
accurately as two intercepts rather than zero. I see three
possibilities:
1. This is the intended result, in which case no fix is required, but
I’d be curious to understand the argument better.
2. This is an unfortunate outcome but not worth fixing as the user can
easily compute the correct R^2. In this case, I'd suggest that this
unintuitive behavior should be explicitly called out in the
documentation.
3. This is a bug worth fixing.
I look forward to hearing the community’s opinion on this.
Thanks in advance!
__
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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] Associate a .R file with the RGui
Hi Jeff,
Please see my original question.
Thanks,
Amarjiit
> On 5 Nov 2022, at 15:03, Jeff Newmiller wrote:
>
> RGui is not an editor. It is a console (aka REPL,
> https://en.wikipedia.org/wiki/Read%E2%80%93eval%E2%80%93print_loop).
>
> When using RGui, it is up to you to edit your R file in an external editor
> like Notepad++ and copy paste code snippets or use source("yourfile.R") as
> desired.
>
>> On November 5, 2022 6:47:54 AM PDT, Amarjit Chandhial via R-help
>> wrote:
>>
>>
>>
>> Hi Andrew/Petr,
>>
>>
>> Thanks for the replies.
>>
>> In R Console if I run:
>>
>> R.home("bin")
>>
>> I get the following
>>
>> "C:/PROGRA~1/R/R-42~1.2/bin/x64"
>>
>> which is where
>>
>> Rgui.exe is (within the x64 folder there are 13 files in total: 8 . exe
>> and 5 .dll).
>>
>>
>> In file Explorer if I right-click on a .R file -> Open With -> R for
>> Windows GUI Front-End
>>
>> RGui (64-bit) opens but the .R file does not appear in the editor.
>>
>>
>> Amarjit
>>
>>
>> -- Original Message --
>> From: "Andrew Simmons"
>> To: "Amarjit Chandhial"
>> Cc: "R-help Mailing List"
>> Sent: Friday, 4 Nov, 2022 At 09:08
>> Subject: Re: [R] Associate a .R file with the RGui
>>
>> In an R session, run this:
>>
>> writeLines(normalizePath(R.home("bin")))
>>
>>
>> Right click your .R file > Open with > Choose another app > Check the
>> box "Always use this app to open .R files" > Look for another app on
>> this PC
>> Paste the directory found above, then select "Rgui.exe"
>>
>>
>> On Fri, Nov 4, 2022, 04:49 Amarjit Chandhial via R-help
>> mailto:r-help@r-project.org> > wrote:
>>
>> Hi,
>>
>>
>> My OS is Windows 11 Pro 64-Bit, I have R 4.2.2 and RStudio installed.
>>
>> If I double-click on a .R file in File Explorer the OS gives me the
>> option of opening the .R in RStudio, or Look for an app in the
>> Microsoft
>> Store, or More Apps. Similarly with a right-click.
>>
>> I would like to associate a .R file with the RGui, not RStudio, thus
>> when I double-click on a .R file in File Explorer the .R file opens in
>> the R Editor in RGui.
>>
>> On my PC R 4.2.2 is located in "C:/Program Files/R/R-4.2.2/etc"
>>
>> Please can someone provide step-by-step instructions on how to
>> associate?
>>
>>
>> thanks,
>> Amarjit
>>
>> [[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.
>>
>>
>>
>>
>>[[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.
>
> --
> Sent from my phone. Please excuse my brevity.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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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] Selecting a minimum value of an attribute associated with point values neighboring a given point and assigning it as a new attribute
Probably better posted on R-sig-geo.
-- Bert
On Sat, Nov 5, 2022 at 12:36 AM Duhl, Tiffany R.
wrote:
> Hello,
>
> I have sets of spatial points with LAT, LON coords (unprojected, WGS84
> datum) and several value attributes associated with each point, from
> numerous csv files (with an average of 6,000-9,000 points in each file) as
> shown in the following example:
>
> data<- read.csv("R_find_pts_testdata.csv")
>
> > data
> ID Date TimeLATLON Conc
> Leg.SpeedCO2 H2O BC61 Hr Min Sec
> 1 76 4/19/2021 21:25:38 42.40066 -70.98802 99300 0.0 mph 428.39 9.57
> 578 21 25 38
> 2 77 4/19/2021 21:25:39 42.40066 -70.98802 96730 0.0 mph 428.04 9.57
> 617 21 25 39
> 3 79 4/19/2021 21:25:41 42.40066 -70.98802 98800 0.2 mph 427.10 9.57
> 1027 21 25 41
> 4 80 4/19/2021 21:25:42 42.40066 -70.98802 96510 2 mph 427.99 9.58
> 1381 21 25 42
> 5 81 4/19/2021 21:25:43 42.40067 -70.98801 95540 3 mph 427.99 9.58
> 1271 21 25 43
> 6 82 4/19/2021 21:25:44 42.40068 -70.98799 94720 4 mph 427.20 9.57
> 910 21 25 44
> 7 83 4/19/2021 21:25:45 42.40069 -70.98797 94040 5 mph 427.18 9.57
> 652 21 25 45
> 8 84 4/19/2021 21:25:46 42.40072 -70.98795 95710 7 mph 427.07 9.57
> 943 21 25 46
> 9 85 4/19/2021 21:25:47 42.40074 -70.98792 96200 8 mph 427.44 9.56
> 650 21 25 47
> 10 86 4/19/2021 21:25:48 42.40078 -70.98789 9375010 mph 428.76 9.57
> 761 21 25 48
> 11 87 4/19/2021 21:25:49 42.40081 -70.98785 9336011 mph 429.25 9.56
> 1158 21 25 49
> 12 88 4/19/2021 21:25:50 42.40084 -70.98781 9434012 mph 429.56 9.57
> 107 21 25 50
> 13 89 4/19/2021 21:25:51 42.40087 -70.98775 9278012 mph 428.62 9.56
> 720 21 25 51
>
>
> What I want to do is, for each point, identify all points within 50m of
> that point, find the minimum value of the "Conc" attribute of each nearby
> set of points (including the original point) and then create a new variable
> ("Conc_min") and assign this minimum value to a new variable added to
> "data".
>
> So far, I have the following code:
>
> library(spdep)
> library(sf)
>
> setwd("C:\\mydirectory\\")
> data<- read.csv("R_find_pts_testdata.csv")
>
> #make sure the data is a data frame
> pts <- data.frame(data)
>
> #create spatial data frame and define projection
> pts_coords <- cbind(pts$LON, pts$LAT)
> data_pts <- SpatialPointsDataFrame(coords= pts_coords,
> data=pts, proj4string = CRS("+proj=longlat +datum=WGS84"))
>
> #Re-project to WGS 84 / UTM zone 18N, so the analysis is in units of m
> ptsUTM <- sf::st_as_sf(data_pts, coords = c("LAT", "LON"), remove = F)%>%
> st_transform(32618)
>
> #create 50 m buffer around each point then intersect with points and
> finally find neighbors within the buffers
> pts_buf <- sf::st_buffer(ptsUTM, 50)
> coords <- sf::st_coordinates(ptsUTM)
> int <- sf::st_intersects(pts_buf, ptsUTM)
> x <- spdep::dnearneigh(coords, 0, 50)
>
> Now at this point, I'm not sure what to either the "int" (a sgbp list) or
> "x" (nb object) objects (or even if I need them both)
>
> > int
> Sparse geometry binary predicate list of length 974, where the predicate
> was `intersects'
> first 10 elements:
> 1: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
> 2: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
> 3: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
> 4: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
> 5: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
> 6: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
> 7: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
> 8: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
> 9: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
>
> > x
> Neighbour list object:
> Number of regions: 974
> Number of nonzero links: 34802
> Percentage nonzero weights: 3.668481
> Average number of links: 35.73101
>
> One thought is that maybe I don't need the dnearneigh function and can
> instead convert "int" into a dataframe and somehow merge or associate
> (perhaps with an inner join) the ID fields of the buffered and intersecting
> points and then compute the minimum value of "Conc" grouping by ID:
>
> > as.data.frame(int)
> row.id col.id
> 11 1
> 21 2
> 31 3
> 41 4
> 51 5
> 61 6
> 71 7
> 81 8
> 91 9
> 10 1 10
> 11 1 11
> 12 1 12
> 13 1 13
> 14 1 14
> 15 1 15
> 16 1 16
> 17 1 17
> 18 1 18
> 19 2 1
> 20 2 2
> 21 2 3
> 22 2 4
> 23 2 5
> 24 2 6
> 25 2 7
> 26 2 8
> 27 2 9
> 28 2 10
>
>
> So in the above example I'd like to take the minimum of "Conc" among the
> col.id points grouped with row.id 1 (i.e., col.ids 1-18) and assign the
> minimum value of this group as a new variable in data (Data$Conc_min), and
> do the same for row.id 2 and all the rest of the rows.
>
> I'm just not sure how to do this and I appreciate any help folks might
>
Re: [R] Associate a .R file with the RGui
RGui is not an editor. It is a console (aka REPL,
https://en.wikipedia.org/wiki/Read%E2%80%93eval%E2%80%93print_loop).
When using RGui, it is up to you to edit your R file in an external editor like
Notepad++ and copy paste code snippets or use source("yourfile.R") as desired.
On November 5, 2022 6:47:54 AM PDT, Amarjit Chandhial via R-help
wrote:
>
>
>
>Hi Andrew/Petr,
>
>
>Thanks for the replies.
>
>In R Console if I run:
>
>R.home("bin")
>
>I get the following
>
>"C:/PROGRA~1/R/R-42~1.2/bin/x64"
>
>which is where
>
>Rgui.exe is (within the x64 folder there are 13 files in total: 8 . exe
>and 5 .dll).
>
>
>In file Explorer if I right-click on a .R file -> Open With -> R for
>Windows GUI Front-End
>
>RGui (64-bit) opens but the .R file does not appear in the editor.
>
>
>Amarjit
>
>
>-- Original Message --
>From: "Andrew Simmons"
>To: "Amarjit Chandhial"
>Cc: "R-help Mailing List"
>Sent: Friday, 4 Nov, 2022 At 09:08
>Subject: Re: [R] Associate a .R file with the RGui
>
>In an R session, run this:
>
>writeLines(normalizePath(R.home("bin")))
>
>
>Right click your .R file > Open with > Choose another app > Check the
>box "Always use this app to open .R files" > Look for another app on
>this PC
>Paste the directory found above, then select "Rgui.exe"
>
>
>On Fri, Nov 4, 2022, 04:49 Amarjit Chandhial via R-help
>mailto:r-help@r-project.org> > wrote:
>
> Hi,
>
>
> My OS is Windows 11 Pro 64-Bit, I have R 4.2.2 and RStudio installed.
>
> If I double-click on a .R file in File Explorer the OS gives me the
> option of opening the .R in RStudio, or Look for an app in the
>Microsoft
> Store, or More Apps. Similarly with a right-click.
>
> I would like to associate a .R file with the RGui, not RStudio, thus
> when I double-click on a .R file in File Explorer the .R file opens in
> the R Editor in RGui.
>
> On my PC R 4.2.2 is located in "C:/Program Files/R/R-4.2.2/etc"
>
> Please can someone provide step-by-step instructions on how to
> associate?
>
>
> thanks,
> Amarjit
>
> [[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.
>
>
>
>
> [[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.
--
Sent from my phone. Please excuse my brevity.
__
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] Associate a .R file with the RGui
Hi Andrew/Petr,
Thanks for the replies.
In R Console if I run:
R.home("bin")
I get the following
"C:/PROGRA~1/R/R-42~1.2/bin/x64"
which is where
Rgui.exe is (within the x64 folder there are 13 files in total: 8 . exe
and 5 .dll).
In file Explorer if I right-click on a .R file -> Open With -> R for
Windows GUI Front-End
RGui (64-bit) opens but the .R file does not appear in the editor.
Amarjit
-- Original Message --
From: "Andrew Simmons"
To: "Amarjit Chandhial"
Cc: "R-help Mailing List"
Sent: Friday, 4 Nov, 2022 At 09:08
Subject: Re: [R] Associate a .R file with the RGui
In an R session, run this:
writeLines(normalizePath(R.home("bin")))
Right click your .R file > Open with > Choose another app > Check the
box "Always use this app to open .R files" > Look for another app on
this PC
Paste the directory found above, then select "Rgui.exe"
On Fri, Nov 4, 2022, 04:49 Amarjit Chandhial via R-help
mailto:r-help@r-project.org> > wrote:
Hi,
My OS is Windows 11 Pro 64-Bit, I have R 4.2.2 and RStudio installed.
If I double-click on a .R file in File Explorer the OS gives me the
option of opening the .R in RStudio, or Look for an app in the
Microsoft
Store, or More Apps. Similarly with a right-click.
I would like to associate a .R file with the RGui, not RStudio, thus
when I double-click on a .R file in File Explorer the .R file opens in
the R Editor in RGui.
On my PC R 4.2.2 is located in "C:/Program Files/R/R-4.2.2/etc"
Please can someone provide step-by-step instructions on how to
associate?
thanks,
Amarjit
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[R] rio: list of extensions for supported formats
Hi, is there a function in the package rio to get the file extensions listed in the vignette under supported formats? Thanks Sigbert __ 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] Selecting a minimum value of an attribute associated with point values neighboring a given point and assigning it as a new attribute
Hello,
I have sets of spatial points with LAT, LON coords (unprojected, WGS84 datum)
and several value attributes associated with each point, from numerous csv
files (with an average of 6,000-9,000 points in each file) as shown in the
following example:
data<- read.csv("R_find_pts_testdata.csv")
> data
ID Date TimeLATLON Conc
Leg.SpeedCO2 H2O BC61 Hr Min Sec
1 76 4/19/2021 21:25:38 42.40066 -70.98802 99300 0.0 mph 428.39 9.57 578
21 25 38
2 77 4/19/2021 21:25:39 42.40066 -70.98802 96730 0.0 mph 428.04 9.57 617
21 25 39
3 79 4/19/2021 21:25:41 42.40066 -70.98802 98800 0.2 mph 427.10 9.57 1027
21 25 41
4 80 4/19/2021 21:25:42 42.40066 -70.98802 96510 2 mph 427.99 9.58 1381
21 25 42
5 81 4/19/2021 21:25:43 42.40067 -70.98801 95540 3 mph 427.99 9.58 1271
21 25 43
6 82 4/19/2021 21:25:44 42.40068 -70.98799 94720 4 mph 427.20 9.57 910
21 25 44
7 83 4/19/2021 21:25:45 42.40069 -70.98797 94040 5 mph 427.18 9.57 652
21 25 45
8 84 4/19/2021 21:25:46 42.40072 -70.98795 95710 7 mph 427.07 9.57 943
21 25 46
9 85 4/19/2021 21:25:47 42.40074 -70.98792 96200 8 mph 427.44 9.56 650
21 25 47
10 86 4/19/2021 21:25:48 42.40078 -70.98789 9375010 mph 428.76 9.57 761
21 25 48
11 87 4/19/2021 21:25:49 42.40081 -70.98785 9336011 mph 429.25 9.56 1158
21 25 49
12 88 4/19/2021 21:25:50 42.40084 -70.98781 9434012 mph 429.56 9.57 107
21 25 50
13 89 4/19/2021 21:25:51 42.40087 -70.98775 9278012 mph 428.62 9.56 720
21 25 51
What I want to do is, for each point, identify all points within 50m of that
point, find the minimum value of the "Conc" attribute of each nearby set of
points (including the original point) and then create a new variable
("Conc_min") and assign this minimum value to a new variable added to "data".
So far, I have the following code:
library(spdep)
library(sf)
setwd("C:\\mydirectory\\")
data<- read.csv("R_find_pts_testdata.csv")
#make sure the data is a data frame
pts <- data.frame(data)
#create spatial data frame and define projection
pts_coords <- cbind(pts$LON, pts$LAT)
data_pts <- SpatialPointsDataFrame(coords= pts_coords,
data=pts, proj4string = CRS("+proj=longlat +datum=WGS84"))
#Re-project to WGS 84 / UTM zone 18N, so the analysis is in units of m
ptsUTM <- sf::st_as_sf(data_pts, coords = c("LAT", "LON"), remove = F)%>%
st_transform(32618)
#create 50 m buffer around each point then intersect with points and finally
find neighbors within the buffers
pts_buf <- sf::st_buffer(ptsUTM, 50)
coords <- sf::st_coordinates(ptsUTM)
int <- sf::st_intersects(pts_buf, ptsUTM)
x <- spdep::dnearneigh(coords, 0, 50)
Now at this point, I'm not sure what to either the "int" (a sgbp list) or "x"
(nb object) objects (or even if I need them both)
> int
Sparse geometry binary predicate list of length 974, where the predicate was
`intersects'
first 10 elements:
1: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
2: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
3: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
4: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
5: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
6: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
7: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
8: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
9: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, ...
> x
Neighbour list object:
Number of regions: 974
Number of nonzero links: 34802
Percentage nonzero weights: 3.668481
Average number of links: 35.73101
One thought is that maybe I don't need the dnearneigh function and can instead
convert "int" into a dataframe and somehow merge or associate (perhaps with an
inner join) the ID fields of the buffered and intersecting points and then
compute the minimum value of "Conc" grouping by ID:
> as.data.frame(int)
row.id col.id
11 1
21 2
31 3
41 4
51 5
61 6
71 7
81 8
91 9
10 1 10
11 1 11
12 1 12
13 1 13
14 1 14
15 1 15
16 1 16
17 1 17
18 1 18
19 2 1
20 2 2
21 2 3
22 2 4
23 2 5
24 2 6
25 2 7
26 2 8
27 2 9
28 2 10
So in the above example I'd like to take the minimum of "Conc" among the col.id
points grouped with row.id 1 (i.e., col.ids 1-18) and assign the minimum value
of this group as a new variable in data (Data$Conc_min), and do the same for
row.id 2 and all the rest of the rows.
I'm just not sure how to do this and I appreciate any help folks might have on
this matter!
Many thanks,
-Tiffany
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