Re: [R] [External] Re: Error in setwd(dir) when initializing R
Hello, Thank you all for your responses. When I initialize R, the folder in which it starts is: getwd() [1] "C:/Users/Ana/OneDrive - Universidad Complutense de Madrid (UCM)/Documentos" So it seems a problem with OneDrive -Kevin: I do not really understand your question... You mean if I set my working directory to my C:// or D:// folder in my computer? It doesn't work either. -Ivan: this is the message I got when running traceback(). So can I move the.Rdata file without affecting the work? -Luke: thank you for the idea, I will try it. Error in setwd(dir) : no es posible cambiar el directorio de trabajo> traceback()4: setwd(dir) 3: .rs.onAvailablePackagesStale(reposString) 2: .rs.availablePackages() 1: .rs.rpc.discover_package_dependencies("3C994FEC", ".R") Best, Ana El mar, 21 nov 2023 a las 0:43, escribió: > On Mon, 20 Nov 2023, Ivan Krylov wrote: > > > On Mon, 20 Nov 2023 12:18:11 +0100 > > Ana de las Heras Molina wrote: > > > >> Error in setwd(dir) : no es posible cambiar el directorio de trabajo > > > > If you run traceback() first thing after getting this error, does it > > say anything useful? (Anything besides "No traceback available" would > > count as useful.) > > > > Do you have a file named .RData in your home directory? If yes, it may > > help to move it away (or remove it if you don't use the saved session). > > Also check for .Rprofile or other profile that might contain a setwd() > call. Starting R with --vanilla should work if the issue is a startup > file. > > Best, > > luke > > > > > > > -- > Luke Tierney > Ralph E. Wareham Professor of Mathematical Sciences > University of Iowa Phone: 319-335-3386 > Department of Statistics andFax: 319-335-3017 > Actuarial Science > 241 Schaeffer Hall email: luke-tier...@uiowa.edu > Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu > -- *Ana de las Heras Molina* Nutrición Animal Departamento de Producción Animal Facultad de Veterinaria Universidad Complutense de Madrid *Contacto*: 913943855/anaher...@ucm.es [[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] Calculating volume under polygons
(Keeping on the list. And consider my suggestion to move this to R-sig-Geo) What is the coordinate reference system of the polygon layer? Can you share these layers? On 21/11/2023 4:58, javad bayat wrote: Dear Micha; Thank you for your reply. The R version is 4.3.2, the raster package is "raster_3.6-26", the sf package is "sf_1.0-14". The str of the raster and polygon is as follow: > str(r) Formal class 'RasterLayer' [package "raster"] with 13 slots ..@ file :Formal class '.RasterFile' [package "raster"] with 13 slots .. .. ..@ name : chr "E:\Base1.tif" .. .. ..@ datanotation: chr "INT2S" .. .. ..@ byteorder : chr "little" .. .. ..@ nodatavalue : num -Inf .. .. ..@ NAchanged : logi FALSE .. .. ..@ nbands : int 1 .. .. ..@ bandorder : chr "BIL" .. .. ..@ offset : int 0 .. .. ..@ toptobottom : logi TRUE .. .. ..@ blockrows : Named int 128 .. .. .. ..- attr(*, "names")= chr "rows" .. .. ..@ blockcols : Named int 128 .. .. .. ..- attr(*, "names")= chr "cols" .. .. ..@ driver : chr "gdal" .. .. ..@ open : logi FALSE ..@ data :Formal class '.SingleLayerData' [package "raster"] with 13 slots .. .. ..@ values : logi(0) .. .. ..@ offset : num 0 .. .. ..@ gain : num 1 .. .. ..@ inmemory : logi FALSE .. .. ..@ fromdisk : logi TRUE .. .. ..@ isfactor : logi FALSE .. .. ..@ attributes: list() .. .. ..@ haveminmax: logi TRUE .. .. ..@ min : num 1801 .. .. ..@ max : num 3289 .. .. ..@ band : int 1 .. .. ..@ unit : chr "" .. .. ..@ names : chr "Base1" ..@ legend :Formal class '.RasterLegend' [package "raster"] with 5 slots .. .. ..@ type : chr(0) .. .. ..@ values : logi(0) .. .. ..@ color : logi(0) .. .. ..@ names : logi(0) .. .. ..@ colortable: logi(0) ..@ title : chr(0) ..@ extent :Formal class 'Extent' [package "raster"] with 4 slots .. .. ..@ xmin: num 330533 .. .. ..@ xmax: num 402745 .. .. ..@ ymin: num 3307321 .. .. ..@ ymax: num 3345646 ..@ rotated : logi FALSE ..@ rotation:Formal class '.Rotation' [package "raster"] with 2 slots .. .. ..@ geotrans: num(0) .. .. ..@ transfun:function () ..@ ncols : int 5777 ..@ nrows : int 3066 ..@ crs :Formal class 'CRS' [package "sp"] with 1 slot .. .. ..@ projargs: chr NA ..@ srs : chr "+proj=utm +zone=40 +datum=WGS84 +units=m +no_defs" ..@ history : list() ..@ z : list() > str(p) sf [12 × 10] (S3: sf/tbl_df/tbl/data.frame) $ Name : chr [1:12] "01" "02" "03" "04" ... $ FolderPath: chr [1:12] ... $ SymbolID : num [1:12] 0 0 0 0 0 0 0 0 0 0 ... $ AltMode : int [1:12] 0 0 0 0 0 0 0 0 0 0 ... $ Base : num [1:12] 0 0 0 0 0 0 0 0 0 0 ... $ Clamped : int [1:12] -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 ... $ Extruded : int [1:12] 0 0 0 0 0 0 0 0 0 0 ... $ Shape_Area: num [1:12] 63.51 15.28 9.23 39.19 642.38 ... $ Area : num [1:12] 64 15 9 39 642 56 36 16 53 39 ... $ geometry :sfc_POLYGON of length 12; first list element: List of 1 ..$ : num [1:18, 1:3] 55.6 55.6 55.6 55.6 55.6 ... ..- attr(*, "class")= chr [1:3] "XYZ" "POLYGON" "sfg" - attr(*, "sf_column")= chr "geometry" - attr(*, "agr")= Factor w/ 3 levels "constant","aggregate",..: NA NA NA NA NA NA NA NA NA ..- attr(*, "names")= chr [1:9] "Name" "FolderPath" "SymbolID" "AltMode" ... Sincerely On Mon, Nov 20, 2023 at 5:15 PM Micha Silver wrote: Hi: Some preliminary comments first 1- You might get a better response posting to R-sig-Geo 2- Probably better to switch to the `terra` package instead of the older `raster` 3- Furthermore, there is the package `exactextractr` that ensures that edge pixels are taken into account, weighted by the actual, partial coverage of each pixel by the polygon. 4- Can you post: your R version, and version of the relevant packages, and information about the polygons and DEM (i.e. `str(p)` and `str(r)` ) On 20/11/2023 14:30, javad bayat wrote: > Dear all; > I am trying to calculate volume under each polygon of a shapefile according > to a DEM. > when I run the code, it gives me an error as follows. > " > Error in h(simpleError(msg, call)) : > error in evaluating the argument 'x' in selecting a method for function > 'addAttrToGeom': sp supports Z dimension only for POINT and MULTIPOINT. > use `st_zm(...)` to coerce to XY dimensions > " > I want to have a table that contains one column corresponding to the > polygon rank and another that contains the volume on that polyon. > I would be more than happy if anyone could help me. > I provided codes at the end of this email. > Sincerely > > > ## > library(raster); > library(sf) > # Load the DEM raster and shapefile > r <- ra
Re: [R] [External] Re: Error in setwd(dir) when initializing R
On Mon, 20 Nov 2023, Ivan Krylov wrote: On Mon, 20 Nov 2023 12:18:11 +0100 Ana de las Heras Molina wrote: Error in setwd(dir) : no es posible cambiar el directorio de trabajo If you run traceback() first thing after getting this error, does it say anything useful? (Anything besides "No traceback available" would count as useful.) Do you have a file named .RData in your home directory? If yes, it may help to move it away (or remove it if you don't use the saved session). Also check for .Rprofile or other profile that might contain a setwd() call. Starting R with --vanilla should work if the issue is a startup file. Best, luke -- Luke Tierney Ralph E. Wareham Professor of Mathematical Sciences University of Iowa Phone: 319-335-3386 Department of Statistics andFax: 319-335-3017 Actuarial Science 241 Schaeffer Hall email: luke-tier...@uiowa.edu Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu __ 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] Cannot calculate confidence intervals NULL
Dear Bert, Dear All, Yes, thanks ! that was the problem! Le mercredi 15 novembre 2023 à 22:21:53 UTC+1, Bert Gunter a écrit : I believe the problem is here: cor1 <- cor(x1, y1, method="spearman") cor2 <- cor(x2, y2, method="spearman") The x's and y's are not looked for in data (i.e. NSE) but in the environment where the function was defined, which is standard evaluation. Change the above to: cor1 <- with(d, cor(x1, y1, method="spearman")) cor2 <- with(d, cor(x2, y2, method="spearman")) and all should be fine. -- Bert On Wed, Nov 15, 2023 at 12:54 PM varin sacha via R-help wrote: > R-Experts, > > Here below my R code working without error message but I don't get the > results I am expecting. > Here is the result I get: > > [1] "All values of t are equal to 0.28611928397257 \n Cannot calculate > confidence intervals" > NULL > > If someone knows how to solve my problem, really appreciate. > Best, > S > > > # > # Difference in Spearman rho > > library(boot) > > x1=c(4,6,5,7,8,4,2,3,5.5,6.7,5.5,3.5,2,1,3,5,6,3.5,2.5,2,1,2,3,2,1,2,3,4,3,4) > > y1=c(10,14,12.5,21,15,16,17.5,11,11.5,21,19,16,17.5,18,18.5,12,13,14,11,11,12,18,20,13,23,12,11,14,16,11) > > x2=c(5,3,4,2,1,1,1,2,3,4,5,4,3,2,1,3,4.5,4.5,5.5,6,5,4,7,8,3,4,2,5,4,3) > > y2=c(11,12,13,11,10,19,21,21,13,15,18,13,12,14,19,18.5,17.5,12.5,10,9,11,13,14,16,11,18,14,13,12,12) > > # Function to calculate the difference in Spearman coefficients > pearson_diff <- function(data, indices) { > > # Sample the data > d <- data[indices, ] > > # Calculate the Spearman correlation coefficients for every sample > cor1 <- cor(x1, y1, method="spearman") > cor2 <- cor(x2, y2, method="spearman") > > # Return the difference > return(cor1 - cor2) > } > > # Create a data.frame with the data > data <- data.frame(x1, y1, x2, y2) > > # Use the boot function to apply the bootstrap > set.seed(123) # For reproducibility > bootstrap_results <- boot(data = data, statistic = pearson_diff, R = 1000) > > # Calculate all the 95% confidence interval > boot.ci(bootstrap_results, type = "all") > ### > > > __ > 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-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] Error in setwd(dir) when initializing R
On Mon, 20 Nov 2023 12:18:11 +0100 Ana de las Heras Molina wrote: > Error in setwd(dir) : no es posible cambiar el directorio de trabajo If you run traceback() first thing after getting this error, does it say anything useful? (Anything besides "No traceback available" would count as useful.) Do you have a file named .RData in your home directory? If yes, it may help to move it away (or remove it if you don't use the saved session). -- Best regards, Ivan __ 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] Error in setwd(dir) when initializing R
I think that you may be correct about OneDrive being related. I have seen OneDrive associated with problems before. What happens if you manually set the working directory to that location? Does it work if your default home directory is local to your machine? > On Nov 20, 2023, at 6:18 AM, Ana de las Heras Molina wrote: > > [You don't often get email from andel...@ucm.es. Learn why this is important > at https://aka.ms/LearnAboutSenderIdentification ] > > Hello, > I am Ana de las Heras, and I write to you because every time I open RStudio > or R directly I have the following message, before I can do anything at > all: > > Error in setwd(dir) : no es posible cambiar el directorio de trabajo > > > At first I didn't pay much attention to it, but I am having lots of > troubles with different programs, including LinDa, ANCOMBC or Genome > InfoDbdata (and thus, phyloseq). After asking in the different forus of > each program, they have told me that the issue is more related to my R > installation and that first message I obtain when I start the program. > > I would be very grateful if someone could help me. This issue started when > I installed the latest version of R (4.3.1. and now 4.3.2.). I have already > uninstalled and reinstalled both programs, as well as Rtools. I am not sure > if the issue could be related to ONe Drive, since the HOME folder is in > OneDrive. I am currently working on Windows 10, 64 bits. > > Yours faithfully, > Ana > -- > *Ana de las Heras Molina* > > > Nutrición Animal > Departamento de Producción Animal > Facultad de Veterinaria > Universidad Complutense de Madrid > > *Contacto*: 913943855/anaher...@ucm.es > >[[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-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] Error in setwd(dir) when initializing R
Hello, I am Ana de las Heras, and I write to you because every time I open RStudio or R directly I have the following message, before I can do anything at all: Error in setwd(dir) : no es posible cambiar el directorio de trabajo At first I didn't pay much attention to it, but I am having lots of troubles with different programs, including LinDa, ANCOMBC or Genome InfoDbdata (and thus, phyloseq). After asking in the different forus of each program, they have told me that the issue is more related to my R installation and that first message I obtain when I start the program. I would be very grateful if someone could help me. This issue started when I installed the latest version of R (4.3.1. and now 4.3.2.). I have already uninstalled and reinstalled both programs, as well as Rtools. I am not sure if the issue could be related to ONe Drive, since the HOME folder is in OneDrive. I am currently working on Windows 10, 64 bits. Yours faithfully, Ana -- *Ana de las Heras Molina* Nutrición Animal Departamento de Producción Animal Facultad de Veterinaria Universidad Complutense de Madrid *Contacto*: 913943855/anaher...@ucm.es [[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] Calculating volume under polygons
Hi: Some preliminary comments first 1- You might get a better response posting to R-sig-Geo 2- Probably better to switch to the `terra` package instead of the older `raster` 3- Furthermore, there is the package `exactextractr` that ensures that edge pixels are taken into account, weighted by the actual, partial coverage of each pixel by the polygon. 4- Can you post: your R version, and version of the relevant packages, and information about the polygons and DEM (i.e. `str(p)` and `str(r)` ) On 20/11/2023 14:30, javad bayat wrote: Dear all; I am trying to calculate volume under each polygon of a shapefile according to a DEM. when I run the code, it gives me an error as follows. " Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'addAttrToGeom': sp supports Z dimension only for POINT and MULTIPOINT. use `st_zm(...)` to coerce to XY dimensions " I want to have a table that contains one column corresponding to the polygon rank and another that contains the volume on that polyon. I would be more than happy if anyone could help me. I provided codes at the end of this email. Sincerely ## library(raster); library(sf) # Load the DEM raster and shapefile r <- raster("E:/Base1.tif") p <- read_sf(dsn = "E:/Sites.shp", layer = " Sites") Now to the question: In `read_sf()`, when the source is a shapefile, you do not need the 'layer' option. It doesn't hurt, but in this case I see that you have an extra space before the layer name. Could that be causing the problem? # Extract the values of the DEM raster for each polygon values <- extract(r, p) Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'addAttrToGeom': sp supports Z dimension only for POINT and MULTIPOINT. use `st_zm(...)` to coerce to XY dimensions # Calculate the volume of each polygon volumes <- sapply(values, function(x) rasterVolume(x, r)) What is this "rasterVolume" function that you call here? # Print the results for (i in 1:length(volumes)) { cat(sprintf("Volume under polygon %d: %f\n", i, volumes[i])) } ## -- Micha Silver Ben Gurion Univ. Sde Boker, Remote Sensing Lab cell: +972-523-665918 __ 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] Calculating volume under polygons
Dear all; I am trying to calculate volume under each polygon of a shapefile according to a DEM. when I run the code, it gives me an error as follows. " Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'addAttrToGeom': sp supports Z dimension only for POINT and MULTIPOINT. use `st_zm(...)` to coerce to XY dimensions " I want to have a table that contains one column corresponding to the polygon rank and another that contains the volume on that polyon. I would be more than happy if anyone could help me. I provided codes at the end of this email. Sincerely ## library(raster); library(sf) # Load the DEM raster and shapefile r <- raster("E:/Base1.tif") p <- read_sf(dsn = "E:/Sites.shp", layer = " Sites") # Extract the values of the DEM raster for each polygon values <- extract(r, p) Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'addAttrToGeom': sp supports Z dimension only for POINT and MULTIPOINT. use `st_zm(...)` to coerce to XY dimensions # Calculate the volume of each polygon volumes <- sapply(values, function(x) rasterVolume(x, r)) # Print the results for (i in 1:length(volumes)) { cat(sprintf("Volume under polygon %d: %f\n", i, volumes[i])) } ## -- Best Regards Javad Bayat M.Sc. Environment Engineering Alternative Mail: bayat...@yahoo.com [[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] anyone having trouble accesing CRAN?
Notice that getCRANmirrors() without the local.only=TRUE gets its list from ...tada cran.r-project.org. Arguably, that might be in for a change. Meanwhile, you might just use cloud.r-project.org right away. -pd > On 15 Nov 2023, at 20:23 , Ivan Krylov wrote: > > On Wed, 15 Nov 2023 14:13:00 -0500 > "Christopher W. Ryan via R-help" wrote: > >> Anyone seeing similar? > > Same for me. > > While it worked, CRAN website had the following message: > >>> The CRAN Admin Team will perform system upgrades during the period >>> Wednesday November 15 until Thursday November 16, 2023. There will >>> be intermittent outages in service during this time. > > Use chooseCRANmirror(local.only = TRUE) (or subset() the return value > of getCRANmirrors(local.only = TRUE)) to access a mirror that works. > > -- > Best regards, > Ivan > > __ > 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. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd@cbs.dk Priv: pda...@gmail.com __ 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.