Differences in geographical division levels between GADM and Nightlights for Vietnam

nreguera commented 4 years ago

I might have done something wrong in some point but I can´t find where.

I am just doing some merging transformations with the data, and they work fine for all the countries except for Vietnam. I have in one variable the divisions from GADM map (in the following screenshot in the variable called VNM.provinces.map) and in another variable the nightlights readings (in the following screenshot called VNM.nl). When I try to do a transformation at first level (similar to province) it tells me that the number of columns is different, and in fact they are:

Untitled

The data from GADM has 63 columns (red square) meanwhile the Nightlights has 28 (1 is NA) (orange square). Also I have realized that in the Nightlights data, the two administrative divisions that have unkonwn and unknown.1 names have the same number of levels, 28.

Is it possible that an error ocurred when I downloaded this data?

Thanks.

nreguera commented 4 years ago

Update:

I extracted the Vietnam nightlights data again from the rasters that I already downloaded (located in the outputrasters folder), deleting previously both STRUCT and DATA related files in the data folder, and the new STRUCT and DATA files generated look the same. You can see them in these links:

I see lots of NAs in the columns unknown, unknown.1 and ward_(xã), so I think this may be the reason why later in the analysis I can only detect part of the admin LEVEL_1 divisions (28 out of the 63 that appear in the GADM dataset).

chrisvwn commented 4 years ago

Hmm. You shouldn't have unknown column names with GADM. Could you provide the step-by-step code you are using?

nreguera commented 4 years ago

Yes, very weird, having into account that I have used the same code for 5 countries, and vietnam is the only one that had this issue. The code is this:

ctry <- "VNM" # KHM, MMR, VNM, LAO, THA
nightlights.data <- getCtryNlData(
                      ctryCode = ctry,
                      admLevel = "admin3", 
                      nlType = "VIIRS.M", 
                      nlPeriods = nlRange("201204", "201812"), 
                      ignoreMissing = FALSE, 
                      nlStats = list("sum", na.rm=TRUE))

chrisvwn commented 4 years ago

I have found a bug that was causing an error that I think was related to what you're experiencing. It was a simple issue but one that would occur in very isolated cases. Interestingly, I could not successfully run the above command as I was getting an error before the data was written to disk.

Could you try the latest github update and let me know if it fixes the issue?

nreguera commented 4 years ago

I uninstalled it and tried to reinstall to catch the last updates, but it gives me this error:

Warning in install.packages : package ‘Rnightlights’ is not available (for R version 3.6.1)

chrisvwn commented 4 years ago

Please install fro.github.

devtools::install_github("chrisvwn/Rnightlights")

nreguera commented 4 years ago

I followed the same process as before, removing the STRUCT and DATA files that I had, and using the rasters previously downloaded located in the outputrasters folder to extract the data in them, and the new files generated still contain the unknown column names and the NAs in lots of rows values (attached in this message as a ZIP). May it be the problem in the rasters?

data.zip

chrisvwn commented 4 years ago

Please post the output from the command

chrisvwn commented 4 years ago

Hey @nreguera . Have you had any luck with this? If not could you post the command you are running as well as the full output it produces? This would help me track down what might be going on. The steps you are following seem correct to me but something weird is going on. The rasters would not cause this issue.

nreguera commented 4 years ago

Hello @chrisvwn sorry for the late reply. This is the code I executed:

library(Rnightlights)
Sys.setlocale("LC_TIME", "English")
Sys.setlocale(locale = "UTF-8")
pkgOptions(downloadMethod="aria")
pkgOptions(extractMethod = "rast", numCores=4)
pkgOptions(deleteTiles=TRUE)

ctry <- "VNM" # KHM, MMR, VNM, LAO, THA
nightlights.data <- getCtryNlData(
                      ctryCode = ctry,
                      admLevel = "admin3",
                      nlType = "VIIRS.M",
                      nlPeriods = nlRange("201204", "201812"),
                      ignoreMissing = FALSE,
                      nlStats = list("sum", na.rm=TRUE))

And this is the output:

2020-01-08 17:07:14: NlRange autodetected nlType: VIIRS.M
2020-01-08 17:07:14: ctryStruct not found. Creating
Processing missing data: VNM:VIIRS.M:VCMCFG:201204:sum, VIIRS.M:VCMCFG:201205:sum, VIIRS.M:VCMCFG:201206:sum, VIIRS.M:VCMCFG:201207:sum, VIIRS.M:VCMCFG:201208:sum, VIIRS.M:VCMCFG:201209:sum, VIIRS.M:VCMCFG:201210:sum, VIIRS.M:VCMCFG:201211:sum, VIIRS.M:VCMCFG:201212:sum, VIIRS.M:VCMCFG:201301:sum, VIIRS.M:VCMCFG:201302:sum, VIIRS.M:VCMCFG:201303:sum, VIIRS.M:VCMCFG:201304:sum, VIIRS.M:VCMCFG:201305:sum, VIIRS.M:VCMCFG:201306:sum, VIIRS.M:VCMCFG:201307:sum, VIIRS.M:VCMCFG:201308:sum, VIIRS.M:VCMCFG:201309:sum, VIIRS.M:VCMCFG:201310:sum, VIIRS.M:VCMCFG:201311:sum, VIIRS.M:VCMCFG:201312:sum, VIIRS.M:VCMCFG:201401:sum, VIIRS.M:VCMCFG:201402:sum, VIIRS.M:VCMCFG:201403:sum, VIIRS.M:VCMCFG:201404:sum, VIIRS.M:VCMCFG:201405:sum, VIIRS.M:VCMCFG:201406:sum, VIIRS.M:VCMCFG:201407:sum, VIIRS.M:VCMCFG:201408:sum, VIIRS.M:VCMCFG:201409:sum, VIIRS.M:VCMCFG:201410:sum, VIIRS.M:VCMCFG:201411:sum, VIIRS.M:VCMCFG:201412:sum, VIIRS.M:VCMCFG:201501:sum, VIIRS.M:VCMCFG:201502:sum, VIIRS.M:VCMCFG:201503:sum, VIIRS.M:VCMCFG:201504:sum, VIIRS.M:VCMCFG:201505:sum, VIIRS.M:VCMCFG:201506:sum, VIIRS.M:VCMCFG:201507:sum, VIIRS.M:VCMCFG:201508:sum, VIIRS.M:VCMCFG:201509:sum, VIIRS.M:VCMCFG:201510:sum, VIIRS.M:VCMCFG:201511:sum, VIIRS.M:VCMCFG:201512:sum, VIIRS.M:VCMCFG:201601:sum, VIIRS.M:VCMCFG:201602:sum, VIIRS.M:VCMCFG:201603:sum, VIIRS.M:VCMCFG:201604:sum, VIIRS.M:VCMCFG:201605:sum, VIIRS.M:VCMCFG:201606:sum, VIIRS.M:VCMCFG:201607:sum, VIIRS.M:VCMCFG:201608:sum, VIIRS.M:VCMCFG:201609:sum, VIIRS.M:VCMCFG:201610:sum, VIIRS.M:VCMCFG:201611:sum, VIIRS.M:VCMCFG:201612:sum, VIIRS.M:VCMCFG:201701:sum, VIIRS.M:VCMCFG:201702:sum, VIIRS.M:VCMCFG:201703:sum, VIIRS.M:VCMCFG:201704:sum, VIIRS.M:VCMCFG:201705:sum, VIIRS.M:VCMCFG:201706:sum, VIIRS.M:VCMCFG:201707:sum, VIIRS.M:VCMCFG:201708:sum, VIIRS.M:VCMCFG:201709:sum, VIIRS.M:VCMCFG:201710:sum, VIIRS.M:VCMCFG:201711:sum, VIIRS.M:VCMCFG:201712:sum, VIIRS.M:VCMCFG:201801:sum, VIIRS.M:VCMCFG:201802:sum, VIIRS.M:VCMCFG:201803:sum, VIIRS.M:VCMCFG:201804:sum, VIIRS.M:VCMCFG:201805:sum, VIIRS.M:VCMCFG:201806:sum, VIIRS.M:VCMCFG:201807:sum, VIIRS.M:VCMCFG:201808:sum, VIIRS.M:VCMCFG:201809:sum, VIIRS.M:VCMCFG:201810:sum, VIIRS.M:VCMCFG:201811:sum, VIIRS.M:VCMCFG:201812:sum. This may take a while. 
Note: Set 'ignoreMissing=TRUE' to return only data found or 
'ignoreMissing=NULL' to return NULL if not all the data is found
2020-01-08 17:07:20: **** START PROCESSING: ctryCodes=VNM, admLevels=list(VNM = "gadm36_VNM_3"), nlTypes=VIIRS.M, configNames=VCMCFG, multiTileStrategy=all, multiTileMergeFun=mean, removeGasFlares=TRUE, nlPeriods=c("201204", "201205", "201206", "201207", "201208", "201209", "201210", "201211", "201212", "201301", "201302", "201303", "201304", "201305", "201306", "201307", "201308", "201309", "201310", "201311", "201312", "201401", "201402", "201403", "201404", "201405", "201406", "201407", "201408", "201409", "201410", "201411", "201412", "201501", "201502", "201503", "201504", "201505", "201506", "201507", "201508", "201509", "201510", "201511", "201512", "201601", "201602", "201603", "201604", "201605", 
"201606", "201607", "201608", "201609", "201610", "201611", "201612", "201701", "201702", "201703", "201704", "201705", "201706", "201707", "201708", "201709", "201710", "201711", "201712", "201801", "201802", "201803", "201804", "201805", "201806", "201807", "201808", "201809", "201810", "201811", "201812"), nlStats=list(list("sum", na.rm = TRUE)), custPolyPath=NULL, gadmVersion=3.6, gadmPolyType=shpZip, downloadMethod=aria, cropMaskMethod=rast, extractMethod=rast****
2020-01-08 17:07:20: Downloading country polygons ...
  |                                                                                       |   0%2020-01-08 17:07:20: Downloading polygon: VNM
2020-01-08 17:07:20: Downloading ctry poly: VNM
2020-01-08 17:07:20: Downloading ctry shpZip: VNM
2020-01-08 17:07:20: Polygon dir for VNM:3.6 already exists
  |=======================================================================================| 100%
2020-01-08 17:07:21: Downloading country polygons ... DONE
2020-01-08 17:07:21: **** PROCESSING nlType:VIIRS.M | configName: VCMCFG | nlPeriod:201204****
2020-01-08 17:07:21: Checking tiles required for VIIRS.M 201204
2020-01-08 17:07:21: VNM: cropped raster exists. Tile not required
2020-01-08 17:07:21: numTiles: 0, Required tiles: 
2020-01-08 17:07:21: No tiles needed for 201204. Processing countries with missing stats and existing cropped rasters
2020-01-08 17:07:21: Processing ctryCode: VNM
2020-01-08 17:07:21: Processing ctryCode: VNM AdmLevel: gadm36_VNM_3
2020-01-08 17:07:21: ProcessNlCountry: ctryCode=VNM, admLevel=gadm36_VNM_3, nlType=VIIRS.M, configName=VCMCFG, multiTileStrategy=all, multiTileMergeFun=mean, removeGasFlares=TRUE, nlPeriod=201204, nlStats=list(list("sum", na.rm = TRUE)), downloadMethod=aria, cropMaskMethod=rast, extractMethod=rast, gadmVersion=3.6, gadmPolyType=shpZip, custPolyPath=NULL****
2020-01-08 17:07:21: Check for existing data file
2020-01-08 17:07:21: Data file not found. Creating ...
2020-01-08 17:07:26: Data file not found. Creating ... DONE
2020-01-08 17:07:26: Begin processing 201204
2020-01-08 17:07:26: E:/Nightligths/.Rnightlights/outputrasters/NL_VNM_VIIRS.M_201204_VCMCFG-MTSALL-MEAN-RGFT_GADM-3.6-SHPZIP.tif already exists
2020-01-08 17:07:26: Begin extracting data from the raster 
  |======================================================================================================================================================| 100%
2020-01-08 17:33:29: Saving nlStat 'sum(...=TRUE)' ...
2020-01-08 17:33:29: Saving nlStat 'sum' ... DONE
2020-01-08 17:33:29: DONE processing VNM 201204
2020-01-08 17:33:29: **COMPLETE. Writing data to disk
2020-01-08 17:33:29: **** PROCESSING nlType:VIIRS.M | configName: VCMCFG | nlPeriod:201205****
2020-01-08 17:33:29: Checking tiles required for VIIRS.M 201205
2020-01-08 17:33:29: VNM: cropped raster exists. Tile not required
2020-01-08 17:33:30: numTiles: 0, Required tiles: 
2020-01-08 17:33:30: No tiles needed for 201205. Processing countries with missing stats and existing cropped rasters
2020-01-08 17:33:30: Processing ctryCode: VNM
2020-01-08 17:33:30: Processing ctryCode: VNM AdmLevel: gadm36_VNM_3
2020-01-08 17:33:30: ProcessNlCountry: ctryCode=VNM, admLevel=gadm36_VNM_3, nlType=VIIRS.M, configName=VCMCFG, multiTileStrategy=all, multiTileMergeFun=mean, removeGasFlares=TRUE, nlPeriod=201205, nlStats=list(list("sum", na.rm = TRUE)), downloadMethod=aria, cropMaskMethod=rast, extractMethod=rast, gadmVersion=3.6, gadmPolyType=shpZip, custPolyPath=NULL****
2020-01-08 17:33:30: Check for existing data file
2020-01-08 17:33:30: Data file found: E:/Nightligths/.Rnightlights/data/NL_DATA_VNM_ADM3_GADM-3.6-SHPZIP.csv
2020-01-08 17:33:30: Processing stats: sum(...=TRUE)
2020-01-08 17:33:30: Load country data file
2020-01-08 17:33:30: Load country polygon admin level
2020-01-08 17:33:30: Begin processing 201205
2020-01-08 17:33:30: E:/Nightligths/.Rnightlights/outputrasters/NL_VNM_VIIRS.M_201205_VCMCFG-MTSALL-MEAN-RGFT_GADM-3.6-SHPZIP.tif already exists
2020-01-08 17:33:30: Begin extracting data from the raster 
  |======                                                                                                                                                |   4%

nreguera commented 4 years ago

Anyway, I am running late, so I will skip Vietnam data...

chrisvwn commented 4 years ago

Noted. Let me have a look at this.

A quick note. For the NAs that you might be getting could you for now quote the arguments so that you have list("sum", "na.rm=TRUE"). There is a bug there that I need to fix.

nreguera commented 4 years ago

Ok, just let me know if you want me to test the bug fix.

chrisvwn commented 4 years ago

I have fixed the bug. Could you try these steps:

delete VNM data and struct files
delete all VNM files and directories under polygons directory
delete all .rds files from gasflares directory (fixed warnings about different proj4 strings)
uninstall Rnightlights
reinstall Rnightlights from github
run getCtryNlData (note numCores pkgOption has been renamed to numThreads)

nreguera commented 4 years ago

I got this error when trying to reinstall Rnightlights:

Error: Failed to install 'Rnightlights' from GitHub:
  (converted from warning) cannot remove prior installation of package ‘fansi’

chrisvwn commented 4 years ago

Could you try restarting R/RStudio after uninstalling Rnightlights then try the reinstall.

On Sun, Jan 12, 2020, 09:47 Natxo notifications@github.com wrote:

I got this error when trying to reinstall Rnightlights:

Error: Failed to install 'Rnightlights' from GitHub:

(converted from warning) cannot remove prior installation of package ‘fansi’

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/chrisvwn/Rnightlights/issues/53?email_source=notifications&email_token=ABQXQOUWUIMZUCMXOVNCSR3Q5K4IPA5CNFSM4J7C73BKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEIWTIWA#issuecomment-573387864, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABQXQOXEWPJDLI3AKTTE2JTQ5K4IPANCNFSM4J7C73BA .

nreguera commented 4 years ago

I got this one:

> devtools::install_github("chrisvwn/Rnightlights")
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘fansi’
In addition: Warning message:
package ‘sp’ was built under R version 3.6.2

chrisvwn commented 4 years ago

Please try to install fansi manually:

install.packages('fansi')

then try to reinstall.

Edit: Also add the dependencies option to install_github so try:

devtools::install_github("chrisvwn/Rnightlights", dependencies=TRUE)

nreguera commented 4 years ago

Fansi was installed successfully:

> install.packages('fansi')
Installing package into ‘D:/Docs/R/win-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/fansi_0.4.1.zip'
Content type 'application/zip' length 223944 bytes (218 KB)
downloaded 218 KB

package ‘fansi’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\Natxo\AppData\Local\Temp\RtmpY7MQ23\downloaded_packages

But I got an error in RNightlights:

> devtools::install_github("chrisvwn/Rnightlights", dependencies=TRUE)
WARNING: Rtools is required to build R packages, but is not currently installed.

Please download and install Rtools custom from http://cran.r-project.org/bin/windows/Rtools/.
Downloading GitHub repo chrisvwn/Rnightlights@master
These packages have more recent versions available.
Which would you like to update?

1: All                                    
2: CRAN packages only                     
3: None                                   
4: bit         (1.1-14 -> 1.1-15.1) [CRAN]
5: stringi     (1.4.4  -> 1.4.5   ) [CRAN]
6: xfun        (0.11   -> 0.12    ) [CRAN]
7: prettyunits (1.0.2  -> 1.1.0   ) [CRAN]

Enter one or more numbers, or an empty line to skip updates:
1
dendextend   (NA     -> 1.13.2  ) [CRAN]
gdalUtils    (NA     -> 2.0.1.14) [CRAN]
ggdendro     (NA     -> 0.1-20  ) [CRAN]
plotly       (NA     -> 4.9.1   ) [CRAN]
shinyjs      (NA     -> 1.1     ) [CRAN]
bit          (1.1-14 -> 1.1-15.1) [CRAN]
stringi      (1.4.4  -> 1.4.5   ) [CRAN]
viridis      (NA     -> 0.5.1   ) [CRAN]
png          (NA     -> 0.1-7   ) [CRAN]
leaflet.p... (NA     -> 1.9.0   ) [CRAN]
tidyr        (NA     -> 1.0.0   ) [CRAN]
hexbin       (NA     -> 1.28.0  ) [CRAN]
gridExtra    (NA     -> 2.3     ) [CRAN]
xfun         (0.11   -> 0.12    ) [CRAN]
prettyunits  (1.0.2  -> 1.1.0   ) [CRAN]
Installing 15 packages: dendextend, gdalUtils, ggdendro, plotly, shinyjs, bit, stringi, viridis, png, leaflet.providers, tidyr, hexbin, gridExtra, xfun, prettyunits
Installing packages into ‘D:/Docs/R/win-library/3.6’
(as ‘lib’ is unspecified)

  There are binary versions available but the source versions are later:
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shinyjs    1.0      1.1             FALSE
bit     1.1-14 1.1-15.1              TRUE
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trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/prettyunits_1.1.0.zip'
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downloaded 36 KB

package ‘dendextend’ successfully unpacked and MD5 sums checked
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The downloaded binary packages are in
    C:\Users\Natxo\AppData\Local\Temp\RtmpY7MQ23\downloaded_packages
installing the source packages ‘shinyjs’, ‘xfun’

trying URL 'https://cran.rstudio.com/src/contrib/shinyjs_1.1.tar.gz'
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** help
*** installing help indices
  converting help for package 'xfun'
    finding HTML links ... done
    Rscript                                 html  
    attr                                    html  
    download_file                           html  
    embed_file                              html  
    file_ext                                html  
    file_string                             html  
    gsub_file                               html  
    in_dir                                  html  
    install_dir                             html  
    install_github                          html  
    isFALSE                                 html  
    is_ascii                                html  
    native_encode                           html  
    normalize_path                          html  
    numbers_to_words                        html  
    optipng                                 html  
    os                                      html  
    parse_only                              html  
    pkg_attach                              html  
    prose_index                             html  
    protect_math                            html  
    raw_string                              html  
    read_utf8                               html  
    rename_seq                              html  
    rev_check                               html  
    rstudio_type                            html  
    same_path                               html  
    session_info                            html  
    split_lines                             html  
    strict_list                             html  
    stringsAsStrings                        html  
    tojson                                  html  
    try_silent                              html  
    upload_ftp                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (xfun)

The downloaded source packages are in
    ‘C:\Users\Natxo\AppData\Local\Temp\RtmpY7MQ23\downloaded_packages’
WARNING: Rtools is required to build R packages, but is not currently installed.

Please download and install Rtools custom from http://cran.r-project.org/bin/windows/Rtools/.
Error: Failed to install 'Rnightlights' from GitHub:emp\RtmpY7MQ23\remotes9444fe54e1a\chrisvwn-Rnightlights-0a9e516/DESCRIPTION' ...
  lazy-load database 'D:/Docs/R/win-library/3.6/prettyunits/R/prettyunits.rdb' is corrupt
In addition: Warning message:
In paste0(" (", pretty_dt(elapsed), ")") :
  internal error -3 in R_decompress1

chrisvwn commented 4 years ago

Okay. That is a step in the right direction. Could you try the suggested solution:

Please download and install Rtools custom from http://cran.r-project.org/bin/windows/Rtools/.

nreguera commented 4 years ago

It looks it´s working:

data.zip

But why there are characters like ? in the names?

chrisvwn commented 4 years ago

Great! The ? characters means that the computer does not have the character set/locale to display the characters correctly. Not sure how to deal with this but you can try to install and set the locale for VNM text

nreguera commented 4 years ago

Ok, we will leave this for the next project I guess.

Thank you so much for your support @chrisvwn I think I won´t disturb you for a while :)

chrisvwn commented 4 years ago

You're welcome @nreguera . Always a pleasure!

chrisvwn / Rnightlights

Differences in geographical division levels between GADM and Nightlights for Vietnam #53