possible bug in "using geospatial data"

[mdlincoln]

reported from twitter:

There seems to be a directory missing in the data provided for "Using Geospatial Data to Inform Historical Research in R." The tutorial reads: Census_Data <- read.csv("./data/County1990_Data/nhgis0027_ts_nominal_county.csv" but there is no County1990_Data folder

I can look into it this weekend unless someone has a chance to take a look sooner.

[mdlincoln]

OK, I've checked through the lesson and the uploaded data have quite a few problems.

Firstly, our reporter is correct - there is no Country1900_Data/nhgist0027_ts_nominal_country.csv file.

Moreover, the County1900 directory data is incomplete - it has data, but no spatial information, such that when I run the very first import command of the lesson, I get the following warning:

County_Aggregate_Data <- st_read("./data/County1990/")
#> Reading layer `US_county_1990' from data source `/Users/mlincoln/Development/geospatial/data/County1990' using driver `ESRI Shapefile'
#> Warning message:
#> no simple feature geometries present: returning a data.frame or tbl_df 

Because of this, none of the rest of the lesson will work. FWIW I also tried opening this shapefile in QGIS (which also ought to be able to read it) and it says that it's not a valid shapefile, so whatever data have been uploaded are corrupt or incomplete.

@JMParr you were the editor for this lesson, can you please check if you have the complete data for it somewhere?

[JMParr]

Hi, @mdlincoln - I've looked through the files, including old clones from Github. Unfortunately, it looks like I do not have complete data. I'm not sure what happened. Correcting it will necessitate contacting the author.

[mdlincoln]

@JMParr ok, please contact them. Without it the lesson is unusable.

[acrymble]

I'm going to put a warning message on this until this can be resolved. We don't want people thinking this lesson is useable.

[acrymble]

@ladew222 you were the author of this tutorial. It looks like there has been an issue getting all of the data files in place. Can you help us rectify this so we can re-publicize the lesson?

[mdlincoln]

Thanks for adding that warning @acrymble, I think that's a reasonable interim action to take. @JMParr have you emailed the author yet?

If we aren't able to get the correct data file within some period of time (1-2 months?), though, I think it would be necessary to retire the lesson This isn't a minor issue in one section - without the correct data almost all of the lesson is broken.

[JMParr]

I have emailed the author, but I haven't heard back. It's possible it went into the spam folder, or he's just busy and hasn't had a chance to reply. The data files were fine when the lesson was originally finalized.

On Sun, Apr 7, 2019 at 9:40 AM Matthew Lincoln notifications@github.com wrote:

Thanks for adding that warning @acrymble https://github.com/acrymble, I think that's a reasonable interim action to take. @JMParr https://github.com/JMParr have you emailed the author yet?

If we aren't able to get the correct data file within some period of time (1-2 months?), though, I think it would be necessary to retire the lesson https://programminghistorian.org/en/lesson-retirement-policy This isn't a minor issue in one section - without the correct data almost all of the lesson is broken.

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[ladew222]

I apologize for the late reply as there was an email issue. I will take a look and get back to you this week. Like Jessica mentioned, the files were functioning at publication so the files may have gotten corrupted somehow if I was to guess. I will look to see what is the source of the issue and repackage the files if necessary.

On Apr 7, 2019, at 7:15 PM, Jessica Parr notifications@github.com wrote:

I have emailed the author, but I haven't heard back. It's possible it went into the spam folder, or he's just busy and hasn't had a chance to reply. The data files were fine when the lesson was originally finalized.

On Sun, Apr 7, 2019 at 9:40 AM Matthew Lincoln notifications@github.com wrote:

Thanks for adding that warning @acrymble https://github.com/acrymble, I think that's a reasonable interim action to take. @JMParr https://github.com/JMParr have you emailed the author yet?

If we aren't able to get the correct data file within some period of time (1-2 months?), though, I think it would be necessary to retire the lesson https://programminghistorian.org/en/lesson-retirement-policy This isn't a minor issue in one section - without the correct data almost all of the lesson is broken.

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[JMParr]

Thank you @ladew22 !

On Sun, Apr 7, 2019 at 9:03 PM ladew222 notifications@github.com wrote:

I apologize for the late reply as there was an email issue. I will take a look and get back to you this week. Like Jessica mentioned, the files were functioning at publication so the files may have gotten corrupted somehow if I was to guess. I will look to see what is the source of the issue and repackage the files if necessary.

On Apr 7, 2019, at 7:15 PM, Jessica Parr notifications@github.com wrote:

I have emailed the author, but I haven't heard back. It's possible it went into the spam folder, or he's just busy and hasn't had a chance to reply. The data files were fine when the lesson was originally finalized.

On Sun, Apr 7, 2019 at 9:40 AM Matthew Lincoln <notifications@github.com

wrote:

Thanks for adding that warning @acrymble https://github.com/acrymble, I think that's a reasonable interim action to take. @JMParr https://github.com/JMParr have you emailed the author yet?

If we aren't able to get the correct data file within some period of time (1-2 months?), though, I think it would be necessary to retire the lesson https://programminghistorian.org/en/lesson-retirement-policy This isn't a minor issue in one section - without the correct data almost all of the lesson is broken.

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[ladew222]

No problem. I compared my archive to the compressed download and there is quite a bit missing; both files and folders. I checked to see very briefly to see the code worked with my archive and it appears to function but I want work through the lesson more completely. Once done, I can send over the files. What is the best means for me to deliver the items.

On Apr 7, 2019, at 8:25 PM, Jessica Parr notifications@github.com wrote:

Thank you @ladew22 !

On Sun, Apr 7, 2019 at 9:03 PM ladew222 notifications@github.com wrote:

I apologize for the late reply as there was an email issue. I will take a look and get back to you this week. Like Jessica mentioned, the files were functioning at publication so the files may have gotten corrupted somehow if I was to guess. I will look to see what is the source of the issue and repackage the files if necessary.

On Apr 7, 2019, at 7:15 PM, Jessica Parr notifications@github.com wrote:

I have emailed the author, but I haven't heard back. It's possible it went into the spam folder, or he's just busy and hasn't had a chance to reply. The data files were fine when the lesson was originally finalized.

On Sun, Apr 7, 2019 at 9:40 AM Matthew Lincoln <notifications@github.com

wrote:

Thanks for adding that warning @acrymble https://github.com/acrymble, I think that's a reasonable interim action to take. @JMParr https://github.com/JMParr have you emailed the author yet?

If we aren't able to get the correct data file within some period of time (1-2 months?), though, I think it would be necessary to retire the lesson https://programminghistorian.org/en/lesson-retirement-policy This isn't a minor issue in one section - without the correct data almost all of the lesson is broken.

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.

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[JMParr]

Sounds good. @acrymble is Managing Editor. He can let us know.

On Sun, Apr 7, 2019 at 9:36 PM ladew222 notifications@github.com wrote:

No problem. I compared my archive to the compressed download and there is quite a bit missing; both files and folders. I checked to see very briefly to see the code worked with my archive and it appears to function but I want work through the lesson more completely. Once done, I can send over the files. What is the best means for me to deliver the items.

On Apr 7, 2019, at 8:25 PM, Jessica Parr notifications@github.com wrote:

Thank you @ladew22 !

On Sun, Apr 7, 2019 at 9:03 PM ladew222 notifications@github.com wrote:

I apologize for the late reply as there was an email issue. I will take a look and get back to you this week. Like Jessica mentioned, the files were functioning at publication so the files may have gotten corrupted somehow if I was to guess. I will look to see what is the source of the issue and repackage the files if necessary.

On Apr 7, 2019, at 7:15 PM, Jessica Parr notifications@github.com wrote:

I have emailed the author, but I haven't heard back. It's possible it went into the spam folder, or he's just busy and hasn't had a chance to reply. The data files were fine when the lesson was originally finalized.

On Sun, Apr 7, 2019 at 9:40 AM Matthew Lincoln < notifications@github.com

wrote:

Thanks for adding that warning @acrymble < https://github.com/acrymble>, I think that's a reasonable interim action to take. @JMParr https://github.com/JMParr have you emailed the author yet?

If we aren't able to get the correct data file within some period of time (1-2 months?), though, I think it would be necessary to retire the lesson https://programminghistorian.org/en/lesson-retirement-policy This isn't a minor issue in one section - without the correct data almost all of the lesson is broken.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <

https://github.com/programminghistorian/jekyll/issues/1181#issuecomment-480591502

,

or mute the thread <

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[acrymble]

Thank you both for the update. @ladew222 can you try to get us the fix by 7 May 2019 please? You can email them to the managing editor (see http://programminghistorian.org/en/project-team)

[ladew222]

I am a day tardy on this due to illness. I am sending the files today.

[JMParr]

Thank you @ladew222 . I hope you are feeling better. Tagging @mdlincoln in case he hasn't seen this yet.

[acrymble]

I've received the data from @ladew222 and he says there are 2 other minor fixes he wants to make. Once I hear what those are I'll do a pull request with the changes.

[acrymble]

I've received the data and the author has suggested the following two fixes:

County_Aggregate_Data$RelativeTotal= ((cntyNCG$AV0AA1990/10000)/cntyNCG$CountMembers )

To

County_Aggregate_Data$RelativeTotal= ((County_Aggregate_Data$AV0AA1990/10000)/County_Aggregate_Data$CountMembers )

And

qtm(shp = cntyNCG, fill = "CountMembers",text="NHGISNAM",text.size="A57AA1980")

to

qtm(shp = County_Aggregate_Data, fill = "CountMembers",text="NHGISNAM",text.size="A57AA1980")

--

I will push up the changes and then we can make sure everything is still working.

[acrymble]

We have a new problem.

The shapefiles for this lesson are too large. The file "County1990/US_county_1990.shp" is 79mb, and as a result, the Archive.zip file that contains everything is also very large. Github will only let me upload files of 25mb. That means that even with these fixes a key file is going to be missing.

@mdlincoln is there a solution we can adopt? I've half-completed these changes on branch "issue-1181".

I have the missing files on my computer

[ladew222]

I will try to reduce the file and try to limit it to the two states I directly analyzed rather than the entire US. I will try to reduce on my end with hat 25mb number as a reference.

On May 17, 2019, at 10:42 AM, Adam Crymble notifications@github.com wrote:

We have a new problem.

The shapefiles for this lesson are too large. The file "County1990/US_county_1990.shp" is 79mb, and as a result, the Archive.zip file that contains everything is also very large. Github will only let me upload files of 25mb. That means that even with these fixes a key file is going to be missing.

@mdlincoln https://github.com/mdlincoln is there a solution we can adopt? I've half-completed these changes on branch "issue-1181".

I have the missing files on my computer

[mdlincoln]

Thanks @ladew222 - yes, please simplify the geometry as this lesson doesn't require anything near the resolution of 79mb. https://mapshaper.org/ is a very simple online tool for doing this, or there are methods in R, QGIS, ArcMap for it as well.

[ladew222]

Thanks,

I used map shaper and simplified the shape file. The files is now 23.2 mb. I can reduce more if needed as well. Here is a link to the modified file: https://we.tl/t-bZ50NVAjwj https://we.tl/t-bZ50NVAjwj.

On May 20, 2019, at 7:31 PM, Matthew Lincoln notifications@github.com wrote:

Thanks @ladew222 https://github.com/ladew222 - yes, please simplify the geometry as this lesson doesn't require anything near the resolution of 79mb. https://mapshaper.org/ https://mapshaper.org/ is a very simple online tool for doing this, or there are methods in R, QGIS, ArcMap for it as well.

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[acrymble]

I've got the smaller file. I'm going to try to do a pull request. @ladew222 I think ideally a much smaller file would make the lesson more globally accessible. We've been reminded recently that some parts of the world still struggle to download files of this size. But this resolves our immediate need.

[acrymble]

Oops @ladew222 I've just noticed that your new file, when extracted from the zip, is still above 25mb. We've uploaded the files individually into the assets folder, so this too needs to be below the threshold. I haven't opened the file itself to see what extra detail is in there, but is there more that can be cut that allows for a minimally functioning tutorial with small file sizes?

[ladew222]

Sure. I will cut a bit more and make is well under to prevent any issues.

On May 22, 2019, at 1:52 AM, Adam Crymble notifications@github.com wrote:

Oops @ladew222 https://github.com/ladew222 I've just noticed that your new file, when extracted from the zip, is still above 25mb. We've uploaded the files individually into the assets folder, so this too needs to be below the threshold. I haven't opened the file itself to see what extra detail is in there, but is there more that can be cut that allows for a minimally functioning tutorial with small file sizes?

[ladew222]

I reduced the file down further. I apologize for the too large file. I uploaded the entire County1990 folder which is now listed at 16.9 mb. Here is the file https://we.tl/t-eumryd43pt https://we.tl/t-eumryd43pt

https://we.tl/t-Y9buBfVS6s https://we.tl/t-Y9buBfVS6s

On May 22, 2019, at 8:07 AM, Eric Weinberg egweinbe@gmail.com wrote:

Sure. I will cut a bit more and make is well under to prevent any issues.

On May 22, 2019, at 1:52 AM, Adam Crymble <notifications@github.com mailto:notifications@github.com> wrote:

Oops @ladew222 https://github.com/ladew222 I've just noticed that your new file, when extracted from the zip, is still above 25mb. We've uploaded the files individually into the assets folder, so this too needs to be below the threshold. I haven't opened the file itself to see what extra detail is in there, but is there more that can be cut that allows for a minimally functioning tutorial with small file sizes?

[acrymble]

I've created a pull request where we can preview this lesson.

https://deploy-preview-1312--ph-dev.netlify.com/en/lessons/geospatial-data-analysis

Is anyone available to try out the code to help us make sure it works now?

[ladew222]

Thanks for anyone willing to help. I will run through the complete lesson again myself as well over the next couple of days.

On May 23, 2019, at 8:40 AM, Adam Crymble notifications@github.com wrote:

I've created a pull request where we can preview this lesson.

https://deploy-preview-1312--ph-dev.netlify.com/en/lessons/geospatial-data-analysis https://deploy-preview-1312--ph-dev.netlify.com/en/lessons/geospatial-data-analysis Is anyone available to try out the code to help us make sure it works now?

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[acrymble]

@ladew222 I'm afraid we're still having problems with this, which @mdlincoln has pointed out in his review of the pull request. https://github.com/programminghistorian/jekyll/pull/1312

Can you please address the comments, and completely re-try the lesson before we try another pull request?

If we aren't able to fix this by the end of June, I'm going to propose retiring the lesson.

[ladew222]

Thanks everyone. I noted similar issues yesterday and was trying alternative toward simplification of the geometry to deal with the size issues but I think @mdlincoln https://github.com/mdlincoln may be right that the best route is to subset North Carolina and South Carolina rather that simplifying the geometry as there appears to have been an issue with map shaper’s simplification. I do cover subsetting as part of the lesson so I may leave in one other state so I can describe that process as long as file size is not an issue. I do have an addendum that address how to obtain the entire shapefile from NHGIS so it should cover users who are interested in other geographic regions at least in the U.S. I will then test the entire lesson with the new files and update you when it is tested and complete.

On May 29, 2019, at 10:39 AM, Adam Crymble notifications@github.com wrote:

@ladew222 https://github.com/ladew222 I'm afraid we're still having problems with this, which @mdlincoln https://github.com/mdlincoln has pointed out in his review of the pull request. #1312 https://github.com/programminghistorian/jekyll/pull/1312 Can you please address the comments, and completely re-try the lesson before we try another pull request?

If we aren't able to fix this by the end of June, I'm going to propose retiring the lesson.

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[mdlincoln]

@ladew222 I like that idea a lot!

[ladew222]

I was able to simplify the entire U.S. map and test the results which saved me from some additional modifications to the actual lesson. I went through the lesson and tested the new files to ensure they work properly. The data directory is available here:https://dropmefiles.com/0OP4Q https://dropmefiles.com/0OP4Q and is 32 MB. The .shp file is no 19.2 MB and is the largest file. I updated the lesson file from ph-submissions at https://github.com/programminghistorian/ph-submissions/blob/gh-pages/lessons/geospatial-data-analysis.md https://github.com/programminghistorian/ph-submissions/blob/gh-pages/lessons/geospatial-data-analysis.md. This is needed to match the new data. The most substantive change is that the data directory is now County1990ussm. If you are able to upload the files, I am more than willing to test again once uploaded or make any additional changes.

Thanks everyone.

On May 31, 2019, at 9:48 AM, Matthew Lincoln notifications@github.com wrote:

@ladew222 https://github.com/ladew222 I like that idea a lot!

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[acrymble]

I believe @JMParr is back in a few days. Can you please take over and re-test this lesson so that we can resolve the issues with the data files?

Let us know if you need help.

[acrymble]

We had suggested retiring this lesson if a fix was not in place by the end of June. @JMParr we're now at that deadline. Can you please let us know your plan so we can proceed appropriately?

[ladew222]

And please let me know if anything is needed from my end.

Sent from my iPhone

On Jun 30, 2019, at 7:26 AM, Adam Crymble notifications@github.com wrote:

We had suggested retiring this lesson if a fix was not in place by the end of June. @JMParr we're now at that deadline. Can you please let us know your plan so we can proceed appropriately?

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[JMParr]

Hi, Adam- I'm just back from medical leave, and was away last week. I will take a look through this tomorrow. Sorry for the delay. I did not see your previous email.

On Sun, Jun 30, 2019 at 8:26 AM Adam Crymble notifications@github.com wrote:

We had suggested retiring this lesson if a fix was not in place by the end of June. @JMParr https://github.com/JMParr we're now at that deadline. Can you please let us know your plan so we can proceed appropriately?

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[JMParr]

Just a confirmation that I am working on testing. I'll provide an update by the end of the week.

[JMParr]

Hi, all. Thank you for your patience. I've hit a bump that's probably minor, and I wanted to double check that it was not an issue local to my fairly elderly laptop. That meant getting into campus to try on some other machines (and you can imagine the traffic getting near a Boston campus the week of July 4th). In trying to run the package installs, I keep getting requests to select HTTPS CRAN mirror.

[JMParr]

@ladew222 is this a step that comes up on your end?

[mdlincoln]

@JMParr If someone has installed R for the first time, then R will prompt them to select a CRAN mirror from the list provided. Once you do that, it ought to continue installation with no problems - were you able to do so?

[JMParr]

I've had R installed on my laptop for 3 years, and had an updated version. Similar issue on campus, and none of them were new installs. Very strange.

[mdlincoln]

@JMParr the setting gets stored in an .Rprofile file in your home directory, so it's possible that got moved somehow? In any event, nothing in the lesson code would trigger that.

Also - AFTER you selected that, were you able to proceed?

[JMParr]

Thanks, @mdlincoln . My R skills are admittedly rusty. New error message, asserting that there's no package called "tmap." Here's the full text of the error:

The downloaded source packages are in ‘/private/var/folders/bb/yy26r_g54_136qgvyj_3c_nm0000gn/T/RtmpFKKvA6/downloaded_packages’ Warning message: In install.packages("sf") : installation of package ‘units’ had non-zero exit status

library(sf) configure: error: in /private/var/folders/bb/yy26r_g54_136qgvyj_3c_nm0000gn/T/RtmpqWzSF2/R.INSTALL814e200d79/units': configure: error: C++ compiler cannot create executables Seeconfig.log' for more details ERROR: configuration failed for package ‘units’

• removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/units’ Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘units’ In addition: Warning message: package ‘sf’ was built under R version 3.3.2 Error: package or namespace load failed for ‘sf’ library(tmap) Error in library(tmap) : there is no package called ‘tmap’

[ladew222]

I will do a raw install on a new machine here today to see if I can replicate any of the issues with the packages in R. I have not had issues but have had R installed for some time on both my machines.

On Jul 9, 2019, at 8:41 AM, Jessica Parr notifications@github.com wrote:

admittedly rusty. New error m

[JMParr]

Thanks @ladew222 - I'm also going do a new one to see if that helps. It's possible that something has gone wrong with my install through an update or something else.

[JMParr]

Hmmm. That didn't help. Very strange.

[mdlincoln]

ooh, units often causes issues because it hooks into a lot of C++ code. First off though, it looks like you're running a very old version of R - the current version is 3.6.1 and it looks like yours is around 3.3? I'm afraid that's the most troubleshooting I can do today, but it may be helpful to just wipe out everything and rebuild from the newest version.

[JMParr]

Thanks! I thought I had recently updated, but it looks like I was mistaken. Am working on another new wipe and re-install, but need to update my OS first.

[mdlincoln]

good luck! I had to do all that last month, myself... 😭

[ladew222]

Yep. I will try a raw here once I get access to another machine to see how that runs as well.

On Jul 9, 2019, at 9:12 AM, Matthew Lincoln notifications@github.com wrote:

good luck! I had to do all that last month, myself... 😭

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[JMParr]

Heh. Thanks! I may have been hedging my bets. New OS update for my laptop is quite recent, but laptop is now 4 years old, "well-loved," and showing its age. Was looking to replace it this summer, but will just have to take the plunge and run those updates now since it's become a productivity/work issue.

[ladew222]

I was able to do a raw install here without problems. Please let me know if I can be of assistance on the checking/update.