README.md

In zevross-spatial/rstudio-conf2020-spatial-ex: Exercises and Solutions for Spatial Data with R Workshop (Part 1)

http://bit.ly/zrsaSpatialWorkshop

To get to dashboard

• Log in as Zev, replace workspace with "admin" in URL

Creation of server

sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo apt-get update
sudo apt-get install r-base

sudo apt-get install gdebi-core
wget https://download2.rstudio.org/server/bionic/amd64/rstudio-server-1.2.5033-amd64.deb
sudo gdebi rstudio-server-1.2.5033-amd64.deb

# units package requires libdunits2-dev
sudo add-apt-repository ppa:ubuntugis/ppa
sudo apt-get update
sudo apt-get install libudunits2-dev libgdal-dev libgeos-dev libproj-dev
sudo apt install libcurl4-openssl-dev libssl-dev libxml2-dev


# BEGIN if you installed old version of R and need to remove
sudo R
.libPaths() # to find where the packages were
sudo apt-get purge --auto-remove r-base
# then manually remove the folders from .libPaths()
sudo apt-get install r-base
# END if you need to remove

# https://github.com/mtennekes/tmap/blob/master/ubuntu_17_installation.sh
sudo apt-get install libv8-dev 
sudo apt-get install libjq-dev 
sudo apt-get install libprotobuf-dev 
sudo apt-get install protobuf-compiler
sudo apt-get install libcairo2-dev

# this only really for OpenStreetMap
sudo apt-get install -y default-jre
sudo apt-get install -y default-jdk
sudo R CMD javareconf

# then

sudo R
install.packages("sf")
install.packages("tmap")
install.packages(c("mapview", "raster"))
install.packages(c("ggplot2", "tidyr", "dplyr", "stringr"))
install.packages("rmapshaper")
install.packages("rJava")
install.packages("shinyjs") # for tmaptools::palette_explorer()
install.packages("OpenStreetMap") # for tmaptools::read_osm()
install.packages(c(“tidycensus”, “FedData”, “osmdata”,  “rnaturalearth”)) 

mkdir uploads
chmod -R 755 uploads
chown ubuntu uploads

This is the repo for the exercise/solutions package

# On your machine
scpspatialworkshop  ~/git-repos/zrsaSpatialWorkshop_0.2.tar.gz
scpspatialworkshop ~/git-repos/workshop-r-spatial-slides/pdfs/Archive.zip 

unzip Archive.zip
# On the server
sudo R
detach(package:zrsaSpatialWorkshop) # error related to name is fine
remove.packages("zrsaSpatialWorkshop")
q()
sudo R

# careful what folder
install.packages('/home/ubuntu/uploads/zrsaSpatialWorkshop_0.2.tar.gz',
  repos = NULL, type="source")

Delete existing users

sudo rstudio-server kill-all
sudo rstudio-server restart

 for i in {1001..1200}
  do
    sudo userdel -r guest$i
done

Delete slides then unzip

cd ~/uploads # not under sudo su
sudo rm -rf -d *.pdf
unzip datascienceRworkshop1_slides.zip
chmod -R 755 ~/uploads

If you just want to delete slides from user folders

# delete slides
for i in {1001..1100}
  do
    echo $i
    user=guest$i
    sudo -u $user rm -rf -d /home/$user/slides/*pdf
done

<<<<<<< HEAD
# delete data
for i in {1001..1100}
  do
    echo $i
    user=guest$i
    sudo -u $user rm -rf -d /home/$user/data/*.*
done

Create users and folders

=======

Added 2020-01-21

install.packages(c("tidycensus", "FedData", "osmdata", "OpenStreetMap", "rnaturalearth"))

Temporary locations for slides and package

files.zevross.com/workshops/spatial/slides/pdf/zrsaSpatialWorkshop-slides.zip files.zevross.com/workshops/spatial/r-package/zrsaSpatialWorkshop_0.2.0.tar.gz

e00a5a7e18c5a8f8d33bcbfaa1ce154778762bb4

for i in {1001..1100}
  do
    echo $i
    echo "guest$i:pass$i:$i:800:RStudio:/home/guest$i:/bin/bash" | sudo newusers
    user=guest$i
    sudo -u $user mkdir -p /home/$user/slides
    sudo -u $user mkdir -p /home/$user/data
    sudo -u $user mkdir -p /home/$user/workshop-package
done

Copy materials to users

for i in {1001..1100}
  do
    echo $i
    user=guest$i
    sudo -u $user cp -a /home/ubuntu/uploads/*.pdf /home/$user/slides/
    sudo -u $user cp -a /usr/local/lib/R/site-library/zrsaSpatialWorkshop/data-raw/* /home/$user/data/
    sudo -u $user cp -a /home/ubuntu/uploads/zrsaSpatialWorkshop_0.2.tar.gz /home/$user/workshop-package/
done


# just for package updates
for i in {1001..1100}
  do
    echo $i
    user=guest$i
    sudo -u $user cp -a /home/ubuntu/uploads/zrsaSpatialWorkshop_0.2.tar.gz /home/$user/workshop-package/
done


# if you only want to move data
for i in {1001..1100}
  do
    echo $i
    user=guest$i
    sudo -u $user cp -a /usr/local/lib/R/site-library/zrsaSpatialWorkshop/data-raw/* /home/$user/data/
done

Fixing a broken session

If a user is experiencing trouble with their session try the following,

1. Connect to the server, ssh -i path/to/file.pem [e-mail]
2. Move to the users folder, cd ~/../user####/
3. Move their .rstudio folder, mv .rstudio .rstudio-old
4. Have the user open a new browser tab or window and connect to the RStudio server

If the problem persists,

1. Connect to the server, if not still connected
2. Find the PID of the users session, sudo rstudio-server active-sessions | grep user#### | cut -d " " -f 3
3. Kill or suspend the user's session, sudo rstudio-server force-suspend-session <PID> or sudo kill <PID>

Here's what was used for first time teaching

But on my local machine 1/12/2020, I have GEOS 3.7.2, GDAL 2.4.2, PROJ 5.2.0

On the Ubuntu (18) machine in prep for the RStudio workshop

zevross-spatial/rstudio-conf2020-spatial-ex documentation built on Jan. 29, 2020, 9:57 a.m.