Help Desk FAQs

Atlas.ti Exporting 

Qualitative Software.
Export entire Atlas.ti project using Menu:
“File” -> “Export” -> “Project Bundle”
“Import & Export” tab with more exporting details.
Atlas.ti Exporting Projects Documentation

Incorporating Jupyter Notebook

I will initiate a jupyter notebook for this demo and use a package with a sample code.

Begin by following the instructions above to create the virtual environment. Install your desired package before starting jupyter notebook.

Use pip or conda commands to install libraries to your virtual environment

pip install keras
pip install tensorflow

Must install ipykernel to initiate from jupyter notebook from Anaconda command prompt

pip install ipykernel

conda install ipykernel

Must install “jupyter” and '"jupyter notebook" libraries to initiate from Anaconda command prompt

pip install jupyter

pip install jupyter notebook

If pip install jupyter gives kernel dead. use pip uninstall jupyter, then use conda

conda install jupyter

Will use “random2” package for my sample code

pip install random2

Initiate jupyter notebook with the command below

jupyter notebook

You may have .ipynb files scattered all over your filing system. You can initiate your environment from any folder so long as you specify the location

jupyter notebook --notebook-dir U:/Documents

The command above opens Jupyter with Documents as the home directory. Now I can access any .ipynb files inside all folders within Documents. This can be done with Desktop, Downloads, etc.

Some information can be gotten from the following link.

Pythonforundergradengineers.com

 

Incorporating Jupyter Lab

Begin by following the instructions above to create the virtual environment. Use pip command to install libraries to your virtual environment

pip install jupyterlab

type ‘jupyter lab’ to initiate. Make sure to open using Firefox or Microsoft Edge browsers, Internet Explorer does not support jupyter lab

jupyter lab

Take the localhost link in the screenshot below and paste it into an acceptable browser, Firefox, or Microsoft Edge. Below is an example of a localhost URL from the screenshot below:

http://localhost:8888/?token=6f0251d09cbd560c97b38faacfd4ddb040dec8d167c770c0

• Jupyter lab opened in an acceptable browser

Sample Program

Use the program below to test once the jupyter notebook has opened within a web browser. This program is dependent on the library “random2”, installed in the commands above.

#!/usr/bin/env python
import random # Get a random number generator.
NTRIALS = 10000 # Enough trials to get a reasonably accurate answer.
NPEOPLE = 30 # How many people in the group?
matches = 0 # Keep track of how many trials have matching birthdays.
for trial in range(NTRIALS): 12# Do a bunch of trials...
taken = {} # A place to keep track of which birthdays
# are already taken on this trial.
for person in range(NPEOPLE): 60# Put the people’s birthdays down, one at a time...
day = random.randint(0, 365) # On a randomly chosen day.
if day in taken:4
matches += 1 # A match! # No need to look for more than one.
taken[day] = 1 # Mark the day as taken.
print("The fraction of trials that have matching birthdays is", float(matches)/NTRIALS)

Using Spyder

Open Anaconda prompt.

Activate the directory using the steps at the beginning of the article.

Must install ipykernel to initiate from jupyter notebook from Anaconda command prompt

conda install ipykernel
pip install spyder
pip install jedi

pip install ipykernel
conda install ipykernel

Use pip command to install other libraries to your virtual environment

pip install random2

Initiate the Spyder application with the command below spyder

Run test program dependent on random2 library.

#!/usr/bin/env python
import random # Get a random number generator.
NTRIALS = 10000 # Enough trials to get a reasonably accurate answer.
NPEOPLE = 30 # How many people in the group?
matches = 0 # Keep track of how many trials have matching birthdays.
for trial in range(NTRIALS): 12# Do a bunch of trials...
taken = {} # A place to keep track of which birthdays
# are already taken on this trial.
for person in range(NPEOPLE): 60# Put the people’s birthdays down, one at a time...
day = random.randint(0, 365) # On a randomly chosen day.
if day in taken:4
matches += 1 # A match! # No need to look for more than one.
taken[day] = 1 # Mark the day as taken.
print("The fraction of trials that have matching birthdays is", float(matches)/NTRIALS)

The following video demonstrates a research account login from a Windows computer:

 

Tutorial Video on using Python on CRADC servers above. Sections of video included below:

• step 1: Sign in to CRADC servers. Create Virtual Environment 0:00-4:30 Python -m venv “path_to_project_folder”
• Step 2 Go to the system with internet access, the same exact version of Python installed to CRADC servers, with pip included for downloading packages. 4:30-11:10 pip download package_name
• Step 3 submit a secure file transfer request to move Python packages to your CRADC account 11:10 - 13:45
• Step 4 Install Python packages to CRADC Virtual Environment from step 1 13:45 - 20:45 pip install --no-index --find-links “path_to_Scripts_Folder” package_name
• Step 5 Activate Environment and use it for running Python commands, script files, and importing packages. Options for running Python commands. 20:45-27:00

 

written instructions

CCSS has removed its installation of Stat Transfer software from our servers. Below are instructions for converting data to different file formats without using Stat Transfer. Reasons for converting data to different formats include:

• Export data to more user-friendly software for sending to fellow researchers.
• Continue your research by further analyzing your data using a different programming language.

Instructions

Nearly all programming languages accept CSV data files. CSV stands for Comma Separated Values. CSV files can be opened and saved using excel as well as notepad for text. Making it an ideal file type for exporting and sharing. Below I include coding syntax, Example commands, Menu guidance, and online documentation for exporting and importing CSV data for CCSS's most popular programs.

Export Python Data to CSV

Requires csv Python library. Syntax/Code Example
Import csv
with open('eggs.csv', 'w', newline='') as csvfile:
spamwriter = csv.writer(csvfile, delimiter=' ',
quotechar='|', quoting=csv.QUOTE_MINIMAL)
spamwriter.writerow(['Spam'] * 5 + ['Baked Beans'])
spamwriter.writerow(['Spam', 'Lovely Spam', 'Wonderful Spam'])
Python can export to a variety of files other than CSV.
Python Exporting CSV Documentation

Import CSV Data into Python

Pandas library helpful for importing and exporting csv files. Syntax/Code Example
Import pandas and pd
data = pd.read_csv("filename.csv")
Import CSV into Python Documentation

CCSS has removed its installation of Stat Transfer software. Below are instructions for converting data to different file formats without using Stat Transfer. Reasons for converting data to different formats include:

• Export data to more user-friendly software for sending to fellow researchers.
• Continue your research by further analyzing your data using a different programming language.

Instructions

Nearly all programming languages accept CSV data files. CSV stands for Comma Separated Values. CSV files can be opened and saved using excel as well as notepad for text. Making it an ideal file type for exporting and sharing. Below I include coding syntax, Example commands, Menu guidance, and online documentation for exporting and importing CSV data for CCSS's most popular programs.

Export R data to CSV

# Uses write.csv command. Syntax:
write.csv(data_object, ‘filename.csv’)
#Example Code

df <- data.frame(name = c("Jon", "Bill", "Maria"), age = c(23, 41, 32))
write.csv(df, 'U:/Downloads/file1.csv')
R Exporting CSV Documentation
R can export to a variety of formats. Some of the formats are included in the following link.
R Exporting to other File Formats

Import csv data into R

Uses the read.csv command. Syntax:
data_object = read.csv(‘filename.csv’)
#Example code

Df = read.csv('U:/Downloads/file1.csv')

Users of the CCSS servers may not write to the C drive of the servers. Therefore, you need to direct the installation of R packages onto your own workspace. By default R packages you install will be located within Documents -> R -> win-library -> Rversion number

To install and load R packages to your workspace, a sample is shown below of installing the SemiPar package for your reference.

First, using Windows Explorer, create a sub-directory on your U drive to store your packages say, RPackages. In the example below, RPackages is inside my Documents folder.

Then in R, type the following commands:

install.packages(“SemiPar”, lib=”U:/Documents/RPackages”)

library(SemiPar, lib=”U:/Documents/RPackages”)

Note that in the install.packages command, SemiPar is enclosed in quotes but not in the library command.

You may need to tell R where to look for your installed packages. Do this by locating the path to R files, copying it, and pasting it in the following command .libPaths("path").

#example: Using the path from the above example, my packages are saved within U:/Documents/RPackages. I will set that as my library path like so.

.libPaths("U:/Documents/RPackages")

You may need to install and load an R package that Github provides. Follow the instructions below to accomplish this.

Example
Sample package taken from following link https://github.com/jamesfeigenbaum/jjfPkg

install.packages("remotes")
library(remotes)
install.packages("bitops")
library(bitops)
remotes::install_github("jamesfeigenbaum/jjfPkg", lib="U:\\Documents\\RPackages", force=TRUE)
#At this point I will be asked to update packages. I select option 3. To update 'None' of the packages.
library(jjfPkg, lib="U:\\Documents\\RPackages")

Q: Why can't I load my Stata dataset with an older version of Stata?

 

A: Stata is backward compatible. Newer versions of Stata can read older versions, but that is not the case for older Stata dealing with more recent versions. Stata’s backward compatibility works for 1 version away. Meaning Stata15 can read Stata14 data, Stata11 can read Stata10 data, and Stata12 has the same form as Stata11, but Stata15 can not read Stata11 because 15 and 11 are more than 1 version apart.

There are two options to load newer Stata data sets into an older version of Stata.

1. You can load the new Stata version data set into the old one with “use#”. Where # is the version of Stata that your data was created in.
   Example: My data is from version 13, but I want to load this data into version 10. Perform the command below
   use13 "my_dataset_path&name", clear
2. You can save to older versions of Stata. Using the “saveold” command.
   Example: My data is of version 15, but I want to save the data to use it in Stata11. Perform the command below
   saveold data_name, version(11)
   
   Important: Stata15 can only save back to version 11. To save to an older version, you must open data in Stata11 and use saveold again to go to an earlier version.
   Note: I included the “version(#)” option at the end of the “saveold” command. This will be talked about more later on in this FAQ.

 

Q: Why are my older STATA commands not running like they used to?

A: Stata is backward compatible; however, command syntax for a previous version of Stata may not be identical to that of a newer version. You can use “version” to run Stata commands of a specific version. The version command was added for Stata14. Version command can be used in 3 ways.

1. First, only typing “version” into the command prompt will output the current Stata version in use.
   Example:
   version *output will be version 16, Stata16 is the most recent version on CCSS servers.
   Note: An asterisk “*” in Stata and this FAQ denote a comment, Stata does not interpret these. Comments are colored in green font.
2. To run a bunch of commands with earlier Stata syntax, use “version #”. Where # is the version of Stata you want the following commands to be run under. The “version” command is treated as an umbrella term. Every command underneath the occurrence of “version #” will be run in compliance with Stata#, where # was specified in the “version” command.
   Example:
   version 11

    

   *{batch of commands I want to run using version 11}
   version 16 *When complete, return back to the version I started with.
3. Lastly, you can run single commands using an older version using version # : command, similar to the point above. Where # is the version number and “command” is the specific command you want to run for the particular version specified. This is useful when switching between multiple Stata versions for many different commands.
   Example:
   version 13:command *single command that I will run using Stata13
   version 15:command *single command that I will run using Stata15, likely as a result of the previous command
   version 11:command *single command that I will run using Stata11, likely as a result of the previous two commands

Installing user-written ado files on the research servers

NOTE:  CCSS requires that each individual researcher follow the instructions below for installing ado files.

Q1:  When I try to download and install user-written programs, I get an “access denied” message. How can I use these?

Q2:  I am running Stata on a research server, and I’m interested in using some commands that are not part of the main software. These commands are written by users and can be installed into Stata through the web. The Stata reference manual makes this sound straightforward, but when I go through the steps on a research server, I can’t install the new command because I don’t have permission to add files to the space where the Stata code is kept on the server. How do I get around this?

 

ANSWER:

Indeed, research server users do not have permission to write to the default path for STB and other user-written files. However, users can still install these files to their U drive. Sample code for installing “reghdfe” package provided under “Example” section.

First, from within Stata, you can issue the command “sysdir” to see the list of the system set directories to which Stata points to by default.  Included in the list of default settings are these entries:

PLUS: C:\ado\plus

PERSONAL: C:\ado\personal

The PLUS folder is the destination for downloaded ado files written by other users.  The PERSONAL folder is intended for ado files you have written.  CCSS computing account users do not have permission to write to the C:\ drive, so there are other options:  If you need to use an ado file, you can install

it yourself by redirecting the PLUS folder to your U-drive (as shown below).   To install user-written ado files (anytime), you’ll need to use  the “sysdir set” commands (case is important) to redirect the PERSONAL or PLUS folders as shown below:

 

sysdir set PLUS "U:\folder"
sysdir set PERSONAL "U:\folder"

 

Where “folder” is the subfolder you wish to save your ado files in (you must create this first). This location used in the “sysdir set” command must be the same as your current working directory location and the same location as where all the files you are working on are.

 

Example

You may copy and paste most of the commands below. Know that for this example, I have a folder in my documents named “Statafiles”

 

sysdir set PLUS "U:\Documents\Statafiles"
sysdir set PERSONAL "U:\Documents\Statafiles"

*Green text is a comment. Set directory to the same location set for PLUS directory. This is also the place where all your Stata working files are saved.

cd "U:\Documents\Statafiles"

*Use the option below if you know the name of the ado file you wish to use

ssc install reghdfe

*You May need to use the option below if you do not know the exact name of the ado file. Search features/commands of ado you want

search reghdfe

*After the search command above, a new window will pop up with options to download packages that fit the search criteria.

*Click on the package name you would like to install. You will be directed to another page. Scroll down to the section "Installation Files", and select "(click here to install)". The package will be installed to the location you set as PLUS or PERSONAL directory

***********************************************

To make this a “permanent” change do this:

Create a shortcut to the Stata application on your desktop

(Start → All Programs → right-click on Stata17 → More → Open File Location → Right-click on StataMP 17(64-bit) → “send to” → Desktop(create shortcut)). 

Then find the newly created shortcut on your desktop, right-click on the icon, and choose “properties” → “Shortcut” tab. 

In the “Start In” field enter the path “U:\Documents”.

In “Target” field enter “C:\Program Files\Stata17\StataMP-64.exe” only.

If you see other text in this field, delete it, you may see “/UseRegistryStartin” within the Target field, delete that. 

Use the Stata do file editor to create a file called “profile.do” file, which contains the sysdir commands you wish to use.  Be sure to place the profile.do file in the directory “U:\Documents”.  Stata will automatically look for the profile.do file when opening and run those commands.

Error: Access to C:\STD2124_0000.temp was denied. Screenshot example below

Solution 1: While signed into the servers begin inside the Notepad application and follow steps below. Open start menu, type “notepad” and select Notepad or Notepad++ desktop applications.

1. Create folder on Desktop called "Statatemp"
2. Open Notepad.

3. Paste following into notepad application:

   set STATATMP=U:\Desktop\statatemp
   cd u:\project
   "C:\Program Files\Stata17\StataMP-64.exe"
   

   Note: Put an empty line after the 3rd line of code. A total of 4 lines in your Notepad. 3 commands and 1 empty line at the end.

   Note: The quotes when pasted from this FAQ to notepad do not come out as standard quotes.  Delete and replace the quotation marks after you have pasted the above commands into notepad. If the text inside the quotes are color coded; delete the quotes and re-enter them in the same position.

4. Save notepad with .bat file extension. File -> Save As -> Save as Type: All Types -> end file name with .bat .Do not save with default .txt file extension

Once complete, double-click on the .bat file. This will open Stata and fix your errors. Moving forward, double click on this file to open Stata and never encounter this error again.

Double clicking the file should open Stata automatically, if it does not there is an issue with the .bat file created.

Example using my research account.

 

set STATATMP=U:\Desktop\statatemp
cd U:\Documents\stata_test
"C:\Program Files\Stata17\StataMP-64.exe"

Example using my CRADC Account.

 

set STATATMP = S:\CR2000\jrg363_cr2000\Desktop\statatemp
cd S:\CR2000\jrg363_cr2000\Desktop
"C:\Program Files\Stata17\StataMP-64.exe"

Solution 2:

Create a shortcut to the Stata application on your desktop. Then use this desktop shortcut to oepn Stata moving forward to avoid the issue.

1. (Start → All Programs → right-click on Stata17 → More → Open File Location → Right-click on StataMP 17(64-bit) → “send to” → Desktop(create shortcut)).
2. Find the newly created shortcut on your desktop, right click on the icon and choose “properties” → “Shortcut” tab.
3. In the “Start In” field enter the path “U:\Desktop”.
4. Use Desktop shortcut to open Stata moving forward. This will fix this issue

Contact the CCSS HelpDesk with any questions or issues.

Working with dates where years are in two-digit formats 

Q.  Dates in my data have only two digits to represent a year. The digit 00 represents the year 2000, but my SAS program interprets this as 1900. What can I do about this?

A.  Use the SAS system option “YEARCUTOFF=” to specify the first year of a 100-year span within which you want your 2-digit dates to fall.   For example:

options yearcutoff=1950;

would interpret the 2-digit year values 50-99 as 1950 to 1999 and values 00-49 as being 2000 to 2049.

For SAS Versions 6.04 –  6.12, the system default value is YEARCUTOFF= 1900.  This means that all two-digit years will be assumed to be between 1900 and 1999 unless you reset the default.

For SAS Version 7.0 — 8.1,  the system default is YEARCUTOFF=1920.  This means that all two-digit years will be assumed to be between 1920 and 2019 unless you reset the default.

The default value for either version can be easily reset by using the “YEARCUTOFF=” option, as shown above.

To find out whether the YEARCUTOFF option has been reset on any version of SAS that you are using, you can submit these statements:

proc options option=yearcutoff;
run;

OR — from SAS 8.1 for Windows, just go to Tools –> Options –> System –> Input Control –> Data Processing.  Then scroll down through the list of options until you see Yearcutoff...

How do I create a SAS data set with compressed observations? 

To create a compressed SAS data set, use the COMPRESS=YES option as an output DATA set option or an OPTIONS statement. Compressing a data set reduces its size by reducing repeated consecutive characters or numbers to 2-byte or 3-byte representations. To uncompress observations, you must use a DATA step to copy the data set and use the option COMPRESS=NO for the new data set.

The advantages of using a SAS compressed data set are reduced storage requirements for the data set and fewer input/output operations necessary to read from and write to the data set during processing. The disadvantages include not being able to use the SAS observation number to access an observation. The CPU time required to prepare compressed observations for input/output observations is increased because of the overhead of compressing and expanding the observations. (Note: If there are few repeated characters, a data set can occupy more space in compressed form than uncompressed form due to the higher overhead per observation.) For more details on SAS compression, see “SAS Language: Reference, Version 6, First Edition, Cary, NC: SAS Institute Inc., 1990”.

The two ways to compress data sets in SAS:

• Using the option in the DATA step to compress a data set:
  • data ssd.income (compress=yes);
• To compress all data sets created within SAS sessions
  • options compress=yes;

Researchers can download and install Excel add-ins while connected to the servers.

Instructions Included with Example of downloading and installing Excel add-in “Open Solver”

• Connect to CCSS computing server.
  Login Instructions
• Open web browser(Internet Explorer, Firefox or Microsoft Edge) and go to URL in which you can download Excel add-in
  Open Solver Link below.
  Open Solver Download Link
• Download and save all the associated files on the U drive(Downloads, Documents, Desktop). More information about CCSS server’s U drive found in the following link.
  CCSS Work Environment If necessary unzip the files
• You only need to perform previous steps once. Recall where you downloaded the files. Following steps may need to be performed every time you want to use Open Solver.
• Open Excel
• Open blank page
• Select File -> Options -> Add-ins
• At bottom in “manage” makes sure “Excel add-ins” is select then press Go

• Click on Browse – search folders to where you downloaded and saved the Add-in files in the earlier steps
• Select the .xlam file. For OpenSolver the file is named “OpenSolver.xlam”
• Close out Add-in box
• Open Solver add-in will be visible within the “Data” tab of excel.

Any questions message CCSS-ResearchSupport@cornell.edu

 

NVivo projects on the CCSS servers can sometimes not save correctly. As a result, you could unknowingly lose hours of hard work. Avoid this frustration by frequently Copying your project file. The steps are as follows.

• Once you have finished working for the day, copy your project file.
• “File” -> “Copy Project”
• Assign a name to your project file. By default date and time are attached. It is suggested to keep that information, so you know which project file is the most recent.
• Save copied project file somewhere on your U: drive. It can open at any time.

When you open the software NVivo, it brings up the most recently worked on and saved projects. Sometimes the recently worked on projects do not appear in the list correctly. This is when a copying project files would be beneficial. If the save does not work correctly, you can always open the copied file.

Instructions for copying the project from the NVivo website are included below.

NVivo Copy Project

Restoring Backups

NVivo on CCSS automatically backs up your projects once a week and stores them as .nvb files in the following location:

U:\Documents\NVivo 12 Recovery

To recover the project, perform the following steps

1. Sign in to CCSS servers
2. Open File Explorer and navigate to the following folder location: U:\Documents\NVivo 12 Recovery

Locate and send the .nvb file to NVivo support by filling out the form at the following link: Technical Support Form. Ask them to recover the project and send it back as .nvp file.

Difficulty loading and using the Spatial Analyst toolbox? Perform the following steps.

1. Open ArcGIS Desktop
2. In Menu Customize -> Extensions
3. Check box for 'Spatial Analyst'
4. Once checked, you will be able to use this toolbox.