https://nd.psychstat.org/ 2026-04-11T10:52:01+00:00 https://nd.psychstat.org/ https://nd.psychstat.org/_media/wiki/dokuwiki.svg text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/an_online_tool_for_text_comparison_finediff An online tool for text comparison (finediff) <http://latex.psychstat.org/tools/diff/viewdiff.php> text/html 2019-03-04T14:41:39+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/apache_log_process_using_goaccess Apache log process using GoAccess sudo zcat /var/log/apache2/access-advstats.*.gz | sudo goaccess /var/log/apache2/access-advstats.log -o report.html --log-format=COMBINED text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/barplot_with_error_bars_annotated_by_kruskal-wallis_or_anova_p-value Barplot with error bars, annotated by Kruskal-Wallis or ANOVA p-value Use the WGCNA package. To install, use the command install.packages('WGCNA') This package requires the installation of the impute package that can be installed using source("http://bioconductor.org/biocLite.R") biocLite("impute") text/html 2016-07-30T20:05:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/batch_convert_youtube_dash_m4a_audio_youtube-dl_to_m4a_aac_dl Batch Convert YouTube DASH m4a audio (youtube-dl) to m4a (AAC DL) The YouTube DASH audio might not be played by some audio players. If you have multiple files with such format, you can convert them using the following command on Windows. FOR %i IN (*) DO C:\Users\Downloads\ffmpeg-20160725-fb91850-win64-static\ffmpeg-20160725-fb91850-win64-static\bin\ffmpeg -i "%i" -vn -acodec copy "new\%i" text/html 2016-02-17T21:32:15+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/bugs_download_files BUGS download files * [Linux version OpenBUGS 3.2.3] * [Windows version OpenBUGS 3.2.3] * [WinBUGS] [WinBUGS key file] [WinBUGS patch] text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/compile_openblas_for_r Compile OpenBLAS for R on Windows * Install MinGW using the installer: <http://sourceforge.net/projects/mingw/files/latest/download?source=files> Make sure install MSYS * Install wget within MinGW: mingw-get install msys-wget * Download OpenBLAS: <https://github.com/xianyi/OpenBLAS/archive/develop.zip> * Compile it using make text/html 2017-01-09T15:12:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/control_r_figure_output_format Control R figure output format To control the site wide option, use nano Rhome/etc/Rprofile.site The home path (Rhome) can be found using R.home(component = "home") On Ubuntu, it is often /usr/lib/R. In the Rprofile.site, input options(device='svg') text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/convert_from_lyx_to_latex Convert from LyX to LaTeX Many ways to use. First, one can use File --> Export --> LaTeX (pdflatex). The .tex file is saved in the same folder as .lyx file. The second way is a little bit more complex, but can be useful. Follow those steps. * Open Tools text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/copy_tables_from_excel_to_lyx Copy Tables from Excel to LyX This is the way to copy tables from Excel to Lyx I found on the web. * In LyX, insert a table with the same dimensions as the one in the excel. * Place the mouse cursor in the top left cell of the table. * From the menu of LyX, choose text/html 2016-02-15T02:33:11+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/delete_large_number_of_files Delete large number of files I had to delete thousands of files. The command “rm” simply took forever. Then I learned you can use rsync to do the job. First, create an empty directory such as mkdir empty Then, rsync it with the folder you want to delete using text/html 2025-01-15T17:54:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/doi_to_bibtex_and_apa_format_references_online DOI to bibtex and APA format references online I create a simple website that can convert one or a set of DOIs to bibtex or APA style references. You can use it here: <https://classes.psychstat.org/apps/doi2bib> You can put dois in the input field, one each line. DOIs with or without the prefix text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/draw_sem_path_diagram_using_websem Draw SEM path diagram using WebSEM WebSEM provides a flexible way to draw path diagram. To use it, go to <https://websem.psychstat.org>. If you are not ready to register yet, try out at <https://websem.psychstat.org/apps/drawsem/> or <https://websem.psychstat.org/apps/drawsem/pathdiag.php>. text/html 2021-04-26T17:07:01+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/estimate_sample_skewness_and_kurtosis_in_popular_statistical_software Estimate univariate and multivariate sample skewness and kurtosis in popular statistical software This tutorial explains four different methods for calculating univariate and multivariate skewness and kurtosis in your data: an online calculator that allows the use of Excel, SPSS, and SAS data sets directly as well as text and csv files, an SPSS program, a SAS program, and instructions for STATA. text/html 2019-09-24T14:51:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/flatten_comments_in_acrobat_pro Flatten comments in Acrobat Pro Bring up the Preflight tool (search preflight), then use the “Flatten annotations and field” in the “PDF Fixups” (search flatten) category. text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/gmail_configuration_for_redmine_on_ubuntu Gmail configuration for redmine on Ubuntu To install redmine, use sudo apt-get install redmine To config redmine to use gmail to send out emails * In the redmine folder /usr/share/redmine/config, copy configuration.yml.example to configuration.yml text/html 2021-06-19T22:06:38+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/hugo_and_php_for_website_building Hugo and PHP for building Websites I built almost all my websites using PHP. Recently, I started to build simple HTML sites using Hugo, which was amazing. However, occasionally, I missed the flexibility of PHP for server side processing. I have tried to output PHP files instead of html files from Hugo but was not successful. Eventually, I resolved to make the change to the web server instead. Basically, one can change the setting of the server to parse .html files as php files. Several ways can… text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/install_an_external_program_within_r Install an external program within R This is an example to download and install an external program / software within R. dotRcheck <- function(){ #Check for audiolyzR installation directory<-getwd() if (.Platform$OS.type=="windows"){ ANSWER <- readline("Do you want to install Graphviz for path diagram generation? \nType y or n\n") if (substr(ANSWER,1,1)=="y"){ tmpdir <- getwd() destfile<-paste(tmpdir, "graphviz-2.30.1.msi", sep="/") download.file("htt… text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/install_and_use_subversion_svn_and_viewvc_on_ubuntu Install and Use Subversion (svn) and ViewVC on Ubuntu Install Subversion with Web Access on Ubuntu * To install subversion, open a terminal and run the following command: sudo apt-get install subversion libapache2-svn * To create a folder for the subversion repository in /svn, use text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/install_gitlab_on_existing_apache2_web_server Install GitLab on existing Apache2 web server First, setup a domain to point to the server such as gitlab.example.com. Second, follow the procedure at <https://gitlab.com/gitlab-org/gitlab-ce/blob/master/doc/install/installation.md> till the end of Step 6. Do not proceed with 7 to install Nginx. If you are using MySQL, remember to setup mysql database. text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/install_openbugs Install OpenBUGS Steps * Download OpenBUGS (Note only OpenBUS 2.2.0 works on unix machines) and upload it to dscratch. First upload it to AFS and then copy it to dscratch. * Unzip the file on the cluster * Create a file called linbugs with the following content and change permission using chmod 755 lingbugs text/html 2016-07-01T21:01:20+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/install_shiny_server_on_godaddy_cloud_server Install shiny server on Godaddy cloud server I am trying out the Goddy cloud server with the following specific: 20GB No more than $5.00 /month ($0.0074 /hour) 512MB memory 1 core processor 20GB SSD disk 1TB transfer However, when I install the shiny package, I got the following error message text/html 2024-09-17T20:03:50+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/install_tensorflow_on_macbook_pro_m1_and_kerns_for_r Install tensorflow on MacBook Pro M1 and kerns for R I have a 2021 MacBook Pro with Apple M1 Pro chip. I tried to install tensor flow on it following the instruction of Apple here <https://developer.apple.com/metal/tensorflow-plugin/> as well as many other instructions online but failed to make it work. text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/installl_openbugs_3.0.7_on_linux_server Install OpenBUGS 3.0.7 on Linux server The following instructions were tested on Red Hat Enterprise Linux Server release 5.4 (Tikanga), Kernel version 2.6.18-164.11.1.el5. Could work for other linux releases. Installation The new version of OpenBUGS (v.3.0.7) can be run on Linux machine very easily. To install it on a linux machine, following these steps (adapted from openbugs.info) text/html 2016-09-20T01:51:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/integrate_mathjax_with_gitlab Integrate Mathjax with Gitlab A quick (not the best way, though) way to integrate Mathjax with Gitlab. Tested on Gitlab 7.9.4 and Gitlab shell 2.6.0. Create the file /home/git/gitlab/app/views/layouts/_mathjax.html.haml, e.g., sudo -u git nano /home/git/gitlab/app/views/layouts/_mathjax.html.haml text/html 2019-11-23T15:05:48+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/let_s_encrypt_ssl Let's encrypt SSL Install SSL for Godaddy web hosting through cpanel. * Install certbot on your local machine: sudo apt-get update sudo apt-get install software-properties-common sudo add-apt-repository universe sudo add-apt-repository ppa:certbot/certbot sudo apt-get update sudo apt-get install certbot python-certbot-apache text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/lyx_customized_reference_list LyX customized reference list This can be used for APA style references in LyX of not want to use the bib file. The following procedure can be used to create a list of references for your own style. * Add a layout in Document -- Settings -- Local Layout with the following text/html 2016-03-29T17:18:59+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/lyx_on_mac_error_converting_to_loadable_format LyX on Mac error converting to loadable format When installing LyX on Mac, one might experience the error “error converting to loadable format” when including pdf files. This is likely because of missing of ImageMagick. To fix the problem, you will need to install ImageMagick. To do it, the following steps need to follow. text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/math_magics Math Magics 1 x 8 + 1 = 9 12 x 8 + 2 = 98 123 x 8 + 3 = 987 1234 x 8 + 4 = 9876 12345 x 8 + 5 = 98765 123456 x 8 + 6 = 987654 1234567 x 8 + 7 = 9876543 12345678 x 8 + 8 = 98765432 123456789 x 8 + 9 = 987654321 0 x 9 + 1 = 1 1 x 9 + 2 = 11 12 x 9 + 3 = 111 123 x 9 + 4 = 1111 1234 x 9 + 5 = 11111 12345 x 9 + 6 = 111111 123456 x 9 + 7 = 1111111 1234567 x 9 + 8 = 11111111 12345678 x 9 + 9 = 11111111… text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/new_york_times_on_bayesian_and_frequentist New York Times on Bayesian and Frequentist <http://www.nytimes.com/2014/09/30/science/the-odds-continually-updated.html> text/html 2019-05-13T15:38:56+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/quantify_the_impact_of_your_r_packages Quantify the impact of your R packages Software development often takes a lot of time but its impact is often difficult to evaluate. If you have developed an R package and upload it to CRAN, you might be able to get some download information but not a lot. text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/r_plot_highlight_an_area_under_an_density_curve R plot highlight an area under a density curve When illustrating p-value for a given distribution, one might want to highlight / mark / shade a specific area. This can be done using the function polygon. Below is an example for an F distribution. x<-seq(0, 10, 0.01) y<-df(x, 2, 6) plot(x,y,type='l', lwd=2,yaxs = "i", xaxs="i") polygon(c(2.33,seq(2.33,10,.01),10),c(0,df(seq(2.33,10,.01),2,6),0), density = c(10, 20), angle = c(45, -45)) text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/r_read_data_from_clipboard_for_windows_and_mac R read data from clipboard for Windows and Mac On Mac On Mac Os X, the function pipe can be used to read and copy to clipboard. I often copy data from excel to clipboard and then read them into R. Specifically, the following code can be used. dset <- read.table(pipe("pbpaste"), sep="\t") text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/record_desktop_videos_using_vlc_media_player Record desktop videos using VLC media player <https://www.vlchelp.com/how-to-record-desktop/> To record mouse, add the following options instead :screen-follow-mouse :screen-mouse-image=file:///C:/Users/Pictures/Mouse.png text/html 2018-11-26T13:33:56+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/regex regex Replace $abc$ with $`abc`$: \$([^$]*)\$ \$`\1`\$ Replace 4. 5 with 4.5 (\d)[.]\s+(\d) $1.$2 ([a-zA-Z])[.]([a-zA-Z]) $1. $2 text/html 2016-04-22T20:37:37+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/setup_up_mattermost_with_existing_gitlab Setup up Mattermost with existing Gitlab Based on * <http://docs.mattermost.com/developer/developer-setup.html#ubuntu> * <http://docs.mattermost.com/install/prod-ubuntu.html> * <https://github.com/mattermost/docs/pull/25/files> * <http://docs.mattermost.com/deployment/sso-gitlab.html> I was trying to set up mattermost with Gitlab I have installed on an Apache2 server in Ubuntu from source. The follow procedure proved to work for me. Install Docker * Download and install Docker text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/springer_multi-author_book_class_for_latex_and_lyx Springer multi-author book class for LaTeX and LyX Windows * Download the class from <ftp://ftp.springer.de/pub/tex/latex/svmultt1.zip> * Extract the files to the folder C:\Program Files\MiKTeX 2.9\tex\latex\svmult.You might need to create the folder svmult (for 64 bit windows, it would be C:\Program Files (x86)\MiKTeX 2.9\tex\latex\svmult) text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/subfigures_in_lyx Subfigures in LyX This is an example form LyX website for using subfigures in LyX. I changed it a little to include multiple figures on multiple rows and columns. The LyX file can be downloaded at The figure used can be downloaded at The output looks like text/html 2022-09-05T00:56:35+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/use_crc_clusters Best (my) way to use CRC clusters Software needed * PuTTY <https://www.putty.org/> * Notepad++ <https://notepad-plus-plus.org/downloads/> * FileZilla <https://filezilla-project.org/download.php?type=client> If you are using a Mac, use the following similar software * Terminal (already installed) to replace PuTTY. * TextWrangler to replace Notepad++ * FileZilla can be equally used on a Mac. text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/useful_statistical_concepts Useful statistical concepts * Cramér–Rao bound text/html 2016-01-24T14:48:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://nd.psychstat.org/blog/welcome Welcome! After I moved to the University of Notre Dame for 4 months, I finally found some time to set my ND website up. This does not replace my old website at <http://www.psychstat.org/us> because it is mainly for the classes I teach. And, unfortunately, for obvious reasons, the class pages cannot be accessed publicly. I will give authorization to the students in my classes. For those who are not on the roster of the classes and are still interested in accessing the class pages, you may have …