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Research knowledge base with Zotero, Highlights, and Obsidian

Ever since I started working on my honours thesis in 2013, I had been tinkering with various workflows to manage references, PDFs, PDF annotations and notes all in some coherent way. The workflow I describe here is the latest one (February 2021 as of writing), and I think I've finally found something that satisfies a lot of the [admittedly very subjective] desiderata.

Knowledge provenance

Being [perhaps overly] wary of mis-citing something, I'd like to be able to quickly go back to the original source, and the exact page and PDF highlight that I'm referring to. For the last couple of years, I have been using the Highlights App (MacOS only, unfortunately; though there may be Windows/Linux equivalents). The two main features of Highlights are that:

1. It automatically extracts PDF highlights and is able to keep them updated in a 'sidecar' file, so for a file like Ram_et_al_2020_Neural_Network.pdf, there'll be

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Launch RStudio server on Ubuntu 20.04

1. Launch server (DigitalOcean, Packet, etc.) with Ubuntu 20.04 and get IP XXX.XXX.XXX.XXX

Test that logging in works

ssh [email protected]

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Allosaurus

• Allosaurus is a pretrained universal phone recognizer: https://github.com/xinjli/allosaurus
• It has been trained on English, Japanese, Mandarin, Tagalog, Turkish, Vietnamese, German, Spanish, Amharic, Italian and Russian

Testing on Kaytetye

• We test this off-the-shelf version on some Kaytetye data. The data are citation form headwords recorded by a female native speaker of Kaytetye in a music studio for a multimedia dictionary.
• For 2,360 headwords, we have ~2 repetitions per word (e.g. palpalpe), and two transcriptions (t_1, t_2) by two independent human transcribers.
• In the table below int_t_dist is the inter-transcriber string distance and min_a_dist is the minimum string distance between the allosaurus transcription and the human transcriptions.

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# Get fauxneticien/kaytetye-medial-vowels
git clone https://github.com/fauxneticien/kaytetye-medial-vowels
# Set read/write permissions for all files
chmod 777 -R kaytetye-medial-vowels
# Run rocker/verse container, name it 'kayv-docker', set login password for 'rstudio' user to 'kayv'
sudo docker run -it --rm -d -p 80:8787 -v ~/kaytetye-medial-vowels:/home/rstudio --name kayv-docker rocker/verse
# Run setup.R inside the container
docker exec kayv-docker Rscript /home/rstudio/src/setup.R

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#!/bin/bash
# Commands taken from https://www.digitalocean.com/community/tutorials/how-to-install-and-use-docker-on-ubuntu-18-04
# Run using:
# bash <(curl -s https://gist.githubusercontent.com/fauxneticien/159529bf6c071f90b7fd70a481e6083b/raw/47c1d9e7c922797deee9fa2ce16387d6a3ed3624/elpis-deploy.sh)
sudo apt update
sudo apt install -y apt-transport-https ca-certificates curl software-properties-common
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu bionic stable"
sudo apt update
sudo apt install -y docker-ce

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#!/bin/bash
# Commands taken from https://www.digitalocean.com/community/tutorials/how-to-install-and-use-docker-on-ubuntu-18-04
sudo apt update
sudo apt install -y apt-transport-https ca-certificates curl software-properties-common
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu bionic stable"
sudo apt update
sudo apt install -y docker-ce
systemctl start docker

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# install.pacakges(...) if you do not have the packages below
library(tidyverse)
library(stringr)
library(wrassp)
library(glue)

wav2formants_csvs <- function(in_file) {
    stopifnot(grepl("\\.wav$", in_file))
    stopifnot(file.exists(in_file))
    

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library(tidyverse)

# Start with likely output of a group_by(...) %>% summarise(...) on raw data
# which computes the mean and error on various distributions of durations
# name each component-measure combination variable in a dot-separated form, e.g.
# clo.dur, clo.err (mean closure duration, standard error for closure duration)
tibble(
    consonant  = c("Pre-stopped nasal", "Nasal", "Oral stop"),
    clo.dur    = c(25, NA, 30),
    clo.err    = c(5, NA, 6),

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library(purrr)
library(stringr)

list.files("~/git-repos/coedl/dbd/public/pdfs", pattern = "PDFsam", full.names = TRUE) %>%
walk(function(path) {
    file.rename(
        path, 
        str_replace(path, "(\\d+)_PDFsam_(dbd-[A-Z]+).pdf", "\\2_\\1.pdf")
    )
})