jonocarroll

## global counters
reset <- function() {
  assign("counts_lt", 0, .GlobalEnv)
  assign("counts_gt", 0, .GlobalEnv)
  assign("counts_eq", 0, .GlobalEnv)
  assign("counts_as", 0, .GlobalEnv)
}

reset()

jonocarroll

using Distances
using Plots

function ninradius(indiv, radius, distances)
    findall(distances[indiv, :] .< radius)
end

function getdists(particlelist)
    pairwise(Euclidean(), reduce(hcat, [[p.x, p.y] for p in particlelist]), dims=2)
end

jonocarroll

>>> def make_a_list(val1 = 0, val2 = 0, lst = []):
...    lst.append(val1)
...    lst.append(val2)
...    return lst

>>> # you need to know that you're modifying base_list
>>> base_list = [1, 2, 3, 4]
>>> extend_list = make_a_list(5, 6, base_list)
>>> print(extend_list)
[1, 2, 3, 4, 5, 6]

jonocarroll

partition <- function(x, cut) {
  v <- rep(0, length(x))
  v[cut] <- 1
  cumsum(v)
}

cumsum_cut <- function(x, cut = NULL) {
    cut <- sort(cut)
    vs <- split(x, partition(x, cut))
    vs <- sapply(vs, \(x) {x[1] <- 0; x})

jonocarroll

`[.vec` <- function(x, i, ...) {
  UseMethod("[.vec", i)
}

`[<-.vec` <- function(x, i, value, ...) {
  UseMethod("[<-.vec", i)
}

`[.vec.default` <- function(x, i, ...) {
  class(x) <- setdiff(class(x), "vec")

jonocarroll

                ts=0.07;ps=0.02;A=B=0;
            while(1){ j=i=0;z=rep(0,1760);
          b=rep(' ',1760); while(j < 6.28){
         j=j+ts;i=0;while(i<6.28){i=i+ps;c=
        sin(i);l=cos(i);      d=cos(j);f=sin(j);
      e=sin(A);g=cos(A         );h=d+2;D=1/(c*h*e+
     f*g+5);m=cos(B)            ;n=sin(B);t=c*h*g-
     f*e;x=as.integer           (40+30*D*(l*h*m-t*n));
    y=as.integer(12+            15*D*(l*h*n+t*m));
    o=as.integer(x+(            80*y));N=as.integer(

jonocarroll

enum <- function(...) {
  vals <- if (is.null(...names())) {
    setNames(seq_len(...length()), c(...))
  } else {
    c(...)
  }
  out <- new.env(parent = emptyenv())
  list2env(as.list(vals), out)
  lapply(names(vals), lockBinding, out)
  lockEnvironment(out)

jonocarroll

## Medical Term Fuzzy Grouping
## J. Carroll 2024
## 
## Uses the {zoomerjoin} package: https://github.com/beniaminogreen/zoomerjoin

## read in a set of medical terms, lowercased
terms <- tolower(readLines("https://raw.githubusercontent.com/socd06/medical-nlp/master/data/vocab.txt"))

## example data with typos and inserted words
gi <- c("gastrointestinal disorders", "gastrointestinal tract disorders", "gastreinstestinal disorder")

jonocarroll

#!/bin/bash

LOG_FILE="/Users/username/output.log"
NOTIFIED_FILE="/Users/username/notified.txt"
EMAIL="username@example.com"

# Read the contents of the notified file, if it exists
notified=$(cat "$NOTIFIED_FILE" 2>/dev/null)

# If the notified file doesn't exist, assume no previous notification

jonocarroll

library(rextendr)

rust_function("
fn rowmin(m: RMatrix::<i32>) -> Vec<i32> {

    // convert to an ndarray
    let matrix = <ArrayView2<i32>>::from_robj(&m).unwrap();

    // store results
    let mut min_values = Vec::with_capacity(matrix.len());