Thomas Lumley tslumley
😐
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| Based on the `rimu` package, the start of an implementation of 'mr' objects using Hadley's `vctrs` package, so they can be used in tibbles. |
tslumley
/ selfharm.csv
Created
March 20, 2022 05:20
Hospital admissions for intentional self-harm (from OIA)
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| Calendar year and month | Total | 00 to 04 | 05 to 09 | 10 to 14 | 15 to 19 | 20 to 24 | 25 to 29 | 30 to 34 | 35 to 39 | 40 to 44 | 45 to 49 | 50 to 54 | 55 to 59 | 60 to 64 | 65 to 69 | 70 to 74 | 75 to 79 | 80 to 84 | 85+ | year | month | date | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 201701 | 801 | NA | 2 | 25 | 169 | 150 | 92 | 59 | 48 | 68 | 49 | 44 | 40 | 19 | 15 | 8 | 3 | 5 | 5 | 2017 | 1 | 2017-01-28 | |
| 2 | 201702 | 828 | NA | NA | 44 | 203 | 139 | 89 | 53 | 54 | 56 | 74 | 46 | 19 | 18 | 11 | 11 | 2 | 1 | 8 | 2017 | 2 | 2017-02-28 | |
| 3 | 201703 | 880 | NA | NA | 38 | 216 | 153 | 81 | 63 | 64 | 70 | 62 | 45 | 37 | 22 | 8 | 7 | 9 | 2 | 3 | 2017 | 3 | 2017-03-28 | |
| 4 | 201704 | 790 | NA | 2 | 40 | 182 | 162 | 96 | 69 | 33 | 45 | 38 | 51 | 24 | 22 | 9 | 8 | 1 | 4 | 4 | 2017 | 4 | 2017-04-28 | |
| 5 | 201705 | 915 | NA | 1 | 48 | 222 | 182 | 105 | 56 | 57 | 58 | 65 | 43 | 22 | 24 | 10 | 6 | 9 | 3 | 4 | 2017 | 5 | 2017-05-28 | |
| 6 | 201706 | 828 | NA | NA | 46 | 212 | 151 | 85 | 62 | 54 | 55 | 54 | 38 | 26 | 15 | 13 | 6 | 3 | 1 | 7 | 2017 | 6 | 2017-06-28 | |
| 7 | 201707 | 830 | NA | NA | 30 | 189 | 148 | 99 | 60 | 63 | 53 | 65 | 45 | 33 | 18 | 11 | 7 | 4 | 1 | 4 | 2017 | 7 | 2017-07-28 | |
| 8 | 201708 | 905 | NA | 1 | 64 | 233 | 151 | 103 | 64 | 55 | 51 | 67 | 35 | 29 | 25 | 14 | 4 | 2 | 3 | 4 | 2017 | 8 | 2017-08-28 | |
| 9 | 201709 | 868 | NA | NA | 35 | 231 | 143 | 98 | 80 | 55 | 56 | 54 | 48 | 22 | 15 | 13 | 10 | 4 | 1 | 3 | 2017 | 9 | 2017-09-28 |
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| expit<-function(eta) exp(eta)/(1+exp(eta)) | |
| logit<-function(p) log(p/(1-p)) | |
| one.sim<-function(beta, N=1000){ | |
| pop<-data.frame(x=rnorm(50000)) | |
| pop$y<-with(pop,rbinom(50000,1,expit(beta*x-3-beta))) | |
| rval<-replicate(N,{ | |
| cases<-which(pop$y==1) | |
| controls<-sample(which(pop$y==0),length(cases)) |
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| pop<-matrix(0,102,102) | |
| ## uniform | |
| vax<-matrix(rbinom(102*102,1,.83),102,102) | |
| ## vertical stripes | |
| vax<-matrix(rep(c(0,1,1,1,1,1,1,0,1,1,1,1),length=102*102),102,102) | |
| ## high-risk square | |
| #vax<-matrix(rbinom(102*102,1,.9),102,102); vax[1:41,1:42]<-rbinom(41*42,1,.5) |
tslumley
/ police-assault.R
Created
August 19, 2021 05:45
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| counts<-c(173,291,320,407,311,292,341,321,188) | |
| times<-c(as.numeric(as.Date("2013-12-31")-as.Date("2013-4-1")),365,365,366,365,365,365,366,as.numeric(as.Date("2021-7-19")-as.Date("2021-1-1"))) | |
| barplot(counts*365/times,width=times,col="royalblue",names=2013:2021,ylab="Assaults, scaled to /year",bg="white") | |
| plot(2013:2021,counts*365/times,ylim=c(200,450),pch=19,col="royalblue",xlab="year",ylab="Assaults, scaled to /year",bg="white") | |
| segments(2013:2021,(sqrt(counts)-1)^2*365/times, y1=(sqrt(counts)+1)^2*365/times,lty=3) | |
| ## from https://fyi.org.nz/request/16238/response/61990/attach/3/Kelly%20P%20IR%2001%2021%2023344%20Final%20Response.pdf |
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| library(rvest) | |
| library(dplyr) | |
| library(DHBins) | |
| a<-read_html("https://www.health.govt.nz/our-work/diseases-and-conditions/covid-19-novel-coronavirus/covid-19-data-and-statistics/covid-19-vaccine-data") | |
| a %>% | |
| html_node("body") %>% | |
| xml2::xml_find_all("//table") %>% nth(n=3) %>%html_text() ->b | |
| gsub("\t"""strsplit(b"\n")[[1]]fixed=TRUE)->d |
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| library(dplyr) | |
| library(rlang) | |
| ma<-read.csv("~/Downloads/weekly-covid-19-municipality-vaccination-report-5-20-2021 (1)/Age - municipality-Table 1.csv",skip=1) | |
| ma %>% | |
| mutate(pop = as.numeric(gsub(",","",Population)), vax=as.numeric(gsub(",","",Fully.vaccinated.individuals))) -> ma_all | |
| ma_all %>% | |
| filter(Age.Group %in% c("65-74 Years","75+ Years")) %>% | |
| select(County,Town,Age.Group,pop,vax) %>% | |
| group_by(County,Town) %>% |
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| svygofchisq<-function(formula, p, design,...){ | |
| means<-svytotal(formula, design,...) | |
| rval<-chisq.test(means,p=p) | |
| nm<-names(coef(means)) | |
| ncat<-length(coef(means)) | |
| means<-svycontrast(means, list(N=rep(1,ncat)), add=TRUE) | |
| pN<-split(cbind(p,0*diag(p)), paste0("p_",nm)) | |
| names(pN)<-paste0("p_",nm) | |
| means<-svycontrast(means, pN,add=TRUE) | |
| for(i in 1:length(nm)){ |
tslumley
/ proflike.R
Created
August 5, 2020 06:02
Conditional profile likelihood for balanced accuracy
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| llprofci<-function(tpos,fpos,tneg,fneg){ | |
| ndis<-tpos+fneg | |
| nnot<-tneg+fpos | |
| lljoint<-function(a,d){ | |
| k<-length(a) |
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| --- | |
| title: "Rogue polls" | |
| author: "Thomas Lumley" | |
| date: "27/07/2020" | |
| output: word_document | |
| --- | |
| ```{r setup, include=FALSE} | |
| knitr::opts_chunk$set(echo = TRUE) | |
| ``` |