thoughtfulbloke’s gists

thoughtfulbloke / MortalityRates.csv

Created October 12, 2024 03:50

NZ Weekly Mortality Rates by Age(<30,30-59,60-79,80+). Date of Death not Registration. Weekly population interpolated from as at Quarter end. source StatsNZ and DIA

Period	Ages	RawDeaths	InterpPop	DeathRateMillion
2000-01-09	30 to 59	74	1569863.62637363	47.1378524585218
2000-01-16	30 to 59	64	1570169.78021978	40.7599234211741
2000-01-23	30 to 59	73	1570475.93406593	46.4827243872527
2000-01-30	30 to 59	60	1570782.08791209	38.1975325933039
2000-02-06	30 to 59	58	1571088.24175824	36.9170861689416
2000-02-13	30 to 59	70	1571394.3956044	44.5464233522841
2000-02-20	30 to 59	76	1571700.54945055	48.3552671827778
2000-02-27	30 to 59	67	1572006.7032967	42.6206833975277
2000-03-05	30 to 59	65	1572312.85714286	41.3403730082799

thoughtfulbloke / KnKplus.R

Created March 11, 2024 08:07

KnKplusGibson

	library(dplyr)
	library(tidyr)
	library(lubridate)
	NZstmf <- read.csv("NZL_NPstmfout.csv") \|>
	filter(Sex == "b")
	NZQTR <- read.csv("TotalQuarterlyPopulationAsAt.csv", skip=3,
	col.names = c("YRQR","Pop")) \|>
	filter(!is.na(Pop)) \|>
	separate(YRQR, into=c("YR", "QR"), sep="Q", convert = TRUE) \|>
	mutate(asDate = ceiling_date(ISOdate(YR,QR*3,25),

thoughtfulbloke / AgeRates.csv

Created December 3, 2023 03:49

We can make this file beautiful and searchable if this error is corrected: It looks like row 8 should actually have 20 columns, instead of 18 in line 7.

	"Age-specific death rates by sex, December years (total population) (Annual-Dec)","","","","","","","","","","","","","","","","","","",""
	"","Total Population","","","","","","","","","","","","","","","","","",""
	" ","0-4 Years","5-9 Years","10-14 Years","15-19 Years","20-24 Years","25-29 Years","30-34 Years","35-39 Years","40-44 Years","45-49 Years","50-54 Years","55-59 Years","60-64 Years","65-69 Years","70-74 Years","75-79 Years","80-84 Years","85-89 Years","90 Years and Over"
	1971,4.31,0.39,0.35,0.96,1.06,0.97,1.29,1.81,2.93,4.70,7.50,12.19,19.17,29.34,44.81,71.51,118.74,192.62,280.73
	1972,4.04,0.37,0.33,1.16,1.13,0.89,1.19,1.71,2.65,4.51,7.33,11.72,19.32,29.64,45.89,74.35,118.35,187.90,309.62
	1973,3.99,0.42,0.35,1.22,1.24,0.98,1.17,1.86,2.70,4.76,7.26,12.57,18.57,30.31,45.92,72.05,114.84,190.45,320.67
	1974,3.68,0.38,0.43,1.16,1.06,1.04,1.15,1.76,2.96,4.74,7.51,11.68,19.02,28.10,46.32,70.63,111.84,190.96,314.86
	1975,3.78,0.46,0.34,1.02,1.11,1.01,1.17,1.75,2.64,4.60,7.39,11.07,19.04,27.29,45.13,65.78,106

thoughtfulbloke / scale graph code.R

Created November 12, 2022 04:22

	library(rmapshaper)
	library(sf)
	library(ggplot2)
	library(dplyr)
	library(patchwork)

	# geographic data from koordinates.com
	start_map <- read_sf("new-zealand-2018-estimated-resident-population-statistical-g/new-zealand-2018-estimated-resident-population-statistical-g.shp")
	coast <- read_sf("nz-coastlines-and-islands-polygons-topo-150k/nz-coastlines-and-islands-polygons-topo-150k.shp")
	# simplify the graph to what is visually useful

thoughtfulbloke / reinfecting_populations.R

Last active September 23, 2022 22:42

	library(dplyr)
	library(lubridate)
	library(readr)
	library(RcppRoll)
	library(ggplot2)
	library(ggthemes)
	sixcols= colorblind_pal()(6)

	case_counts <- read_csv("https://raw.githubusercontent.com/minhealthnz/nz-covid-data/main/cases/covid-case-counts.csv")

thoughtfulbloke / ESR_wastewater_notes.Rmd

Created July 25, 2022 09:21


	```{r}
	library(readr)
	library(dplyr)
	library(lubridate)
	```

	David's usage notes for the wastewater data at: https://github.com/ESR-NZ/covid_in_wastewater

	I am reading the files directly of github, rather than downloading and then reading locally.

thoughtfulbloke / extract_from_demographics.R

Created May 21, 2022 08:49

	library(rvest) # process web pages
	library(dplyr) # general data pipeleine tools
	library(lubridate) # date functions

	# saving demographic pages as html into a folder
	# called case_demografics_html_asof
	# with a datestamp name for the contents
	Demographs <- list.files("../case_demografics_html_asof", pattern=".*html$")

	extract_vax <- function(x) {

thoughtfulbloke / Update_Daily_Covid_Thread.R

Created May 20, 2022 01:38

	# source this file so it pauses for input,
	# check the graphs
	# add comments via the readline input
	# post using rtweet

	library(rvest)
	library(dplyr)
	library(ggplot2)
	library(lubridate)
	library(rtweet)

thoughtfulbloke / case_hospitalisation_rate.R

Created May 13, 2022 23:45

	library(rvest)
	library(dplyr)
	library(lubridate)
	library(stringr)
	library(readr)
	library(ggplot2)
	library(ggthemes)
	library(RcppRoll)

	sixcol <- colorblind_pal()(6)

thoughtfulbloke / excess_mort_2022.R

Created May 6, 2022 01:49

Population Data from Infoshare (quarterly, as at, DPE). Deaths from StatsNZ open data API, but also in their Covid data portal

	legpos="right"
	theme_davidhood <- function(){
	# theme_minimal(base_family="OpenSans") %+replace%
	theme_minimal() %+replace%
	theme(panel.grid = element_blank(),
	axis.line.x = element_line(size=0.1),
	axis.line.y = element_line(size=0.1),
	axis.ticks = element_line(size=0.2),
	strip.background = element_rect(fill= "#FFFFFF", colour="#EFEFEF"),
	strip.text = element_text(size = 13,

David Hood thoughtfulbloke