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child_born = "child_born", child_dead = "child_dead",
agegrp = "agegrp", iso3 = "KHM", svy_date = "svy_date") {
agegrp <- data[[agegrp]]
women <- data[[women]]
child_born <- data[[child_born]]
=======
>>>>>>> 25019f6af33b3b11092c9899e82431ba3bb30468
child_dead <- data[[child_dead]]
pi <- child_born / women
di <- child_dead / child_born
logit_di <- log(di / (1 - di))
pr1 <- pi[1] / pi[2]
pr2 <- pi[2] / pi[3]
re <- rjn_mac_re$re[rjn_mac_re$iso3 == iso3]
## if there is no country that matches, then re = 0
if (length(re) == 0) re <- 0
## calculate logit 5q0 values
logit_5q0 <- rjn_mac_5q0$coef_intercept + re + rjn_mac_5q0$coef_log_cdceb *
logit_di + rjn_mac_5q0$coef_ceb * pi + rjn_mac_5q0$coef_pr1 * pr1 +
rjn_mac_5q0$coef_pr2 * pr2
## convert back to normal values by exponentiating
v5q0 <- exp(logit_5q0) / (1 + exp(logit_5q0))
## calculate reference time
reftime <- rjn_mac_reftime$coef_intercept + rjn_mac_reftime$coef_cdceb * di +
rjn_mac_reftime$coef_ceb * pi + rjn_mac_reftime$coef_pr1 * pr1 +
rjn_mac_reftime$coef_pr2 * pr2
year <- svy_date - reftime
data.frame(drop = agegrp, iso3, svy_date, method = "MAC", agegrp, reftime, year, v5q0)[, -1]
}
u5mr_mac(mcd, "n", "ceb", "cd", "agegroup", "KHM", 1234)
message(paste0("c(", paste0("\"", MAC_random_effects$agegroup, "\"", collapse = ", "), ")"))
message(paste0("c(", paste0("'", MAC_random_effects$iso3, "'", collapse = ", "), ")"))
message(paste0("c(", paste0(MAC_random_effects$random_effect, collapse = ", "), ")"))
u5mr_mac <- function(data, women = "women",
child_born = "child_born", child_dead = "child_dead",
agegrp = "agegrp", iso3 = "KHM", svy_date = "svy_date") {
agegrp <- data[[agegrp]]
women <- data[[women]]
child_born <- data[[child_born]]
child_dead <- data[[child_dead]]
pi <- child_born / women
di <- child_dead / child_born
logit_di <- log(di / (1 - di))
pr1 <- pi[1] / pi[2]
pr2 <- pi[2] / pi[3]
re <- rjn_mac_re$re[rjn_mac_re$iso3 == iso3]
## if there is no country that matches, then re = 0
if (length(re) == 0) re <- 0
## calculate logit 5q0 values
logit_5q0 <- rjn_mac_5q0$coef_intercept + re + rjn_mac_5q0$coef_log_cdceb *
logit_di + rjn_mac_5q0$coef_ceb * pi + rjn_mac_5q0$coef_pr1 * pr1 +
rjn_mac_5q0$coef_pr2 * pr2
## convert back to normal values by exponentiating
q5 <- exp(logit_5q0) / (1 + exp(logit_5q0))
## calculate reference time
reftime <- rjn_mac_reftime$coef_intercept + rjn_mac_reftime$coef_cdceb * di +
rjn_mac_reftime$coef_ceb * pi + rjn_mac_reftime$coef_pr1 * pr1 +
rjn_mac_reftime$coef_pr2 * pr2
year <- svy_date - reftime
data.frame(drop = agegrp, iso3, svy_date, method = "MAC", agegrp, reftime, year, q5)[, -1]
}
u5mr_mac(mcd, "n", "ceb", "cd", "agegroup", "KHM", 1234)
# source("../beta/datasets.R")
rm(list = ls())
# lapply(paste0("./R/", dir("R")), source, echo = TRUE)
library(u5mr)
library(tidyverse)
library(mStats)
options(scipen = 100)
rjn_mac_5q0 <- data.frame(
agegrp = c('15-19', '20-24', '25-29', '30-34', '35-39', '40-44', '45-49'),
coef_intercept = c(-0.6975273, 0.1258313, 0.0167552, -0.1034484, -0.0852121, -0.237591, 0.044768),
coef_log_cdceb = c(0.5555944, 0.8853436, 0.9853121, 0.9679322, 0.9728206, 0.9951801, 1.01955),
coef_ceb = c(2.573548, 0.2111931, 0.0523679, 0.0180773, 0.0147395, 0.0206229, 0.0016674),
coef_pr1 = c(-3.923797, -0.0087424, 0.0705175, -0.0029778, 0.2246798, 0.162713, 0.8637883),
coef_pr2 = c(-0.2960762, -1.110689, -0.2891437, -0.0033048, -0.2317203, -0.0566164, -0.8015343)
)
rjn_mac_re <- data.frame(
agegrp = c("15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29",
"30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39",
"40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49"),
iso3 = c('ARM', 'AZE', 'BDI', 'BEN', 'BFA', 'BGD', 'BOL', 'BRA', 'BWA', 'CAF', 'CIV', 'CMR', 'COG', 'COL', 'COM', 'DOM', 'ECU', 'EGY', 'ERI', 'ETH', 'GAB', 'GHA', 'GIN', 'GTM', 'HND', 'HTI', 'IDN', 'IND', 'JOR', 'KAZ', 'KEN', 'KGZ', 'KHM', 'LBR', 'LKA', 'LSO', 'MAR', 'MDG', 'MEX', 'MLI', 'MOZ', 'MRT', 'MWI', 'NAM', 'NER', 'NGA', 'NIC', 'NPL', 'PAK', 'PER', 'PHL', 'PRY', 'RWA', 'SDN', 'SEN', 'SWZ', 'TCD', 'TGO', 'THA', 'TTO', 'TUN', 'TUR', 'TZA', 'UGA', 'UZB', 'VNM', 'YEM', 'ZAF', 'ZMB', 'ZWE', 'ARM', 'AZE', 'BDI', 'BEN', 'BFA', 'BGD', 'BOL', 'BRA', 'BWA', 'CAF', 'CIV', 'CMR', 'COG', 'COL', 'COM', 'DOM', 'ECU', 'EGY', 'ERI', 'ETH', 'GAB', 'GHA', 'GIN', 'GTM', 'HND', 'HTI', 'IDN', 'IND', 'JOR', 'KAZ', 'KEN', 'KGZ', 'KHM', 'LBR', 'LKA', 'LSO', 'MAR', 'MDG', 'MEX', 'MLI', 'MOZ', 'MRT', 'MWI', 'NAM', 'NER', 'NGA', 'NIC', 'NPL', 'PAK', 'PER', 'PHL', 'PRY', 'RWA', 'SDN', 'SEN', 'SWZ', 'TCD', 'TGO', 'THA', 'TTO', 'TUN', 'TUR', 'TZA', 'UGA', 'UZB', 'VNM', 'YEM', 'ZAF', 'ZMB', 'ZWE', 'ARM', 'AZE', 'BDI', 'BEN', 'BFA', 'BGD', 'BOL', 'BRA', 'BWA', 'CAF', 'CIV', 'CMR', 'COG', 'COL', 'COM', 'DOM', 'ECU', 'EGY', 'ERI', 'ETH', 'GAB', 'GHA', 'GIN', 'GTM', 'HND', 'HTI', 'IDN', 'IND', 'JOR', 'KAZ', 'KEN', 'KGZ', 'KHM', 'LBR', 'LKA', 'LSO', 'MAR', 'MDG', 'MEX', 'MLI', 'MOZ', 'MRT', 'MWI', 'NAM', 'NER', 'NGA', 'NIC', 'NPL', 'PAK', 'PER', 'PHL', 'PRY', 'RWA', 'SDN', 'SEN', 'SWZ', 'TCD', 'TGO', 'THA', 'TTO', 'TUN', 'TUR', 'TZA', 'UGA', 'UZB', 'VNM', 'YEM', 'ZAF', 'ZMB', 'ZWE', 'ARM', 'AZE', 'BDI', 'BEN', 'BFA', 'BGD',
'BOL', 'BRA', 'BWA', 'CAF', 'CIV', 'CMR', 'COG', 'COL', 'COM', 'DOM', 'ECU', 'EGY', 'ERI', 'ETH', 'GAB', 'GHA', 'GIN', 'GTM', 'HND', 'HTI', 'IDN', 'IND', 'JOR', 'KAZ', 'KEN', 'KGZ', 'KHM', 'LBR', 'LKA', 'LSO', 'MAR', 'MDG', 'MEX', 'MLI', 'MOZ', 'MRT', 'MWI', 'NAM', 'NER', 'NGA', 'NIC', 'NPL', 'PAK', 'PER', 'PHL', 'PRY', 'RWA', 'SDN', 'SEN', 'SWZ', 'TCD', 'TGO', 'THA', 'TTO', 'TUN', 'TUR', 'TZA', 'UGA', 'UZB', 'VNM', 'YEM', 'ZAF', 'ZMB', 'ZWE', 'ARM', 'AZE', 'BDI', 'BEN', 'BFA', 'BGD', 'BOL', 'BRA', 'BWA', 'CAF', 'CIV', 'CMR', 'COG', 'COL', 'COM', 'DOM', 'ECU', 'EGY', 'ERI', 'ETH', 'GAB', 'GHA', 'GIN', 'GTM', 'HND', 'HTI', 'IDN', 'IND', 'JOR', 'KAZ', 'KEN', 'KGZ', 'KHM', 'LBR', 'LKA', 'LSO', 'MAR', 'MDG', 'MEX', 'MLI', 'MOZ', 'MRT', 'MWI', 'NAM', 'NER', 'NGA', 'NIC', 'NPL', 'PAK', 'PER', 'PHL', 'PRY', 'RWA', 'SDN', 'SEN', 'SWZ', 'TCD', 'TGO', 'THA', 'TTO', 'TUN', 'TUR', 'TZA', 'UGA', 'UZB', 'VNM', 'YEM', 'ZAF', 'ZMB', 'ZWE', 'ARM', 'AZE', 'BDI', 'BEN', 'BFA', 'BGD', 'BOL', 'BRA', 'BWA', 'CAF', 'CIV', 'CMR', 'COG', 'COL', 'COM', 'DOM', 'ECU', 'EGY', 'ERI', 'ETH', 'GAB', 'GHA', 'GIN', 'GTM', 'HND', 'HTI', 'IDN',
'IND', 'JOR', 'KAZ', 'KEN', 'KGZ', 'KHM', 'LBR', 'LKA', 'LSO', 'MAR', 'MDG', 'MEX', 'MLI', 'MOZ', 'MRT', 'MWI', 'NAM', 'NER', 'NGA', 'NIC', 'NPL', 'PAK', 'PER', 'PHL', 'PRY', 'RWA', 'SDN', 'SEN', 'SWZ', 'TCD', 'TGO', 'THA', 'TTO', 'TUN', 'TUR', 'TZA', 'UGA', 'UZB', 'VNM', 'YEM', 'ZAF', 'ZMB', 'ZWE', 'ARM', 'AZE', 'BDI', 'BEN', 'BFA', 'BGD', 'BOL', 'BRA', 'BWA', 'CAF', 'CIV', 'CMR', 'COG', 'COL', 'COM', 'DOM', 'ECU', 'EGY', 'ERI', 'ETH', 'GAB', 'GHA', 'GIN', 'GTM', 'HND', 'HTI', 'IDN', 'IND', 'JOR', 'KAZ', 'KEN', 'KGZ', 'KHM', 'LBR', 'LKA', 'LSO', 'MAR', 'MDG', 'MEX', 'MLI', 'MOZ', 'MRT', 'MWI', 'NAM', 'NER', 'NGA', 'NIC', 'NPL', 'PAK', 'PER', 'PHL', 'PRY', 'RWA', 'SDN', 'SEN', 'SWZ', 'TCD', 'TGO', 'THA', 'TTO', 'TUN', 'TUR', 'TZA', 'UGA', 'UZB', 'VNM', 'YEM', 'ZAF', 'ZMB', 'ZWE'),
re = c(-0.0740473806025451, -0.795791117654689, 0.0155759526158037, 0.167607916035274,
0.312169911719107, -0.296688023813686, -0.0347382273558816, -0.0807181991540473,
-0.00587074151497604, 0.0341199997542009, 0.0987730517784896, 0.214199601121983,
0.101434384497789, -0.252926194970638, 0.201941057537439, -0.335415771831015,
-0.13894049257474, -0.17633911342114, 0.308017811901251, 0.0622887918523105,
0.0495851202778916, 0.348063608603817, 0.269097292481718, -0.0822907533315262,
-0.45401938813222, 0.242555390947918, -0.0414108708084773, -0.235634428567539,
-0.410657587622013, 0.461005429816519, -0.114078617228897, 0.124042825789835,
0.112012316556841, 0.177191559784913, -0.533245228365606, 0.244690752241358,
-0.253770138470807, 0.0427130903724443, -0.151949500816286, 0.221563125229524,
0.121359808817806, 0.251304137747192, 0.141382927962772, 0.0979680619614078,
0.362533204668132, 0.468893124782236, -0.238506315601834, -0.215977145004483,
-0.268123473779954, -0.131684862494324, -0.256291791064001, -0.503895050382619,
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rjn_mac_reftime <- data.frame(
agegrp = c('15-19', '20-24', '25-29', '30-34', '35-39', '40-44', '45-49'),
coef_intercept = c(0.9432311, 2.533395, 4.303299, 7.268542, 11.42926, 15.48549, 19.90218),
coef_cdceb = c(0.0015192, 0.0006606, -0.0017479, -0.0000676, -0.0012584, -0.002121, -0.001287),
coef_ceb = c(0.1923932, 0.2812458, 0.1005495, -0.3103958, -0.4738352, -0.5497375, -0.5534297),
coef_pr1 = c(0.7542738, 0.8857344, 0.2908919, 0.5750943, 1.502711, 3.027917, 6.079983),
coef_pr2 = c(0.543375, 0.6180932, 2.843069, 4.691129, 4.441438, 3.965783, 0.9077534)
)
microdata <- haven::read_dta("C:/Users/minnmy/Downloads/pmed.1000253.s004/microdata.dta")
mcd <- microdata %>%
filter(sex == 2) %>%
## 281,809
filter(age >= 15 & age < 50)
## 227,690
mcd <- mcd %>%
egen(age, seq(15, 45, 5), new_var = "agegroup") %>%
generate(n, 1 * wtper) %>%
replace(ceb, ceb * wtper) %>%
replace(cd, cd * wtper) %>%
group_by(iso3, svdate, agegroup) %>%
summarise(n = sum(n),
ceb = sum(ceb),
cd = sum(cd)) %>%
data.frame()
u5mr_cohort <- function(data, women = "women",
child_born = "child_born", child_dead = "child_dead",
agegrp = "agegrp", iso3 = "KHM", svy_date = "svy_date") {
agegrp <- data[[agegrp]]
women <- data[[women]]
child_born <- data[[child_born]]
child_dead <- data[[child_dead]]
pi <- child_born / women
di <- child_dead / child_born
logit_di <- log(di / (1 - di))
pr1 <- pi[1] / pi[2]
pr2 <- pi[2] / pi[3]
re <- rjn_mac_re$re[rjn_mac_re$iso3 == iso3]
## if there is no country that matches, then re = 0
if (length(re) == 0) re <- 0
## calculate logit 5q0 values
logit_5q0 <- rjn_mac_5q0$coef_intercept + re + rjn_mac_5q0$coef_log_cdceb *
logit_di + rjn_mac_5q0$coef_ceb * pi + rjn_mac_5q0$coef_pr1 * pr1 +
rjn_mac_5q0$coef_pr2 * pr2
## convert back to normal values by exponentiating
q5 <- exp(logit_5q0) / (1 + exp(logit_5q0))
## calculate reference time
reftime <- rjn_mac_reftime$coef_intercept + rjn_mac_reftime$coef_cdceb * di +
rjn_mac_reftime$coef_ceb * pi + rjn_mac_reftime$coef_pr1 * pr1 +
rjn_mac_reftime$coef_pr2 * pr2
year <- svy_date - reftime
data.frame(drop = agegrp, iso3, svy_date, agegrp, reftime, year, q5)[, -1]
}
u5mr_cohort(mcd, "n", "ceb", "cd", "agegroup", "KHM", 1234)
# source("../beta/datasets.R")
rm(list = ls())
# lapply(paste0("./R/", dir("R")), source, echo = TRUE)
library(u5mr)
library(tidyverse)
library(mStats)
options(scipen = 100)
mac_5q0 <- data.frame(
agegrp = c('15-19', '20-24', '25-29', '30-34', '35-39', '40-44', '45-49'),
coef_intercept = c(-0.6975273, 0.1258313, 0.0167552, -0.1034484, -0.0852121, -0.237591, 0.044768),
coef_log_cdceb = c(0.5555944, 0.8853436, 0.9853121, 0.9679322, 0.9728206, 0.9951801, 1.01955),
coef_ceb = c(2.573548, 0.2111931, 0.0523679, 0.0180773, 0.0147395, 0.0206229, 0.0016674),
coef_pr1 = c(-3.923797, -0.0087424, 0.0705175, -0.0029778, 0.2246798, 0.162713, 0.8637883),
coef_pr2 = c(-0.2960762, -1.110689, -0.2891437, -0.0033048, -0.2317203, -0.0566164, -0.8015343)
)
mac_re <- data.frame(
agegrp = c("15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "15-19", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "20-24", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29", "25-29",
"30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "30-34", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39", "35-39",
"40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "40-44", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49", "45-49"),
iso3 = c('ARM', 'AZE', 'BDI', 'BEN', 'BFA', 'BGD', 'BOL', 'BRA', 'BWA', 'CAF', 'CIV', 'CMR', 'COG', 'COL', 'COM', 'DOM', 'ECU', 'EGY', 'ERI', 'ETH', 'GAB', 'GHA', 'GIN', 'GTM', 'HND', 'HTI', 'IDN', 'IND', 'JOR', 'KAZ', 'KEN', 'KGZ', 'KHM', 'LBR', 'LKA', 'LSO', 'MAR', 'MDG', 'MEX', 'MLI', 'MOZ', 'MRT', 'MWI', 'NAM', 'NER', 'NGA', 'NIC', 'NPL', 'PAK', 'PER', 'PHL', 'PRY', 'RWA', 'SDN', 'SEN', 'SWZ', 'TCD', 'TGO', 'THA', 'TTO', 'TUN', 'TUR', 'TZA', 'UGA', 'UZB', 'VNM', 'YEM', 'ZAF', 'ZMB', 'ZWE', 'ARM', 'AZE', 'BDI', 'BEN', 'BFA', 'BGD', 'BOL', 'BRA', 'BWA', 'CAF', 'CIV', 'CMR', 'COG', 'COL', 'COM', 'DOM', 'ECU', 'EGY', 'ERI', 'ETH', 'GAB', 'GHA', 'GIN', 'GTM', 'HND', 'HTI', 'IDN', 'IND', 'JOR', 'KAZ', 'KEN', 'KGZ', 'KHM', 'LBR', 'LKA', 'LSO', 'MAR', 'MDG', 'MEX', 'MLI', 'MOZ', 'MRT', 'MWI', 'NAM', 'NER', 'NGA', 'NIC', 'NPL', 'PAK', 'PER', 'PHL', 'PRY', 'RWA', 'SDN', 'SEN', 'SWZ', 'TCD', 'TGO', 'THA', 'TTO', 'TUN', 'TUR', 'TZA', 'UGA', 'UZB', 'VNM', 'YEM', 'ZAF', 'ZMB', 'ZWE', 'ARM', 'AZE', 'BDI', 'BEN', 'BFA', 'BGD', 'BOL', 'BRA', 'BWA', 'CAF', 'CIV', 'CMR', 'COG', 'COL', 'COM', 'DOM', 'ECU', 'EGY', 'ERI', 'ETH', 'GAB', 'GHA', 'GIN', 'GTM', 'HND', 'HTI', 'IDN', 'IND', 'JOR', 'KAZ', 'KEN', 'KGZ', 'KHM', 'LBR', 'LKA', 'LSO', 'MAR', 'MDG', 'MEX', 'MLI', 'MOZ', 'MRT', 'MWI', 'NAM', 'NER', 'NGA', 'NIC', 'NPL', 'PAK', 'PER', 'PHL', 'PRY', 'RWA', 'SDN', 'SEN', 'SWZ', 'TCD', 'TGO', 'THA', 'TTO', 'TUN', 'TUR', 'TZA', 'UGA', 'UZB', 'VNM', 'YEM', 'ZAF', 'ZMB', 'ZWE', 'ARM', 'AZE', 'BDI', 'BEN', 'BFA', 'BGD',
'BOL', 'BRA', 'BWA', 'CAF', 'CIV', 'CMR', 'COG', 'COL', 'COM', 'DOM', 'ECU', 'EGY', 'ERI', 'ETH', 'GAB', 'GHA', 'GIN', 'GTM', 'HND', 'HTI', 'IDN', 'IND', 'JOR', 'KAZ', 'KEN', 'KGZ', 'KHM', 'LBR', 'LKA', 'LSO', 'MAR', 'MDG', 'MEX', 'MLI', 'MOZ', 'MRT', 'MWI', 'NAM', 'NER', 'NGA', 'NIC', 'NPL', 'PAK', 'PER', 'PHL', 'PRY', 'RWA', 'SDN', 'SEN', 'SWZ', 'TCD', 'TGO', 'THA', 'TTO', 'TUN', 'TUR', 'TZA', 'UGA', 'UZB', 'VNM', 'YEM', 'ZAF', 'ZMB', 'ZWE', 'ARM', 'AZE', 'BDI', 'BEN', 'BFA', 'BGD', 'BOL', 'BRA', 'BWA', 'CAF', 'CIV', 'CMR', 'COG', 'COL', 'COM', 'DOM', 'ECU', 'EGY', 'ERI', 'ETH', 'GAB', 'GHA', 'GIN', 'GTM', 'HND', 'HTI', 'IDN', 'IND', 'JOR', 'KAZ', 'KEN', 'KGZ', 'KHM', 'LBR', 'LKA', 'LSO', 'MAR', 'MDG', 'MEX', 'MLI', 'MOZ', 'MRT', 'MWI', 'NAM', 'NER', 'NGA', 'NIC', 'NPL', 'PAK', 'PER', 'PHL', 'PRY', 'RWA', 'SDN', 'SEN', 'SWZ', 'TCD', 'TGO', 'THA', 'TTO', 'TUN', 'TUR', 'TZA', 'UGA', 'UZB', 'VNM', 'YEM', 'ZAF', 'ZMB', 'ZWE', 'ARM', 'AZE', 'BDI', 'BEN', 'BFA', 'BGD', 'BOL', 'BRA', 'BWA', 'CAF', 'CIV', 'CMR', 'COG', 'COL', 'COM', 'DOM', 'ECU', 'EGY', 'ERI', 'ETH', 'GAB', 'GHA', 'GIN', 'GTM', 'HND', 'HTI', 'IDN',
'IND', 'JOR', 'KAZ', 'KEN', 'KGZ', 'KHM', 'LBR', 'LKA', 'LSO', 'MAR', 'MDG', 'MEX', 'MLI', 'MOZ', 'MRT', 'MWI', 'NAM', 'NER', 'NGA', 'NIC', 'NPL', 'PAK', 'PER', 'PHL', 'PRY', 'RWA', 'SDN', 'SEN', 'SWZ', 'TCD', 'TGO', 'THA', 'TTO', 'TUN', 'TUR', 'TZA', 'UGA', 'UZB', 'VNM', 'YEM', 'ZAF', 'ZMB', 'ZWE', 'ARM', 'AZE', 'BDI', 'BEN', 'BFA', 'BGD', 'BOL', 'BRA', 'BWA', 'CAF', 'CIV', 'CMR', 'COG', 'COL', 'COM', 'DOM', 'ECU', 'EGY', 'ERI', 'ETH', 'GAB', 'GHA', 'GIN', 'GTM', 'HND', 'HTI', 'IDN', 'IND', 'JOR', 'KAZ', 'KEN', 'KGZ', 'KHM', 'LBR', 'LKA', 'LSO', 'MAR', 'MDG', 'MEX', 'MLI', 'MOZ', 'MRT', 'MWI', 'NAM', 'NER', 'NGA', 'NIC', 'NPL', 'PAK', 'PER', 'PHL', 'PRY', 'RWA', 'SDN', 'SEN', 'SWZ', 'TCD', 'TGO', 'THA', 'TTO', 'TUN', 'TUR', 'TZA', 'UGA', 'UZB', 'VNM', 'YEM', 'ZAF', 'ZMB', 'ZWE'),
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0.0372205349685101, 0.0286088658079497, 0.0495226431349513, -0.0817897920820907,
-0.0550754578194008, -0.0173507323465471, -0.233359007285683, -0.0200965193440001,
-0.0257971261778375, -0.0255853450503265, 0.00647100123906467, 0.0318723146782486,
0.0160438492107449, -0.0208932257641941, -0.0301389877507251, 0.0484910844562105,
0.0390538656561936, 0.073374159746082, -0.0275506681624441, -0.0152452314243491,
-0.0221773426872071, -0.00000000658142803654897, 0.00000000549001592993776,
0.0000000198668591825604, 0.00000000197995328154996, 0.0000000448093576761179,
0.000000000169939626248278, 0.0000000192195042644619, 0.0000000630062388694952,
0.000000117132438271513, -0.0000000598742144712409, -0.0000000806352906505957,
-0.0000000780524006437864, -0.000000120670454488179, -0.0000000438402718308179,
0.0000000566560029230225, 0.000000110416386162676, 0.0000000428397241626569,
0.000000179741440726228, -0.0000000093390309668003, -0.0000000229723188360878,
-0.0000000667412279715967, 0.000000107303954089799, 0.00000000726226116061813,
0.0000000204651542059649, -0.00000000931714564373454, 0.0000000260977268342249,
-0.0000000464800393356342, -0.0000000406485729182893, -0.0000000975574631004335,
0.000000037495526370434, -0.000000216334914430975, 0.0000000672466193275683,
-0.0000000704750921453968, 0.0000000557289692336193, -0.0000000634406485811656,
-0.000000111121851964046, 0.0000000714285958987262, 0.0000000903404887561128,
0.00000000601874472391811, 0.000000113834365478908, -0.0000000252773183735804,
0.0000000422100272933371, 0.0000000530364394390656, 0.0000000694030549637975,
0.000000128680694103497, -0.0000000335656290890042, -0.000000082676743810319,
-0.00000000780778548620502, 0.0000000814160259104205, 0.000000130238700617509,
0.0000000371865678372784, 0.000000000283632031076552, -0.000000220653175685402,
0.0000000147793572008302, 0.0000000940275214266338, -0.000000251933753016487,
-0.0000000626644220445201, 0.00000000834203637173992, -0.000000053818817085844,
0.0000000295402880926745, 0.0000000226628658428821, -0.0000000429021714301435,
-0.00000000988591405273897, 0.00000000214314254121632, 0.0000000993402384095545,
-0.00000000735372412943671, 0.0000000784846845721814, 0.0000000331550688313437,
-0.000000172322181425369, -0.0000000745366109870467)
)
mac_reftime <- data.frame(
agegrp = c('15-19', '20-24', '25-29', '30-34', '35-39', '40-44', '45-49'),
coef_intercept = c(0.9432311, 2.533395, 4.303299, 7.268542, 11.42926, 15.48549, 19.90218),
coef_cdceb = c(0.0015192, 0.0006606, -0.0017479, -0.0000676, -0.0012584, -0.002121, -0.001287),
coef_ceb = c(0.1923932, 0.2812458, 0.1005495, -0.3103958, -0.4738352, -0.5497375, -0.5534297),
coef_pr1 = c(0.7542738, 0.8857344, 0.2908919, 0.5750943, 1.502711, 3.027917, 6.079983),
coef_pr2 = c(0.543375, 0.6180932, 2.843069, 4.691129, 4.441438, 3.965783, 0.9077534)
)
microdata <- haven::read_dta("C:/Users/minnmy/Downloads/pmed.1000253.s004/microdata.dta")
mcd <- microdata %>%
filter(sex == 2) %>%
## 281,809
filter(age >= 15 & age < 50)
## 227,690
mcd <- mcd %>%
egen(age, seq(15, 45, 5), new_var = "agegroup") %>%
generate(n, 1 * wtper) %>%
replace(ceb, ceb * wtper) %>%
replace(cd, cd * wtper) %>%
group_by(iso3, svdate, agegroup) %>%
summarise(n = sum(n),
ceb = sum(ceb),
cd = sum(cd)) %>%
data.frame()
u5mr_cohort <- function(data, women = "women",
child_born = "child_born", child_dead = "child_dead",
agegrp = "agegrp", iso3 = "KHM", svy_date = "svy_date") {
agegrp <- data[[agegrp]]
women <- data[[women]]
child_born <- data[[child_born]]
child_dead <- data[[child_dead]]
pi <- child_born / women
di <- child_dead / child_born
logit_di <- log(di / (1 - di))
pr1 <- pi[1] / pi[2]
pr2 <- pi[2] / pi[3]
re <- mac_re$re[mac_re$iso3 == iso3]
## if there is no country that matches, then re = 0
if (length(re) == 0) re <- 0
## calculate logit 5q0 values
logit_5q0 <- mac_5q0$coef_intercept + re + mac_5q0$coef_log_cdceb *
logit_di + mac_5q0$coef_ceb * pi + mac_5q0$coef_pr1 * pr1 +
mac_5q0$coef_pr2 * pr2
## convert back to normal values by exponentiating
q5 <- exp(logit_5q0) / (1 + exp(logit_5q0))
## calculate reference time
reftime <- mac_reftime$coef_intercept + mac_reftime$coef_cdceb * di +
mac_reftime$coef_ceb * pi + mac_reftime$coef_pr1 * pr1 +
mac_reftime$coef_pr2 * pr2
year <- svy_date - reftime
data.frame(drop = agegrp, iso3, svy_date, agegrp, reftime, year, q5)[, -1]
}
u5mr_cohort(mcd, "n", "ceb", "cd", "agegroup", "KHM", 1234)
microdata
microdata$country <- "Cambodia"
microdata$svydate <- 2000
microdata
microdata %>% rename(svy_wt = wtper)
microdata %>% rename(svy_wt = wtper) %>%
select(iso3, region, country, svy_wt:cd)
microdata %>% rename(svy_wt = wtper) %>% select(iso3, region, country, svy_wt:cd) -> microdata
microdata <- data.frame(microdata)
microdata
usethis::use_data(microdata)
library(u5mr)
?microdata
library(u5mr)
u5mr::microdata
microdata
?panama
library(u5mr)
devtools::release()
devtools::release()
devtools::release()
devtools::check_rhub()
devtools::release()
devtools::check_win_devel()
install.packages("pdflatex")
devtools::release()
inytex::install_tinytex()
tinytex::install_tinytex()
install.packages("pdflatex")
devtools::release()
install.packages("Rd2pdf")
devtools::release()
library(tidyverse)
?pivot_longer