Nothing
## ---- warning = FALSE, echo = FALSE, message = FALSE--------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>", fig.width = 7.5, fig.height = 5, fig.align = "center")
options(datatable.print.nrows = 8)
library(tidyvpc)
library(ggplot2)
library(magrittr)
library(data.table)
set.seed(1014)
## ---- echo=FALSE--------------------------------------------------------------
data.table::setDTthreads(2)
## ----tidyvpc_setup------------------------------------------------------------
library(tidyvpc)
library(data.table)
obs_cat_data <- tidyvpc::obs_cat_data
sim_cat_data <- tidyvpc::sim_cat_data
obs_cat_data <- obs_cat_data[order(PID_code, agemonths)]
sim_cat_data <- sim_cat_data[order(Replicate, PID_code, IVAR)]
## ----echo=FALSE---------------------------------------------------------------
sim_cat_data <- sim_cat_data[Replicate <= 30]
## ----binning_1----------------------------------------------------------------
vpc <- observed(obs_cat_data, x = agemonths, yobs = zlencat) %>%
simulated(sim_cat_data, ysim = DV) %>%
binning(bin = round(agemonths, 0)) %>%
vpcstats(vpc.type = "categorical")
plot(vpc, facet = TRUE, legend.position = "bottom", facet.scales = "fixed")
## ----binning_2----------------------------------------------------------------
vpc <- observed(obs_cat_data, x = agemonths, yobs = zlencat) %>%
simulated(sim_cat_data, ysim = DV) %>%
stratify(~ Country_ID_code) %>%
binning(bin = "pam", nbins = 6) %>%
vpcstats(vpc.type = "categorical", conf.level = .9, quantile.type = 6)
plot(vpc, facet = TRUE, legend.position = "bottom", facet.scales = "fixed")
## -----------------------------------------------------------------------------
vpc <- observed(obs_cat_data, x = agemonths, yobs = zlencat) %>%
simulated(sim_cat_data, ysim = DV) %>%
binless(optimize = TRUE) %>%
vpcstats(vpc.type = "categorical", quantile.type = 6)
plot(vpc, facet = TRUE, legend.position = "bottom", facet.scales = "fixed")
## -----------------------------------------------------------------------------
vpc <- observed(obs_cat_data, x = agemonths, yobs = zlencat) %>%
simulated(sim_cat_data, ysim = DV) %>%
stratify(~ Country_ID_code) %>%
binless(optimize = TRUE, optimization.interval = c(0,300)) %>%
vpcstats(vpc.type = "categorical")
plot(vpc, facet = TRUE, legend.position = "bottom", facet.scales = "fixed")
## -----------------------------------------------------------------------------
sort(unique(obs_cat_data$zlencat))
## -----------------------------------------------------------------------------
sp_user <- list(p0 = 300,
p1 = 50,
p2 = 100)
## -----------------------------------------------------------------------------
vpc <- observed(obs_cat_data, x = agemonths, yobs = zlencat) %>%
simulated(sim_cat_data, ysim = DV) %>%
binless(optimize = FALSE, sp = sp_user) %>%
vpcstats(vpc.type = "categorical", quantile.type = 6)
plot(vpc, facet = TRUE, legend.position = "bottom", facet.scales = "fixed")
## -----------------------------------------------------------------------------
sort(unique(obs_cat_data$Country_ID_code))
sort(unique(obs_cat_data$zlencat))
## -----------------------------------------------------------------------------
user_sp <- list(
Country1_prob0 = 100,
Country1_prob1 = 3,
Country1_prob2 = 4,
Country2_prob0 = 90,
Country2_prob1 = 3,
Country2_prob2 = 4,
Country3_prob0 = 55,
Country3_prob1 = 3,
Country3_prob2 = 200)
## -----------------------------------------------------------------------------
vpc <- observed(obs_cat_data, x = agemonths, yobs = zlencat) %>%
simulated(sim_cat_data, ysim = DV) %>%
stratify(~ Country_ID_code) %>%
binless(optimize = FALSE, sp = user_sp) %>%
vpcstats(vpc.type = "categorical"
, conf.level = 0.9
, quantile.type = 6
)
plot(vpc, facet = TRUE)
## -----------------------------------------------------------------------------
library(dplyr)
obs_cat_data <- obs_cat_data %>%
mutate(gender = ifelse(PID_code %% 2 == 1, "male", "female"))
## -----------------------------------------------------------------------------
vpc <- observed(obs_cat_data, x = agemonths, yobs = zlencat) %>%
simulated(sim_cat_data, ysim = DV) %>%
stratify(~ gender + Country_ID_code)
## -----------------------------------------------------------------------------
sort(unique(obs_cat_data$gender))
sort(unique(obs_cat_data$Country_ID_code))
sort(unique(obs_cat_data$zlencat))
## -----------------------------------------------------------------------------
user_sp <- list(
female.1.prob0 = 1,
female.1.prob1 = 3,
female.1.prob2 = 9,
female.2.prob0 = 5,
female.2.prob1 = 10,
female.2.prob2 = 12,
female.3.prob0 = 33,
female.3.prob1 = 44,
female.3.prob2 = 88,
male.1.prob0 = 4,
male.1.prob1 = 12,
male.1.prob2 = 15,
male.2.prob0 = 800,
male.2.prob1 = 19,
male.2.prob2 = 28,
male.3.prob0 = 22,
male.3.prob1 = 88,
male.3.prob2 = 11
)
## -----------------------------------------------------------------------------
vpc <- observed(obs_cat_data, x = agemonths, yobs = zlencat) %>%
simulated(sim_cat_data, ysim = DV) %>%
stratify(~ gender + Country_ID_code) %>%
binless(optimize = FALSE, sp = user_sp) %>%
vpcstats(vpc.type = "categorical", conf.level = 0.9, quantile.type = 6)
plot(vpc, facet=TRUE)
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