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02_table2_plmlmm.Rmd
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---
title: "02_table2_plmlmm"
author: "randy"
date: "`r Sys.Date()`"
output:
pdf_document: default
html_document: default
---
```{r setup, include=FALSE}
# knitr::opts_chunk$set(echo = TRUE,
# warnings = FALSE,
# message = FALSE,
# comment = "#>",
# results = "hide",
# error = FALSE)
## clean the R environment
graphics.off()
rm(list = ls())
freshr::freshr()
## load packages
library(here, quietly = TRUE)
library(tidyverse, quietly = TRUE)
library(splines)
library(tibble)
library(nlme)
library(gamlss)
library(JMbayes)
## check the directory for the file
# here::dr_here()
here::set_here()
## the figure or results should be saved
# paste0("foldername/Sfilename_workingresult_",
#. Sys.Date(), ".filetype")
```
The results are generated by `02_table2_plmlmm_code.R` with different setups with anchor time points
```{r}
source("R/00_functions.R")
## the R file below is the code for results
# source("02_table2_plmlmm_code.R")
file_location <- "results/result_anchors_2023-08-23/"
files <- list.files(path = "results/result_anchors_2023-08-23/", pattern = ".Rdata")
files
```
```{r}
anchortime <- map_dfr(files, ~pullout(file_location, .)) %>%
mutate(term = rep(c("bias", "mse", "cov50", "cov80", "cov90"), 7))
```
```{r}
options(digits = 4)
bias <- anchortime %>%
filter(term == "bias") %>%
unnest() %>%
mutate(Time = c("t(3, 6, 9, 12)",
"t(4, 8, 12)",
"t(5, 10, 15)",
"t(6, 10, 11, 12)",
"t(6, 9, 12, 15)",
"t(6, 9, 12)",
"t(8, 10, 12)")) %>%
mutate(Time = factor(Time, levels = c("t(4, 8, 12)",
"t(5, 10, 15)",
"t(6, 9, 12)",
"t(8, 10, 12)",
"t(3, 6, 9, 12)",
"t(6, 10, 11, 12)",
"t(6, 9, 12, 15)"))) %>%
arrange(Time) %>%
dplyr::select(-term) %>%
dplyr::select(Time, sgl_n, eld_n, mhl_n, mhl_p)
rmse <- anchortime %>%
filter(term == "mse") %>%
unnest() %>%
mutate(Time = c("t(3, 6, 9, 12)",
"t(4, 8, 12)",
"t(5, 10, 15)",
"t(6, 10, 11, 12)",
"t(6, 9, 12, 15)",
"t(6, 9, 12)",
"t(8, 10, 12)")) %>%
mutate(Time = factor(Time, levels = c("t(4, 8, 12)",
"t(5, 10, 15)",
"t(6, 9, 12)",
"t(8, 10, 12)",
"t(3, 6, 9, 12)",
"t(6, 10, 11, 12)",
"t(6, 9, 12, 15)"))) %>%
mutate_if(is.numeric, sqrt) %>%
arrange(Time) %>%
dplyr::select(-term) %>%
dplyr::select(Time, sgl_n, eld_n, mhl_n, mhl_p)
cov50 <- anchortime %>%
filter(term == "cov50") %>%
unnest() %>%
unnest() %>%
mutate(Time = c("t(3, 6, 9, 12)",
"t(4, 8, 12)",
"t(5, 10, 15)",
"t(6, 10, 11, 12)",
"t(6, 9, 12, 15)",
"t(6, 9, 12)",
"t(8, 10, 12)")) %>%
mutate(Time = factor(Time, levels = c("t(4, 8, 12)",
"t(5, 10, 15)",
"t(6, 9, 12)",
"t(8, 10, 12)",
"t(3, 6, 9, 12)",
"t(6, 10, 11, 12)",
"t(6, 9, 12, 15)"))) %>%
arrange(Time) %>%
dplyr::select(-term) %>%
dplyr::select(Time, sgl_n, eld_n, mhl_n, mhl_p)
cov80 <- anchortime %>%
filter(term == "cov80") %>%
unnest() %>%
mutate(Time = c("t(3, 6, 9, 12)",
"t(4, 8, 12)",
"t(5, 10, 15)",
"t(6, 10, 11, 12)",
"t(6, 9, 12, 15)",
"t(6, 9, 12)",
"t(8, 10, 12)")) %>%
mutate(Time = factor(Time, levels = c("t(4, 8, 12)",
"t(5, 10, 15)",
"t(6, 9, 12)0.8",
"t(6, 9, 12)0.9",
"t(8, 10, 12)",
"t(3, 6, 9, 12)",
"t(6, 10, 11, 12)",
"t(6, 9, 12, 15)"))) %>%
arrange(Time) %>%
dplyr::select(-term) %>%
dplyr::select(Time, sgl_n, eld_n, mhl_n, mhl_p)
cov90 <- anchortime %>%
filter(term == "cov90") %>%
unnest() %>%
mutate(Time = c("t(3, 6, 9, 12)",
"t(4, 8, 12)",
"t(5, 10, 15)",
"t(6, 10, 11, 12)",
"t(6, 9, 12, 15)",
"t(6, 9, 12)",
"t(8, 10, 12)")) %>%
mutate(Time = factor(Time, levels = c("t(4, 8, 12)",
"t(5, 10, 15)",
"t(6, 9, 12)",
"t(8, 10, 12)",
"t(3, 6, 9, 12)",
"t(6, 10, 11, 12)",
"t(6, 9, 12, 15)"))) %>%
arrange(Time) %>%
dplyr::select(-term) %>%
dplyr::select(Time, sgl_n, eld_n, mhl_n, mhl_p)
bias
rmse
cov50
cov80
cov90
```
## saving the files as .tex
```{r eval=FALSE, include=FALSE}
library(xtable)
print(xtable(bias, type = "latex"),
file = paste0("figure/S02_anchor_time_090_bias_", Sys.Date(), ".tex"))
print(xtable(rmse, type = "latex"),
file = paste0("figure/S02_anchor_time_090_rmse_", Sys.Date(), ".tex"))
print(xtable(cov50, type = "latex"),
file = paste0("figure/S02_anchor_time_090_cov50_", Sys.Date(), ".tex"))
print(xtable(cov80, type = "latex"),
file = paste0("figure/S02_anchor_time_090_cov80_", Sys.Date(), ".tex"))
print(xtable(cov90, type = "latex"),
file = paste0("figure/S02_anchor_time_090_cov90_", Sys.Date(), ".tex"))
```
```{r}
sessionInfo()
```