Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.align = "center"
)
library(loewesadditivity)
## ----eval = FALSE-------------------------------------------------------------
# if(!require(loewesadditivity)){
# library(devtools)
# devtools::install_github("shannong19/loewesadditivity")
# }
# library(loewesadditivity)
## ----echo = F, message = F, warning = F---------------------------------------
# hidden load currently
#library(devtools)
devtools::load_all()
## ----setup, message = FALSE, warning = FALSE----------------------------------
library(ggplot2)
library(dplyr)
library(knitr)
library(kableExtra)
results <- rh5_ama1ron2 %>%
rename(dose_A = "RH5", dose_B = "AMA1RON2") %>%
fortify_gia_data() %>%
estimate_params()
results$params_est
## ----data, message = FALSE, warning = FALSE-----------------------------------
data(rh5_ama1ron2)
rh5_ama1ron2 %>% head() %>% knitr::kable() %>%
kableExtra::kable_styling(full_width = T, font_size = 7)
## ----data_f, message = FALSE, warning = FALSE---------------------------------
rh5_ama1ron2_f <-
rh5_ama1ron2 %>% rename(dose_A = 'RH5', dose_B = 'AMA1RON2') %>%
fortify_gia_data()
rh5_ama1ron2_f %>% head() %>% kable(align = "c") %>%
kableExtra::kable_styling(full_width = F)
## ----est, message = FALSE, warning = FALSE------------------------------------
## Set up initial guesses and parameters
model_params <- c(
"beta_A" = .5,
"beta_B" = .5,
"gamma_A" = .5,
"gamma_B" = .5,
"tau_1" = 0,
"tau_2" = 0
)
n_boot <- 10
fn_list <- NULL
alpha <- .05
verbose <- TRUE
out <- estimate_params(
data = rh5_ama1ron2_f,
init_params = model_params,
n_boot = n_boot,
alpha = alpha,
verbose = verbose
)
## ----S, message = FALSE, warning = FALSE--------------------------------------
out$S_est %>% kable(align = "c", digits = 3) %>%
kableExtra::kable_styling(full_width = F)
## ----par_est, message = FALSE, warning = FALSE--------------------------------
out$params_est %>% kable(align = "c", digits = 3) %>%
kableExtra::kable_styling(full_width = F)
## ----GIA_est, message = FALSE, warning = FALSE--------------------------------
out$GIA_est %>% head() %>% kable(align = "c", digits = 3) %>%
kableExtra::kable_styling(full_width = F)
## ---- message = FALSE, warning = FALSE, fig.width=8, fig.height = 6-----------
# Note xlab is dose_A and ylab is dose_B
g1 <- plot_surface(out, xlab = "RH5", ylab = "AMA1RON2")
## ---- message = FALSE, warning = FALSE, fig.width=8, fig.height = 12----------
g2 <- plot_curves(out, dose_A = "RH5", dose_B = "AMA1RON2" )
## ---- message = FALSE, warning = FALSE, fig.width=8, fig.height = 6-----------
g3 <- plot_isobologram(out, dose_A = "RH5", dose_B = "AMA1RON2" )
## ----coverage, message = FALSE, warning = FALSE-------------------------------
model_params <- c("beta_A" = .250, "beta_B" = .146,
"gamma_A" = .527, "gamma_B" = .921,
"tau_1" = -.058, "tau_2" = -.289)
experimental_grid <- make_grid(par = model_params,
n = 5)
n_boot <- 3
n_sims <- 5
GIA_fn <- base_GIA
S_fn <- calc_S_base
fn_list <- NULL
alpha <- .05
verbose <- TRUE
out <- simulate_coverage(n_sims = n_sims,
n_boot = n_boot,
verbose = FALSE,
experimental_grid = experimental_grid,
model_par = model_params,
alpha = .05,
noise_par = c("a0" = 3, "a1" = .01),
GIA_fn = base_GIA,
fn_list = NULL)
out
## -----------------------------------------------------------------------------
out <- design_experiment(n_rep = 2)
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