From 30cbcf924110e1b2da405ddf72df4b111d33536a Mon Sep 17 00:00:00 2001
From: dj44vuri <julian.sagebiel@idiv.de>
Date: Wed, 27 Dec 2023 18:49:32 +0100
Subject: [PATCH] added examples in tests and readme file
---
.Rbuildignore | 1 +
.Rhistory | 77 -------------------
.gitignore | 2 +
R/globals.R | 2 +-
R/sim_all.R | 12 +--
R/sim_choice.R | 5 +-
R/simulate_choices.R | 4 +-
README.md | 51 ++++++++++++
.../Rbookfull.R} | 0
9 files changed, 65 insertions(+), 89 deletions(-)
delete mode 100644 .Rhistory
create mode 100644 README.md
rename tests/{manualtests.R => manual-tests/Rbookfull.R} (100%)
diff --git a/.Rbuildignore b/.Rbuildignore
index 350519f..fc17ab1 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -2,3 +2,4 @@
^\.Rproj\.user$
^LICENSE\.md$
^data-raw$
+^README\.Rmd$
diff --git a/.Rhistory b/.Rhistory
deleted file mode 100644
index e3e3d24..0000000
--- a/.Rhistory
+++ /dev/null
@@ -1,77 +0,0 @@
-options(prompt = prompt::prompt_git() )
-install.packages("prompt")
-options(prompt = prompt::prompt_git() )
-usethis::edit_r_profile()
-options(prompt = prompt::prompt_git() )
-options(prompt = "hello" )
-asdf
-options(prompt = prompt::prompt_git() )
-fasjh
-prompt::prompt_git()
-git_branch()
-prompt::prompt_git(git_branch())
-prompt::git_branch()
-usethis::edit_r_profile()
-options(prompt = prompt::git_branch() )
-options(prompt = paste0(prompt::git_branch(), "> ") )
-options(prompt = paste0(prompt::git_branch(), " > ") )
-if (interactive()) prompt::set_prompt(prompt::prompt_git))
-if (interactive()) prompt::set_prompt(prompt::prompt_git)
-if (interactive()) prompt::set_prompt(prompt::prompt_git)
-devtools::check()
-devtools::load_all
-devtools::load_all()
-devtools::document()
-devtools::document()
-devtools::check()
-usethis::use_package("formula.tools")
-usethis::use_package("formula.tools")
-devtools::check()
-usethis::use_package("purrr")
-devtools::check()
-devtools::document()
-devtools::check()
-usethis::use_package(c(‘mixl’, ‘psych’, ‘rmarkdown’, ‘tibble’, ‘tictoc’))
-usethis::use_package(c("mixl", "psych", "rmarkdown", "tibble", "tictoc"))
-usethis::use_package(c("mixl"))
-usethis::use_package(c( "tictoc"))
-usethis::use_package(c(tibble",))
-l
-)
-,
-}
-q
-.
-ajsdflakjdf
-"
-usethis::use_package(c("tibble"))
-usethis::use_package(c("mixl", "psych", "rmarkdown", "tibble", "tictoc"))
-usethis::use_package(c( "rmarkdown"))
-usethis::use_package(c("psych"))
-devtools::check()
-load_all()
-devtools::load_all()
-system.file("extdata","Rbook" ,package = "simulateDCE")
-source("~/share/groups/bioecon/Julian/simulateDCE/tests/manualtests.R")
-source("~/share/groups/bioecon/Julian/simulateDCE/tests/manualtests.R")
-source("~/share/groups/bioecon/Julian/simulateDCE/tests/manualtests.R")
-source("~/share/groups/bioecon/Julian/simulateDCE/R/simulate_choices.R")
-source("~/share/groups/bioecon/Julian/simulateDCE/tests/manualtests.R")
-devtools::document()
-devtools::load_all()
-?basename
-devtools::document()
-usethis::use_package("evd")
-source("~/share/groups/bioecon/Julian/simulateDCE/tests/manualtests.R")
-source("~/share/groups/bioecon/Julian/simulateDCE/tests/manualtests.R")
-package_version(dplyr)
-package_version("dplyr")
-packageVersion("dplyr")
-usethis::use_package("dplyr, 1.1.4)
-""
-"
-usethis::use_package("dplyr",min_version = "1.1.4")
-devtools::document()
-packageVersion("dplyr")
-packageVersion("dplyr")
-install.packages("dplyr")
diff --git a/.gitignore b/.gitignore
index cd67eac..a331156 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,3 @@
.Rproj.user
+.Rhistory
+README.rmd
diff --git a/R/globals.R b/R/globals.R
index 7acdf7a..eaa2250 100644
--- a/R/globals.R
+++ b/R/globals.R
@@ -1 +1 @@
-utils::globalVariables(c("designfile", "destype", "Choice.situation", "Design", "." ,"ID", ":=", "..density.."))
+utils::globalVariables(c("designfile", "destype", "Choice.situation", "Design", "." ,"ID", ":=", "..density..", "sou_gis", "block", "Block"))
diff --git a/R/sim_all.R b/R/sim_all.R
index f051369..39e90c4 100644
--- a/R/sim_all.R
+++ b/R/sim_all.R
@@ -23,7 +23,7 @@ sim_all <- function(){
all_designs<- purrr::map(designfile, sim_choice,
no_sim= nosim,respondents = resps, mnl_U = mnl_U, destype=destype) %>% ## iterate simulation over all designs
- setNames(designname)
+ stats::setNames(designname)
time <- tictoc::toc()
@@ -38,19 +38,19 @@ sim_all <- function(){
summaryall <- as.data.frame(purrr::map(all_designs, ~.x$summary)) %>%
- dplyr::select(!ends_with("vars")) %>%
- dplyr::relocate(ends_with(c(".n", "mean","sd", "min" ,"max", "range" , "se" )))
+ dplyr::select(!dplyr::ends_with("vars")) %>%
+ dplyr::relocate(dplyr::ends_with(c(".n", "mean","sd", "min" ,"max", "range" , "se" )))
coefall <- purrr::map(all_designs, ~ .x$coefs)
pat<-paste0("(",paste(designname,collapse = "|"),").") # needed to identify pattern to be replaced
s<-as.data.frame(coefall) %>%
- dplyr::select(!matches("pval|run")) %>%
+ dplyr::select(!dplyr::matches("pval|run")) %>%
dplyr::rename_with(~ sub("est_b", "", .x), dplyr::everything()) %>%
dplyr::rename_with( ~ paste0(.,"_",stringr::str_extract(.,pat )), dplyr::everything() ) %>% # rename attributes for reshape part 1
- dplyr::rename_with( ~ stringr::str_replace(.,pattern = pat,replacement=""), everything() ) %>%
- reshape(varying =1:ncol(.), sep = "_" , direction = "long" ,timevar = "design", idvar = "run" )
+ dplyr::rename_with( ~ stringr::str_replace(.,pattern = pat,replacement=""), dplyr::everything() ) %>%
+ stats::reshape(varying =1:ncol(.), sep = "_" , direction = "long" ,timevar = "design", idvar = "run" )
p=list()
diff --git a/R/sim_choice.R b/R/sim_choice.R
index de9f961..4cc3dc0 100644
--- a/R/sim_choice.R
+++ b/R/sim_choice.R
@@ -24,7 +24,6 @@
sim_choice <- function(designfile, no_sim=10, respondents=330, mnl_U,utils=u[[1]] ,destype) {
- require("rlang")
## Function that transforms user written utiliy for simulation into utility function for mixl.
transform_util <- function() {
@@ -90,7 +89,7 @@ mnl_U <- transform_util()
model_spec <- mixl::specify_model(mnl_U, database, disable_multicore=F)
- est=setNames(rep(0,length(model_spec$beta_names)), model_spec$beta_names)
+ est=stats::setNames(rep(0,length(model_spec$beta_names)), model_spec$beta_names)
availabilities <- mixl::generate_default_availabilities(
@@ -111,7 +110,7 @@ mnl_U <- transform_util()
output[["coefs"]] <-coefs
- pvals <- output[["coefs"]] %>% dplyr::select(starts_with("rob_pval0"))
+ pvals <- output[["coefs"]] %>% dplyr::select(dplyr::starts_with("rob_pval0"))
output[["power"]] <- 100*table(apply(pvals,1, function(x) all(x<0.05)))/nrow(pvals)
diff --git a/R/simulate_choices.R b/R/simulate_choices.R
index 4aa5d2d..def513d 100644
--- a/R/simulate_choices.R
+++ b/R/simulate_choices.R
@@ -14,7 +14,7 @@ simulate_choices <- function(data=datadet, utility =utils, setspp) { #the part
by_formula <- function(equation){ #used to take formulas as inputs in simulation utility function
# //! cur_data_all may get deprecated in favor of pick
- dplyr::pick(everything()) |>
+ dplyr::pick(dplyr::everything()) |>
#cur_data_all() |>
dplyr::transmute(!!formula.tools::lhs(equation) := !!formula.tools::rhs(equation) )
}
@@ -41,7 +41,7 @@ simulate_choices <- function(data=datadet, utility =utils, setspp) { #the part
if(exists("decisiongroups")) { ### create a new variable to classify decision groups.
- data = dplyr::mutate(data,group = as.numeric(cut(row_number(),
+ data = dplyr::mutate(data,group = as.numeric(cut(dplyr::row_number(),
breaks = decisiongroups * n(),
labels = seq_along(decisiongroups[-length(decisiongroups)]),
include.lowest = TRUE)))
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..c60ae4a
--- /dev/null
+++ b/README.md
@@ -0,0 +1,51 @@
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# simulateDCE
+
+<!-- badges: start -->
+<!-- badges: end -->
+
+The goal of simulateDCE is to make it easy to simulate choice experiment
+datasets using designs from NGENE or `spdesign`. You have to store the
+design file in a subfolder and need to specify certain parameters and
+the utility functions for the data generating process. The package is
+useful for
+
+1. Test different designs in terms of statistical power, efficiency and
+ unbiasedness
+
+2. To test the effects of deviations from RUM, e.g. heuristics, on
+ model performance for different designs.
+
+3. In teaching, using simulated data is useful, if you want to know the
+ data generating process. It helps to demonstrate Maximum likelihood
+ and choice models, knowing exactly what you should expect.
+
+4. You can use simulation in pre-registration to justify your sample
+ size and design choice.
+
+5. Before data collection, you can use simulated data to estimate the
+ models you plan to use in the actual analysis. You can thus make
+ sure, you can estimate all effects for given sample sizes.
+
+## Installation
+
+You can install the development version of simulateDCE from gitlab. You
+need to install the `remotes` package first. The current version is
+alpha and there is no version on cran:
+
+``` r
+# FILL THIS IN! HOW CAN PEOPLE INSTALL YOUR DEV PACKAGE?
+install.packages("remotes")
+remotes::install_gitlab(repo = "dj44vuri/simulateDCE" , host = "https://git.idiv.de")
+```
+
+## Example
+
+This is a basic example which shows you how to solve a common problem:
+
+``` r
+library(simulateDCE)
+## basic example code
+```
diff --git a/tests/manualtests.R b/tests/manual-tests/Rbookfull.R
similarity index 100%
rename from tests/manualtests.R
rename to tests/manual-tests/Rbookfull.R
--
GitLab