From e9d70b08968e2177ffc19cbd3cf6bc73f44d6839 Mon Sep 17 00:00:00 2001
From: samuelsmock <smock.samuel@gmail.com>
Date: Mon, 19 Feb 2024 09:32:03 -0600
Subject: [PATCH] manipulations argument added where necessary. two notes on
namespace and unused imports persist
---
DESCRIPTION | 7 ++++--
R/sim_all.R | 6 ++---
R/sim_choice.R | 7 +++---
R/simulate_choices.R | 5 ++--
man/sim_all.Rd | 4 ++-
man/sim_choice.Rd | 5 +++-
man/simulate_choices.Rd | 7 ++++--
tests/manual-tests/SE-Agri.R | 45 ++++++++++++++++++++++++++++++++++
tests/testthat/test-sim_all.R | 1 -
vignettes/SE_Agri-vignette.Rmd | 2 +-
10 files changed, 73 insertions(+), 16 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index 310da68..fd09377 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,8 +2,9 @@ Package: simulateDCE
Title: Simulate data for discrete choice experiments
Version: 0.1.1
Authors@R:
- person("Julian", "Sagebiel", , "julian.sagebiel@idiv.de", role = c("aut", "cre"),
+ person(given = "Julian", family = "Sagebiel", email = "julian.sagebiel@idiv.de", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-0253-6875"))
+ person(given = "Samuel", family = "Smock", email = "samuel.smock@idiv.de", role = c("aut", "cre"))
Description: A package that supports simulating choice experiment data for given designs. It helps to quickly test different designs against each other.
License: MIT + file LICENSE
Encoding: UTF-8
@@ -20,8 +21,10 @@ Imports:
psych,
purrr,
readr,
- rlang,
rmarkdown,
+ stats,
+ rlang,
+ utils,
stringr,
tibble,
tictoc,
diff --git a/R/sim_all.R b/R/sim_all.R
index f140b5e..9af5058 100644
--- a/R/sim_all.R
+++ b/R/sim_all.R
@@ -7,7 +7,7 @@
#' @param u A list with utility functions. The list can incorporate as many decision rule groups as you want. However, each group must be in a list in this list. If you just use one group (the normal), this group still has to be in a list in the u list. As a convention name beta coefficients starting with a lower case "b"
#' @param bcoeff List of initial coefficients for the utility function. List content/length can vary based on application, but should all begin with b and be the same as those entered in the utility functions
#' @param decisiongroups A vector showing how decision groups are numerically distributed
-#' @param manipulations A variable to change terms of the utility functions eg shift be a factor of ten or apply selectively to different groups
+#' @param manipulations A variable to alter terms of the utility functions examples may be applying a factor or applying changes to terms selectively for different groups
#'
#' @return A list, with all information on the simulation. This list an be easily processed by the user and in the rmarkdown template.
#' @export
@@ -28,7 +28,7 @@
#' bheight2=0.25,
#' bheight3=0.50)
#'
-sim_all <- function(nosim=2, resps, destype="ngene", designpath, u, bcoeff, decisiongroups = c(0,1)){
+sim_all <- function(nosim=2, resps, destype="ngene", designpath, u, bcoeff, decisiongroups = c(0,1), manipulations = list()){
#################################################
########## Input Validation Test ###############
@@ -112,7 +112,7 @@ sim_all <- function(nosim=2, resps, destype="ngene", designpath, u, bcoeff, deci
tictoc::tic()
all_designs<- purrr::map(designfile, sim_choice,
- no_sim= nosim,respondents = resps, destype=destype, ut=u, bcoefficients = bcoeff, decisiongroups = decisiongroups) %>% ## iterate simulation over all designs
+ no_sim= nosim,respondents = resps, destype=destype, ut=u, bcoefficients = bcoeff, decisiongroups = decisiongroups, manipulations = manipulations) %>% ## iterate simulation over all designs
stats::setNames(designname)
diff --git a/R/sim_choice.R b/R/sim_choice.R
index 45296f8..d361701 100644
--- a/R/sim_choice.R
+++ b/R/sim_choice.R
@@ -15,6 +15,7 @@
#' @param destype Specify which type of design you use. Either ngene or spdesign
#' @param bcoefficients List of initial coefficients for the utility function. List content/length can vary based on application, but should all begin with b and be the same as those entered in the utility functions
#' @param decisiongroups A vector showing how decision groups are numerically distributed
+#' @param manipulations A variable to alter terms of the utility functions examples may be applying a factor or applying changes to terms selectively for different groups
#'
#' @return a list with all information on the run
#' @export
@@ -22,7 +23,7 @@
#' @examples \dontrun{ simchoice(designfile="somefile", no_sim=10, respondents=330,
#' mnl_U,ut=u[[1]] ,destype="ngene")}
#'
-sim_choice <- function(designfile, no_sim=10, respondents=330,ut ,destype=destype, bcoefficients, decisiongroups=c(0,1)) {
+sim_choice <- function(designfile, no_sim=10, respondents=330,ut ,destype=destype, bcoefficients, decisiongroups=c(0,1), manipulations = list()) {
@@ -40,7 +41,7 @@ sim_choice <- function(designfile, no_sim=10, respondents=330,ut ,destype=destyp
cat("This is Run number ", run)
- database <- simulate_choices(datadet, utility = ut, setspp=setpp, bcoefficients = bcoefficients, decisiongroups = decisiongroups)
+ database <- simulate_choices(datadet, utility = ut, setspp=setpp, bcoefficients = bcoefficients, decisiongroups = decisiongroups, manipulations = manipulations)
cat("This is the utility functions \n" , mnl_U)
@@ -99,7 +100,7 @@ designs_all <- list()
as.data.frame()
- database <- simulate_choices(data=datadet, utility = ut, setspp = setpp, bcoefficients = bcoefficients, decisiongroups = decisiongroups)
+ database <- simulate_choices(data=datadet, utility = ut, setspp = setpp, bcoefficients = bcoefficients, decisiongroups = decisiongroups, manipulations = manipulations)
diff --git a/R/simulate_choices.R b/R/simulate_choices.R
index cb40c14..9676bd3 100644
--- a/R/simulate_choices.R
+++ b/R/simulate_choices.R
@@ -3,15 +3,16 @@
#' @param data a dataframe that includes a design repeated for the number of observations
#' @param utility a list with the utility functions, one utility function for each alternatives
#' @param setspp an integer, the number of choice sets per person
-#' @param destype Is it a design created with ngene or with spdesign. Ngene desings should be stored as the standard .ngd output. spdesign should be the spdesign object design$design
+#' @param destype Is it a design created with ngene or with spdesign. Ngene designs should be stored as the standard .ngd output. spdesign should be the spdesign object design$design
#' @return a dataframe that includes simulated choices and a design
#' @param bcoefficients List of initial coefficients for the utility function. List content/length can vary based on application, but should all begin with b and be the same as those entered in the utility functions
#' @param decisiongroups A vector showing how decision groups are numerically distributed
+#' @param manipulations A variable to alter terms of the utility functions examples may be applying a factor or applying changes to terms selectively for different groups
#'
#' @export
#'
#' @examples \dontrun{simulate_choices(datadet, ut,setspp)}
-simulate_choices <- function(data, utility, setspp, destype, bcoefficients, decisiongroups = c(0,1)) { #the part in dataset that needs to be repeated in each run
+simulate_choices <- function(data, utility, setspp, destype, bcoefficients, decisiongroups = c(0,1), manipulations = list()) { #the part in dataset that needs to be repeated in each run
diff --git a/man/sim_all.Rd b/man/sim_all.Rd
index 38cf5e8..1cc6d88 100644
--- a/man/sim_all.Rd
+++ b/man/sim_all.Rd
@@ -13,7 +13,7 @@ sim_all(
u,
bcoeff,
decisiongroups = c(0, 1),
- manipulations
+ manipulations = list()
)
}
\arguments{
@@ -30,6 +30,8 @@ sim_all(
\item{bcoeff}{List of initial coefficients for the utility function. List content/length can vary based on application, but should all begin with b and be the same as those entered in the utility functions}
\item{decisiongroups}{A vector showing how decision groups are numerically distributed}
+
+\item{manipulations}{A variable to alter terms of the utility functions examples may be applying a factor or applying changes to terms selectively for different groups}
}
\value{
A list, with all information on the simulation. This list an be easily processed by the user and in the rmarkdown template.
diff --git a/man/sim_choice.Rd b/man/sim_choice.Rd
index 02579d3..7e85f8a 100644
--- a/man/sim_choice.Rd
+++ b/man/sim_choice.Rd
@@ -11,7 +11,8 @@ sim_choice(
ut,
destype = destype,
bcoefficients,
- decisiongroups = c(0, 1)
+ decisiongroups = c(0, 1),
+ manipulations = list()
)
}
\arguments{
@@ -28,6 +29,8 @@ sim_choice(
\item{bcoefficients}{List of initial coefficients for the utility function. List content/length can vary based on application, but should all begin with b and be the same as those entered in the utility functions}
\item{decisiongroups}{A vector showing how decision groups are numerically distributed}
+
+\item{manipulations}{A variable to alter terms of the utility functions examples may be applying a factor or applying changes to terms selectively for different groups}
}
\value{
a list with all information on the run
diff --git a/man/simulate_choices.Rd b/man/simulate_choices.Rd
index 6163827..cf76d0a 100644
--- a/man/simulate_choices.Rd
+++ b/man/simulate_choices.Rd
@@ -10,7 +10,8 @@ simulate_choices(
setspp,
destype,
bcoefficients,
- decisiongroups = c(0, 1)
+ decisiongroups = c(0, 1),
+ manipulations = list()
)
}
\arguments{
@@ -20,11 +21,13 @@ simulate_choices(
\item{setspp}{an integer, the number of choice sets per person}
-\item{destype}{Is it a design created with ngene or with spdesign. Ngene desings should be stored as the standard .ngd output. spdesign should be the spdesign object design$design}
+\item{destype}{Is it a design created with ngene or with spdesign. Ngene designs should be stored as the standard .ngd output. spdesign should be the spdesign object design$design}
\item{bcoefficients}{List of initial coefficients for the utility function. List content/length can vary based on application, but should all begin with b and be the same as those entered in the utility functions}
\item{decisiongroups}{A vector showing how decision groups are numerically distributed}
+
+\item{manipulations}{A variable to alter terms of the utility functions examples may be applying a factor or applying changes to terms selectively for different groups}
}
\value{
a dataframe that includes simulated choices and a design
diff --git a/tests/manual-tests/SE-Agri.R b/tests/manual-tests/SE-Agri.R
index e69de29..af380da 100644
--- a/tests/manual-tests/SE-Agri.R
+++ b/tests/manual-tests/SE-Agri.R
@@ -0,0 +1,45 @@
+rm(list=ls())
+devtools::load_all()
+
+
+library(rlang)
+
+designpath<- system.file("extdata","SE_AGRI", package = "simulateDCE")
+
+destype = 'ngene'
+resps =360 # number of respondents
+nosim=2 # number of simulations to run (about 500 is minimum)
+
+#betacoefficients should not include "-"
+bcoeff <- list(
+ basc = 4.2, ## very high asc
+ bprof = 0.3,
+ bexp = 0.3,
+ bdomestic = 0.3,
+ bforeign = 0.3,
+ bdamage = 0.6,
+ bprice = 0.2)
+
+
+
+manipulations = list(alt1.professional= expr(alt1.initiator==1),
+ alt2.professional= expr(alt2.initiator==1),
+ alt1.expert = expr(alt1.initiator==2),
+ alt2.expert = expr(alt2.initiator==2),
+ alt1.domestic = expr(alt1.funding==1),
+ alt2.domestic = expr(alt2.funding==1),
+ alt1.foreign = expr(alt1.funding==2),
+ alt2.foreign = expr(alt2.funding==2))
+
+
+#place your utility functions here
+ul<- list(u1=
+ list(
+ v1 =V.1 ~ bprof*alt1.professional+ bexp * alt1.expert + bdomestic * alt1.domestic + bforeign * alt1.foreign + bdamage*alt1.damage + bprice * alt1.compensation,
+ v2 =V.2 ~ bprof*alt2.professional + bexp * alt2.expert + bdomestic * alt2.domestic + bforeign * alt2.foreign + bdamage*alt2.damage + bprice * alt2.compensation,
+ v3 =V.3 ~ basc)
+)
+
+seagri <- sim_all(nosim = nosim, resps=resps, destype = destype,
+ designpath = designpath, u=ul, bcoeff = bcoeff, manipulations = manipulations)
+
diff --git a/tests/testthat/test-sim_all.R b/tests/testthat/test-sim_all.R
index a1ea894..8176a8c 100644
--- a/tests/testthat/test-sim_all.R
+++ b/tests/testthat/test-sim_all.R
@@ -1,4 +1,3 @@
-
library(rlang)
library(formula.tools)
diff --git a/vignettes/SE_Agri-vignette.Rmd b/vignettes/SE_Agri-vignette.Rmd
index 0cd051c..f69d31c 100644
--- a/vignettes/SE_Agri-vignette.Rmd
+++ b/vignettes/SE_Agri-vignette.Rmd
@@ -118,7 +118,7 @@ The sim_all function returns a multidimensional R list containing graphs, simula
```{r output}
seagri <- simulateDCE::sim_all(nosim = nosim, resps=resps, destype = destype,
- designpath = designpath, u= ul, bcoeff = bcoeff)
+ designpath = designpath, u= ul, bcoeff = bcoeff, manipulations = manipulations)
--
GitLab