exported getCoefTable() + lots of small edits to vignettes

jhelvy · Dec 7, 2020 · 69a04d7 · 69a04d7
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,14 +1,14 @@
 Package: logitr
 Title: Random utility logit models with preference and willingness to pay space parameterizations
-Date: 2020-12-04
-Version: 0.0.4
+Date: 2020-12-07
+Version: 0.0.5
 Authors@R: c(
     person(given   = "John",
            family  = "Helveston",
            role    = c("aut", "cre", "cph"),
            email   = "[email protected]",
            comment = c(ORCID = "0000-0002-2657-9191")))
-Description: logitr estimates multinomial (MNL) and mixed logit (MXL) models in R. Models can be estimated using "Preference" space or "Willingness-to-pay" (WTP) space utility parameterizations. The program includes an option to run a multistart optimization loop with random starting points in each iteration, which is useful for non-convex problems like MXL models or models with WTP space utility parameterizations. The main optimization loop uses the nloptr function to minimize the negative log-likelihood function. The package has additional functions for computing and comparing WTP from both preference space and WTP space models and for simulating the expected shares of a set of alternatives using an estimated model.
+Description: logitr estimates multinomial (MNL) and mixed logit (MXL) models in R. Models can be estimated using "Preference" space or "Willingness-to-pay" (WTP) space utility parameterizations. The program includes an option to run a multistart optimization loop with random starting points in each iteration, which is useful for non-convex problems like MXL models or models with WTP space utility parameterizations. The main optimization loop uses the {nloptr} package to minimize the negative log-likelihood function. The package has additional functions for computing and comparing WTP from both preference space and WTP space models and for simulating the expected shares of a set of alternatives using an estimated model.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true

diff --git a/NAMESPACE b/NAMESPACE
@@ -3,6 +3,7 @@
 S3method(coef,logitr)
 S3method(summary,logitr)
 export(dummyCode)
+export(getCoefTable)
 export(logitr)
 export(simulateShares)
 export(statusCodes)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,19 @@
+
+# logitr 0.0.5
+
+## Summary of larger updates:
+
+- Added support for auto creating interactions amongst variables
+
+## Summary of smaller updates:
+
+- Added new documentation for prepping data:
+    - overall structure
+    - dummyCode() function
+    - handling interactions
+- All vignettes proof-read with lots of small changes to examples
+- Added a hex sticker
+
 # logitr 0.0.4
 
 Weighted models, new dataset, new encoding features

diff --git a/R/.DS_Store b/R/.DS_Store
diff --git a/R/main.R → R/logitr.R b/R/main.R → R/logitr.R
@@ -76,17 +76,30 @@
 #'
 #' @export
 #' @examples
-#' # For detailed examples, visit https://jhelvy.github.io/logitr/articles/examples.html
+#' \dontrun{
+#' # For more detailed examples, visit
+#' https://jhelvy.github.io/logitr/articles/
 #'
-#' # Run a MNL model in the Preference Space:
 #' library(logitr)
 #'
+#' # Run a MNL model in the Preference Space:
 #' mnl_pref <- logitr(
 #'   data = yogurt,
 #'   choiceName = "choice",
 #'   obsIDName = "obsID",
 #'   parNames = c("price", "feat", "dannon", "hiland", "yoplait")
 #' )
+#'
+#' # Run a MNL model in the WTP Space:
+#' mnl_wtp <- logitr(
+#'   data = yogurt,
+#'   choiceName = "choice",
+#'   obsIDName = "obsID",
+#'   parNames = c("feat", "dannon", "hiland", "yoplait"),
+#'   priceName = "price",
+#'   modelSpace = "wtp"
+#' )
+#' }
 logitr <- function(data, choiceName, obsIDName, parNames, priceName = NULL,
                    randPars = NULL, randPrice = NULL, modelSpace = "pref",
                    weightsName = NULL, options = list()) {

diff --git a/R/summary.R b/R/summary.R
@@ -86,10 +86,7 @@ printMultistartSummary <- function(model) {
 }
 
 printModelSummary <- function(model) {
-  coefTable <- getCoefTable(
-    model$coef, model$standErrs, model$numObs,
-    model$numParams
-  )
+  coefTable <- getCoefTable(model)
   statTable <- getStatTable(
     model$logLik, model$nullLogLik, model$numObs,
     model$numParams
@@ -136,7 +133,37 @@ getBasicInfoTable <- function(model) {
   return(basicInfoSummary)
 }
 
-getCoefTable <- function(coef, se, numObs, numParams) {
+#' Get the coefficient summary table as a data frame
+#'
+#' Returns a data frame of the coefficient summary table of a model estimated using the `logitr()` function.
+#' @keywords logitr, summary, coefTable
+#' @param object The output of a model estimated model using the `logitr()` function.
+#' @return Returns a data frame of the coefficient summary table of a model estimated using the `logitr()` function.
+#' @export
+#' @examples
+#' library(logitr)
+#'
+#' # Run a MNL model in the preference space
+#' mnl_pref <- logitr(
+#'   data = yogurt,
+#'   choiceName = "choice",
+#'   obsIDName = "obsID",
+#'   parNames = c("price", "feat", "dannon", "hiland", "yoplait")
+#' )
+#'
+#' # Get the coefficient summary table as a data frame
+#' getCoefTable(mnl_pref)
+getCoefTable <- function(object) {
+  coefTable <- getCoefSummaryTable(
+    coef      = object$coef,
+    se        = object$standErrs,
+    numObs    = object$numObs,
+    numParams = object$numParams
+  )
+  return(coefTable)
+}
+
+getCoefSummaryTable <- function(coef, se, numObs, numParams) {
   tStat <- rep(NA, length(coef))
   pVal <- rep(NA, length(coef))
   signif <- rep("", length(coef))

diff --git a/R/wtp.R b/R/wtp.R
@@ -42,7 +42,8 @@ wtp <- function(model, priceName) {
   } else if (model$modelSpace == "wtp") {
     wtp_mean <- stats::coef(model)
     wtp_se <- model$standErrs
-    return(getCoefTable(wtp_mean, wtp_se, model$numObs, model$numParams))
+    return(getCoefSummaryTable(
+      wtp_mean, wtp_se, model$numObs, model$numParams))
   }
 }
 
@@ -60,7 +61,7 @@ getPrefSpaceWtp <- function(model, priceName) {
   wtpDraws <- draws / priceDraws
   wtpDraws[, priceID] <- draws[, priceID]
   wtp_se <- apply(wtpDraws, 2, stats::sd)
-  return(getCoefTable(wtp_mean, wtp_se, model$numObs, model$numParams))
+  return(getCoefSummaryTable(wtp_mean, wtp_se, model$numObs, model$numParams))
 }
 
 #' Compare WTP from preference and WTP space models

diff --git a/README.Rmd b/README.Rmd
@@ -6,11 +6,11 @@ output: github_document
 
 ```{r, include = FALSE}
 knitr::opts_chunk$set(
-  collapse = TRUE,
-  warning = FALSE,
-  message = FALSE,
-  comment = "#>",
-  fig.path = "man/figures/",
+  collapse   = TRUE,
+  warning    = FALSE,
+  message    = FALSE,
+  comment    = "#>",
+  fig.path   = "man/figures/",
   fig.retina = 3
 )
 ```
@@ -28,16 +28,13 @@ status](https://www.r-pkg.org/badges/version/logitr)](https://CRAN.R-project.org
 R. Models can be estimated using “Preference” space or
 “Willingness-to-pay” (WTP) space [utility
 parameterizations](https://jhelvy.github.io/logitr/articles/utility_models.html).
-The current version includes support for:
+The latest version includes support for:
 
 - Homogeneous multinomial logit (MNL) models
 - Heterogeneous mixed logit (MXL) models (with normal and log-normal parameter distributions).
 - Preference space utility parameterization.
 - WTP space utility parameterization.
-- An optional multistart optimization that uses different random starting points in each iteration (useful for non-convex problems like MXL models or models with WTP space parameterizations).
-
-The package also has additional functions for:
-
+- An option to run a multistart optimization loop that uses different random starting points in each iteration (useful for non-convex problems like MXL models or models with WTP space parameterizations).
 - Computing and comparing WTP from both preference space and WTP space models.
 - Simulating the expected shares of a set of alternatives using an estimated model.
 
@@ -55,6 +52,7 @@ devtools::install_github("jhelvy/logitr")
 ```
 
 Load the library with:
+
 ```{r, eval=FALSE}
 library(logitr)
 ```
@@ -69,11 +67,11 @@ library(logitr)
 - Date First Written: *Sunday, September 28, 2014*
 - Most Recent Update: `r format(Sys.Date(), format="%B %d %Y")`
 - License: [MIT](https://github.com/jhelvy/logitr/blob/master/LICENSE.md)
-- [Latest Release](https://github.com/jhelvy/logitr/releases/latest): 0.0.4
+- [Latest Release](https://github.com/jhelvy/logitr/releases/latest): 0.0.5
 
 ## Citation Information
 
-If you use this package for in a publication, I would greatly appreciate it if you cited it. You can get the citation information by typing `citation("logitr")` into R:
+If you use this package for in a publication, I would greatly appreciate it if you cited it - you can get the citation by typing `citation("logitr")` into R:
 
 ```{r}
 citation("logitr")

diff --git a/README.md b/README.md
@@ -15,19 +15,17 @@ status](https://www.r-pkg.org/badges/version/logitr)](https://CRAN.R-project.org
 R. Models can be estimated using “Preference” space or
 “Willingness-to-pay” (WTP) space [utility
 parameterizations](https://jhelvy.github.io/logitr/articles/utility_models.html).
-The current version includes support for:
+The latest version includes support for:
 
   - Homogeneous multinomial logit (MNL) models
   - Heterogeneous mixed logit (MXL) models (with normal and log-normal
     parameter distributions).
   - Preference space utility parameterization.
   - WTP space utility parameterization.
-  - An optional multistart optimization that uses different random
-    starting points in each iteration (useful for non-convex problems
-    like MXL models or models with WTP space parameterizations).
-
-The package also has additional functions for:
-
+  - An option to run a multistart optimization loop that uses different
+    random starting points in each iteration (useful for non-convex
+    problems like MXL models or models with WTP space
+    parameterizations).
   - Computing and comparing WTP from both preference space and WTP space
     models.
   - Simulating the expected shares of a set of alternatives using an
@@ -77,12 +75,12 @@ probabilities).
   - License:
     [MIT](https://github.com/jhelvy/logitr/blob/master/LICENSE.md)
   - [Latest Release](https://github.com/jhelvy/logitr/releases/latest):
-    0.0.4
+    0.0.5
 
 ## Citation Information
 
 If you use this package for in a publication, I would greatly appreciate
-it if you cited it. You can get the citation information by typing
+it if you cited it - you can get the citation by typing
 `citation("logitr")` into R:
 
 ``` r

diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -24,17 +24,15 @@ navbar:
           href: articles/utility_models.html
         - text: "Data Formatting and Encoding"
           href: articles/data_formatting.html
-        - text: "Models with Interactions"
-          href: articles/interactions.html
-    - text: "Examples"
-      menu:
-        - text: "Estimating multinomial logit models"
+        - text: "Estimating Multinomial Logit Models"
           href: articles/mnl_models.html
-        - text: "Estimating mixed logit models"
+        - text: "Estimating Mixed Logit Models"
           href: articles/mxl_models.html
-        - text: "Estimating weighted logit models"
+        - text: "Estimating Models with Interactions"
+          href: articles/interactions.html
+        - text: "Estimating Weighted Logit Models"
           href: articles/weighted_models.html
-        - text: "Simulating shares"
+        - text: "Simulating Shares from Estimated Models"
           href: articles/simulations.html
     - text: "Changelog"
       href: news/index.html
@@ -43,30 +41,30 @@ navbar:
      href: https://github.com/jhelvy/logitr
 
 reference:
-- title: "Encoding data"
+- title: "Encoding Data"
   desc: "Functions for encoding data prior to model estimation."
   contents:
   - dummyCode
-- title: "Estimating models"
+- title: "Estimating Models"
   desc: "Functions for estimating multinomial logit models with preference space and WTP space utility parameterizations."
   contents:
   - logitr
-- title: "Viewing results"
+- title: "Viewing Results"
   desc: "Functions for viewing the results of estimated models."
   contents:
   - summary.logitr
   - coef.logitr
   - statusCodes
-- title: "Computing and comparing WTP"
+- title: "Computing and Comparing WTP"
   desc: "Functions for computing and comparing WTP from estimated models."
   contents:
   - wtp
   - wtpCompare
-- title: "Simulating shares"
+- title: "Simulating Shares from Estimated Models"
   desc: "Functions for simulating expected shares from a set of alternatives."
   contents:
   - simulateShares
-- title: "Example data sets"
+- title: "Example Data Sets"
   desc: "Descriptions of data included with this package"
   contents:
   - yogurt

diff --git a/build.R b/build.R
@@ -4,8 +4,8 @@ devtools::document()
 # Install the package
 devtools::install(force = TRUE)
 
-# Build the pkgdown site
-pkgdown::build_site()
+# # Build the pkgdown site
+# pkgdown::build_site()
 
 # Check package
 devtools::check()

diff --git a/inst/CITATION b/inst/CITATION
@@ -5,7 +5,7 @@ citEntry(
   title    = "logitr: Random utility logit models with preference and willingness to pay space parameterizations",
   author   = "John Paul Helveston",
   year     = "2020",
-  note     = "R package version 0.0.4",
+  note     = "R package version 0.0.5",
   url      = "https://jhelvy.github.io/logitr/",
-  textVersion = "John Paul Helveston. logitr: Random utility logit models with preference and willingness to pay space parameterizations (2020)"
+  textVersion = "John Paul Helveston (2020). logitr: Random utility logit models with preference and willingness to pay space parameterizations."
 )
diff --git a/inst/example/data_formatting.R b/inst/example/data_formatting.R
@@ -53,6 +53,8 @@ model_dummy_price <- logitr(
     'bev150', 'american', 'japanese', 'chinese', 'skorean',
     'phevFastcharge', 'bevFastcharge','opCost', 'accelTime'))
 
+summary(model_dummy_price)
+
 # Save results
 saveRDS(model_default,
   here::here('inst', 'extdata', 'encoding_model_default.Rds'))

diff --git a/inst/extdata/encoding_model_character_price.Rds b/inst/extdata/encoding_model_character_price.Rds
diff --git a/inst/extdata/encoding_model_default.Rds b/inst/extdata/encoding_model_default.Rds
diff --git a/inst/extdata/encoding_model_dummy_price.Rds b/inst/extdata/encoding_model_dummy_price.Rds
diff --git a/man/getCoefTable.Rd b/man/getCoefTable.Rd