all but vignette

Author: CoryMcCartan

.gitignore

@@ -7,3 +7,4 @@
 *.bak
 
 .Rproj.user
+inst/doc

DESCRIPTION

@@ -1,4 +1,6 @@
 Package: adjustr
+Encoding: UTF-8
+Type: Package
 Title: Stan Model Adjustments and Sensitivity Analyses using Importance Sampling
 Version: 0.0.0.9000
 Authors@R: person("Cory", "McCartan", email = "[email protected]",
@@ -12,22 +14,26 @@ License: BSD_3_clause + file LICENSE
 Depends: R (>= 3.6.0)
 Imports:
     tibble,
+    tidyselect,
     dplyr,
     purrr,
     methods,
     utils,
     stats,
     rlang,
     rstan,
-    ggplot2,
     stringr,
     dparser,
+    ggplot2,
     loo
 Suggests:
-    tidyr,
     extraDistr,
+    tidyr,
     testthat,
-    covr
-Encoding: UTF-8
+    covr,
+    knitr,
+    rmarkdown
+URL: https://corymccartan.github.io/adjustr/
 LazyData: true
 RoxygenNote: 7.1.0
+VignetteBuilder: knitr

NAMESPACE

@@ -3,6 +3,7 @@
 S3method(arrange,adjustr_spec)
 S3method(as.data.frame,adjustr_spec)
 S3method(length,adjustr_spec)
+S3method(plot,adjustr_weighted)
 S3method(print,adjustr_spec)
 S3method(pull,adjustr_weighted)
 S3method(rename,adjustr_spec)

R/adjust_weights.R

@@ -28,8 +28,25 @@
 #'   method. The returned object also includes the model sample draws, in the
 #'   \code{draws} attribute.
 #'
+#' @examples \dontrun{
+#' model_data = list(
+#'     J = 8,
+#'     y = c(28, 8, -3, 7, -1, 1, 18, 12),
+#'     sigma = c(15, 10, 16, 11, 9, 11, 10, 18)
+#' )
+#'
+#' spec = make_spec(eta ~ student_t(df, 0, 1), df=1:10)
+#' adjust_weights(spec, eightschools_m)
+#' adjust_weights(spec, eightschools_m, keep_bad=TRUE)
+#'
+#' spec = make_spec(y ~ student_t(df, theta, sigma), df=1:10)
+#' adjust_weights(spec, eightschools_m, data=model_data)
+#' # will throw an error because `y` and `sigma` aren't provided
+#' adjust_weights(spec, eightschools_m)
+#' }
+#'
 #' @export
-adjust_weights = function(spec, object, data=NULL, keep_bad=F) {
+adjust_weights = function(spec, object, data=NULL, keep_bad=FALSE) {
     # CHECK ARGUMENTS
     object = get_fit_obj(object)
     model_code = object@stanmodel@model_code
@@ -59,12 +76,12 @@ adjust_weights = function(spec, object, data=NULL, keep_bad=F) {
         psis_wgt = suppressWarnings(loo::psis(lratio, r_eff=r_eff))
         pareto_k = loo::pareto_k_values(psis_wgt)
         if (all(psis_wgt$log_weights == psis_wgt$log_weights[1])) {
-            warning("New specification equal to old specification.", call.=F)
+            warning("New specification equal to old specification.", call.=FALSE)
             pareto_k = -Inf
         }
 
         list(
-            weights = loo::weights.importance_sampling(psis_wgt, log=F),
+            weights = loo::weights.importance_sampling(psis_wgt, log=FALSE),
             pareto_k = pareto_k
         )
     })
@@ -84,7 +101,7 @@ adjust_weights = function(spec, object, data=NULL, keep_bad=F) {
 
 # Generic methods
 is.adjustr_weighted = function(x) inherits(x, "adjustr_weighted")
-#' Extract Weights From an \code{adjustr_spec_weighted} Object
+#' Extract Weights From an \code{adjustr_weighted} Object
 #'
 #' This function modifies the default behavior of \code{dplyr::pull} to extract
 #' the \code{.weights} column.
@@ -96,10 +113,11 @@ is.adjustr_weighted = function(x) inherits(x, "adjustr_weighted")
 #'
 #' @export
 pull.adjustr_weighted = function(.data, var=".weights") {
+    var = tidyselect::vars_pull(names(.data), !!enquo(var))
     if (nrow(.data) == 1 && var == ".weights") {
         .data$.weights[[1]]
     } else {
-        NextMethod(.data, var=var)
+        .data[[var]]
     }
 }
 
@@ -113,6 +131,12 @@ pull.adjustr_weighted = function(.data, var=".weights") {
 #'
 #' @return Invisbly returns a list of sampling formulas.
 #'
+#' @examples \dontrun{
+#' extract_samp_stmts(eightschools_m)
+#' #> Sampling statements for model 2c8d1d8a30137533422c438f23b83428:
+#' #>   parameter   eta ~ std_normal()
+#' #>   data        y ~ normal(theta, sigma)
+#' }
 #' @export
 extract_samp_stmts = function(object) {
     model_code = get_fit_obj(object)@stanmodel@model_code

R/adjustr-package.R

@@ -16,6 +16,7 @@
 #'     \item \code{\link{make_spec}}
 #'     \item \code{\link{adjust_weights}}
 #'     \item \code{\link{summarize}}
+#'     \item \code{\link{plot}}
 #' }
 #'
 #' @importFrom methods is
@@ -35,6 +36,7 @@ pkg_env = new_environment()
     # create the Stan parser
     tryCatch(get_parser(), error = function(e) {})
 
-    utils::globalVariables(c("name", "pos", "value"))
+    utils::globalVariables(c("name", "pos", "value", ".y", ".y_ol", ".y_ou",
+                             ".y_il", ".y_iu", ".y_med"))
 }  # nocov end
 #> NULL

R/logprob.R

@@ -51,7 +51,7 @@ get_base_data = function(object, samps, parsed_vars, data, extra_names=NULL) {
         if (!all(found)) stop(paste(vars_indata[!found], collapse=", "), " not found")
         # combine draws and data
         base_data = append(
-            map(vars_indraws, ~ rstan::extract(object, ., permuted=F)) %>%
+            map(vars_indraws, ~ rstan::extract(object, ., permuted=FALSE)) %>%
                 set_names(vars_indraws),
             map(vars_indata, ~ reshape_data(data[[.]])) %>%
                 set_names(vars_indata),

R/make_spec.R

@@ -42,6 +42,16 @@
 #' \code{\link[dplyr]{rename}}, and \code{\link[dplyr]{slice}}) are
 #' supported and operate on the underlying table of specification parameters.
 #'
+#' @examples
+#' make_spec(eta ~ cauchy(0, 1))
+#'
+#' make_spec(eta ~ student_t(df, 0, 1), df=1:10)
+#'
+#' params = tidyr::crossing(df=1:10, infl=c(1, 1.5, 2))
+#' make_spec(eta ~ student_t(df, 0, 1),
+#'           y ~ normal(theta, infl*sigma),
+#'           params)
+#'
 #' @export
 make_spec = function(...) {
     args = dots_list(..., .check_assign=T)
@@ -151,6 +161,14 @@ as.data.frame.adjustr_spec = function(x, ...) {
 #' @param ... additional arguments to underlying method
 #' @param .preserve as in \code{filter} and \code{slice}
 #' @name dplyr.adjustr_spec
+#'
+#' @examples \dontrun{
+#' spec = make_spec(eta ~ student_t(df, 0, 1), df=1:10)
+#'
+#' arrange(spec, desc(df))
+#' slice(spec, 4:7)
+#' filter(spec, df == 2)
+#' }
 NULL
 # dplyr generics
 dplyr_handler = function(dplyr_func, x, ...) {
@@ -165,7 +183,7 @@ dplyr_handler = function(dplyr_func, x, ...) {
 
 # no @export because R CMD CHECK didn't like it
 #' @rdname dplyr.adjustr_spec
-filter.adjustr_spec = function(.data, ..., .preserve=F) {
+filter.adjustr_spec = function(.data, ..., .preserve=FALSE) {
     dplyr_handler(dplyr::filter, .data, ..., .preserve=.preserve)
 }
 #' @rdname dplyr.adjustr_spec
@@ -185,7 +203,7 @@ select.adjustr_spec = function(.data, ...) {
 }
 #' @rdname dplyr.adjustr_spec
 #' @export
-slice.adjustr_spec = function(.data, ..., .preserve=F) {
+slice.adjustr_spec = function(.data, ..., .preserve=FALSE) {
     dplyr_handler(dplyr::slice, .data, ..., .preserve=.preserve)
 }
 

R/use_weights.R

@@ -17,6 +17,14 @@
 #' containing the sampled indices. If any weights are \code{NA}, the indices
 #' will also be \code{NA}.
 #'
+#' @examples \dontrun{
+#' spec = make_spec(eta ~ student_t(df, 0, 1), df=1:10)
+#' adjusted = adjust_weights(spec, eightschools_m)
+#'
+#' get_resampling_idxs(adjusted)
+#' get_resampling_idxs(adjusted, frac=0.1, replace=FALSE)
+#' }
+#'
 #' @export
 get_resampling_idxs = function(x, frac=1, replace=T) {
     if (frac < 0) stop("`frac` parameter must be nonnegative")
@@ -48,7 +56,10 @@ get_resampling_idxs = function(x, frac=1, replace=T) {
 #'   posterior distribution of eight alternative specification. For example,
 #'   a value of \code{mean(theta)} will compute the posterior mean of
 #'   \code{theta} for each alternative specification.
-#' @param .resampling Wether to compute summary statistics by first resampling
+#'
+#'   The arguments in \code{...} are automatically quoted and evaluated in the
+#'   context of \code{.data}. They support unquoting and splicing.
+#' @param .resampling Whether to compute summary statistics by first resampling
 #'  the data according to the weights. Defaults to \code{FALSE}, but will be
 #'  used for any summary statistic that is not \code{mean}, \code{var} or
 #'  \code{sd}.
@@ -58,9 +69,24 @@ get_resampling_idxs = function(x, frac=1, replace=T) {
 #' @return An \code{adjustr_weighted} object, wth the new columns specified in
 #' \code{...} added.
 #'
+#' @examples \dontrun{
+#' model_data = list(
+#'     J = 8,
+#'     y = c(28, 8, -3, 7, -1, 1, 18, 12),
+#'     sigma = c(15, 10, 16, 11, 9, 11, 10, 18)
+#' )
+#'
+#' spec = make_spec(eta ~ student_t(df, 0, 1), df=1:10)
+#' adjusted = adjust_weights(spec, eightschools_m)
+#'
+#' summarize(adjusted, mean(mu), var(mu))
+#' summarize(adjusted, diff_1 = mean(y[1] - theta[1]), .model_data=model_data)
+#' summarize(adjusted, quantile(tau, probs=c(0.05, 0.5, 0.95)))
+#' }
+#'
 #' @rdname summarize.adjustr_weighted
 #' @export
-summarise.adjustr_weighted = function(.data, ..., .resampling=F, .model_data=NULL) {
+summarise.adjustr_weighted = function(.data, ..., .resampling=FALSE, .model_data=NULL) {
     stopifnot(is.adjustr_weighted(.data)) # just in case called manually
     args = enexprs(...)
 
@@ -89,7 +115,7 @@ summarise.adjustr_weighted = function(.data, ..., .resampling=F, .model_data=NUL
         expr = expr_deparse(call_args(call)[[1]])
         expr = stringr::str_replace_all(expr, "\\[(\\d)", "[,\\1")
         expr = stringr::str_replace_all(expr, "(?<![a-zA-Z0-9._])mean\\(", "rowMeans(")
-        expr = stringr::str_replace_all(expr, "(?<![a-zA-Z0-9._])sum\\(", "rowSum(")
+        expr = stringr::str_replace_all(expr, "(?<![a-zA-Z0-9._])sum\\(", "rowSums(")
         computed = as.array(eval_tidy(parse_expr(expr), data))
         if (length(dim(computed)) == 1) dim(computed) = c(dim(computed), 1)
 
@@ -124,3 +150,75 @@ funs_env = new_environment(list(
     var = wtd_array_var,
     sd = wtd_array_sd
 ))
+
+
+#' Plot Posterior Quantities of Interest Under Alternative Model Specifications
+#'
+#' Uses weights computed in \code{\link{adjust_weights}} to plot posterior
+#' quantities of interest versus
+#'
+#' @param x An \code{adjustr_weighted} object.
+#' @param by The x-axis variable, which is usually one of the specification
+#'   parameters. Can be set to \code{1} if there is only one specification.
+#'   Automatically quoted and evaluated in the context of \code{x}.
+#' @param post The posterior quantity of interest, to be computed for each
+#'   resampled draw of each specificaiton. Should evaluate to a single number
+#'   for each draw. Automatically quoted and evaluated in the context of \code{x}.
+#' @param only_mean Whether to only plot the posterior mean. May be more stable.
+#' @param ci_level The inner credible interval to plot. Central
+#'   100*ci_level% intervals are computed from the quantiles of the resampled
+#'   posterior draws.
+#' @param outer_level The outer credible interval to plot.
+#' @param ... Ignored.
+#'
+#' @return A \code{\link[ggplot2]{ggplot}} object which can be further
+#'   customized with the \strong{ggplot2} package.
+#'
+#' @examples \dontrun{
+#' spec = make_spec(eta ~ student_t(df, 0, scale),
+#'                  df=1:10, scale=seq(2, 1, -1/9))
+#' adjusted = adjust_weights(spec, eightschools_m)
+#'
+#' plot(adjusted, df, theta[1])
+#' plot(adjusted, df, mu, only_mean=TRUE)
+#' plot(adjusted, scale, tau)
+#' }
+#'
+#' @export
+plot.adjustr_weighted = function(x, by, post, only_mean=FALSE, ci_level=0.8,
+                                 outer_level=0.95, ...) {
+    if (!requireNamespace("ggplot2", quietly=TRUE)) { # nocov start
+        stop("Package `ggplot2` must be installed to plot posterior quantities of interest.")
+    } # nocov end
+    if (ci_level > outer_level) stop("`ci_level` should be less than `outer_level`")
+
+    post = enexpr(post)
+    if (!only_mean) {
+        outer = (1 - outer_level) / 2
+        inner = (1 - ci_level) / 2
+        q_probs = c(outer, inner, 0.5, 1-inner, 1-outer)
+        sum_arg = quo(stats::quantile(!!post, probs = !!q_probs))
+
+        summarise.adjustr_weighted(x, .y = !!sum_arg) %>%
+            rowwise() %>%
+            mutate(.y_ol = .y[1],
+                   .y_il = .y[2],
+                   .y_med = .y[3],
+                   .y_iu = .y[4],
+                   .y_ou = .y[5]) %>%
+        ggplot(aes({{ by }}, .y_med)) +
+            geom_ribbon(aes(ymin=.y_ol, ymax=.y_ou), alpha=0.4) +
+            geom_ribbon(aes(ymin=.y_il, ymax=.y_iu), alpha=0.5) +
+            geom_line() +
+            geom_point(size=3) +
+            theme_minimal() +
+            labs(y= expr_name(post))
+    } else {
+        summarise.adjustr_weighted(x, .y = mean(!!post)) %>%
+        ggplot(aes({{ by }}, .y)) +
+            geom_line() +
+            geom_point(size=3) +
+            theme_minimal() +
+            labs(y = expr_name(post))
+    }
+}

_pkgdown.yml

@@ -13,10 +13,10 @@ template:
 navbar:
   title: "adjustr"
   left:
-    #- text: "Vignettes"
-    #  href: articles/
+    - text: "Vignettes"
+      href: articles/index.html
     - text: "Functions"
-      href: reference/
+      href: reference/index.html
     - text: "Other Packages"
       menu:
         - text: "rstan"
@@ -72,7 +72,8 @@ reference:
     contents:
       - make_spec
       - adjust_weights
-      - summarise.adjustr_weighted
+      - summarize.adjustr_weighted
+      - plot.adjustr_weighted
   - title: "Helper Functions"
     desc: >
       Various helper functions for examining a model or building sampling