Merge pull request #80 from fasrc/polish_doc

make compile_pseudo_population public.

NAMESPACE

@@ -11,6 +11,7 @@ S3method(summary,gpsm_pspop)
 export(absolute_corr_fun)
 export(absolute_weighted_corr_fun)
 export(check_covar_balance)
+export(compile_pseudo_pop)
 export(estimate_gps)
 export(estimate_npmetric_erf)
 export(estimate_pmetric_erf)

R/check_arguments.R

@@ -30,9 +30,17 @@ check_args <- function(pred_model, ci_appr,
 
   # ------------------------------------------------------
 
-  required_args <- NULL
+  required_args <- max_attempt <-  NULL
+
+  dot_args <- list(...)
+  arg_names <- names(dot_args)
+
+  for (i in arg_names){
+    assign(i,unlist(dot_args[i],use.names = FALSE))
+  }
 
   check_args_estimate_gps(pred_model, gps_model, ...)
+  check_args_generate_pseudo_pop(max_attempt = max_attempt)
   check_args_compile_pseudo_pop(ci_appr, use_cov_transform,
                                 transformers, trim_quantiles,
                                 optimized_compile, ...)
@@ -93,6 +101,17 @@ check_args_estimate_gps <- function(pred_model, gps_model, ...){
   invisible(TRUE)
 }
 
+check_args_generate_pseudo_pop <- function(max_attempt){
+
+  if (!is.numeric(max_attempt)){
+    stop(paste(max_attempt, " is not acceptible for max_attempt. Should be a
+                 numeric value."))
+  }
+
+  invisible(TRUE)
+}
+
+
 
 #' @title
 #' Check compile_pseudo_pop function arguments
@@ -146,7 +165,7 @@ check_args_compile_pseudo_pop <- function(ci_appr, use_cov_transform,
   # checkpoint 2 ------------------------------------------
   if (ci_appr == 'matching'){
     required_args <- c(required_args, 'covar_bl_method', 'covar_bl_trs',
-                       'max_attempt', 'matching_fun', 'delta_n', 'scale')
+                       'matching_fun', 'delta_n', 'scale')
   }
 
   # checkpoint 3 ------------------------------------------
@@ -182,10 +201,7 @@ check_args_compile_pseudo_pop <- function(ci_appr, use_cov_transform,
                  scale))
     }
 
-    if (!is.numeric(max_attempt)){
-      stop(paste(max_attempt, " is not acceptible for max_attempt. Should be a
-                 numeric value."))
-    }
+
   }
   invisible(TRUE)
 }

R/compile_pseudo_pop.R

@@ -1,5 +1,5 @@
 #' @title
-#' Compile pseudo population
+#' Compile Pseudo Population
 #'
 #' @description
 #' Compiles pseudo population based on the original population and estimated GPS
@@ -13,13 +13,58 @@
 #'   - gps_mx (min and max of gps)
 #'   - w_mx (min and max of w).
 #' @param ci_appr Causal inference approach.
+#' @param gps_model Model type which is used for estimating GPS value, including
+#' parametric and non-parametric.
+#' @param bin_seq Sequence of w (treatment) to generate pseudo population. If
+#' NULL is passed the default value will be used, which is
+#' `seq(min(w)+delta_n/2,max(w), by=delta_n)`.
+#' @param nthread An integer value that represents the number of threads to be
+#' used by internal packages.
+#' @param trim_quantiles A numerical vector of two. Represents the trim quantile
+#' level. Both numbers should be in the range of \[0,1] and in increasing order
+#' (default: c(0.01,0.99)).
+#' @param optimized_compile If TRUE, uses counts to keep track of number of
+#' replicated pseudo population.
 #' @param ... Additional parameters.
 #'
-#' @keywords internal
+#' @note
+#' The input data set should be output of estimate_gps function with
+#' internal_use flag activated.
+#'
+#' @export
 #'
 #' @return
 #' `compile_pseudo_pop` returns the pseudo population data that is compiled based
-#' on selected causal inference approach.
+#' on the selected causal inference approach.
+#'
+#' @examples
+#'
+#' m_d <- generate_syn_data(sample_size = 100)
+#' data_with_gps <- estimate_gps(m_d$Y,
+#'                               m_d$treat,
+#'                               m_d[c("cf1","cf2","cf3","cf4","cf5","cf6")],
+#'                               pred_model = "sl",
+#'                               gps_model = "parametric",
+#'                               internal_use = TRUE,
+#'                               params = list(xgb_max_depth = c(3,4,5),
+#'                                        xgb_nrounds=c(10,20,30,40,50,60)),
+#'                               nthread = 1,
+#'                               sl_lib = c("m_xgboost")
+#'                              )
+#'
+#'
+#' pd <- compile_pseudo_pop(dataset = data_with_gps,
+#'                          ci_appr = "matching",
+#'                          gps_model = "parametric",
+#'                          bin_seq = NULL,
+#'                          nthread = 1,
+#'                          trim_quantiles = c(0.01, 0.99),
+#'                          optimized_compile=TRUE,
+#'                          matching_fun = "matching_l1",
+#'                          covar_bl_method = 'absolute',
+#'                          covar_bl_trs = 0.1,
+#'                          delta_n = 0.5,
+#'                          scale = 1)
 #'
 compile_pseudo_pop <- function(dataset, ci_appr, gps_model = "parametric",
                                bin_seq = NULL, nthread = 1, trim_quantiles,

R/generate_pseudo_pop.R

@@ -39,8 +39,8 @@
 #' file will be detected by the file name extension.
 #' @param params Includes list of params that is used internally. Unrelated
 #'  parameters will be ignored.
-#' @param nthread An integer value that represents then number threads to use by
-#'  internal packages.
+#' @param nthread An integer value that represents the number of threads to be
+#' used by internal packages.
 #' @param ...  Additional arguments passed to different models.
 #' @details
 #' ## Additional parameters

_pkgdown.yml

@@ -12,6 +12,7 @@ reference:
   - title: Generate pseudo population
     contents:
     - generate_pseudo_pop
+    - compile_pseudo_pop
     - check_covar_balance
   - title: Outcome models
     contents: