Merge pull request #56 from fasrc/hotfix_doc

Hotfix doc
NSAPH-Software · May 12, 2021 · d7ea9f3 · d7ea9f3
2 parents 490ea4f + 55d94df
commit d7ea9f3
Show file tree

Hide file tree

Showing 68 changed files with 167 additions and 126 deletions.
diff --git a/.gitignore b/.gitignore
@@ -13,3 +13,4 @@ src/.DS_Store
 /doc/
 /Meta/
 src-i386
+.DS_Store
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: CausalGPS
 Type: Package
 Title: Matching on generalized propensity scores with continuous exposures
-Version: 0.2.2
+Version: 0.2.3
 Authors@R: c(
     person("Naeem", "Khoshnevis", email = "[email protected]",
            role=c("aut","cre"), 

diff --git a/NEWS.md b/NEWS.md
@@ -1,16 +1,25 @@
-## CausalGPS (2021-05-12)
+## CausalGPS 0.2.3 (2021-05-12)
 
 ### Added
+### Changed
+### Fixed
+
+*  Fixed documentations
+
+### Removed
+
 
+
+## CausalGPS 0.2.2 (2021-05-12)
+
+### Added
 * estimate_semi_erf
 * estimate_hr
 
 ### Changed
-
 * Package name: GPSmatching --> CausalGPS 
 
 ### Fixed
-
 ### Removed
 
 

diff --git a/R/GPSmatching_smooth.R → R/causalgps_smooth.R b/R/GPSmatching_smooth.R → R/causalgps_smooth.R
diff --git a/R/generate_synthetic_data.R b/R/generate_synthetic_data.R
@@ -1,5 +1,5 @@
 #' @title
-#' Generate synthetic data for GPSmatching package
+#' Generate synthetic data for CausalGPS package
 #'
 #' @description
 #' Generates synthetic dataset

diff --git a/R/print.R b/R/print.R
@@ -12,7 +12,7 @@ print.gpsm_erf <- function(x, ...){
 
   x <- unclass(x)
 
-  cat(" GPSmatching exposure rate function object\n")
+  cat(" CausalGPS exposure rate function object\n")
   cat(" function call: \n")
   cat("      ***       \n")
   print(x$fcall, ...)
@@ -74,7 +74,7 @@ print.gpsm_pspop <- function(x, ...){
 
   x <- unclass(x)
 
-  cat(" GPSmatching pseudo population object\n")
+  cat(" CausalGPS pseudo population object\n")
   cat(" function call: \n")
   cat("      ***       \n")
   print(x$fcall, ...)
@@ -96,7 +96,7 @@ print.gpsm_pspop <- function(x, ...){
 #' @export
 summary.gpsm_pspop <- function(object, ...){
 
-  cat("GPSmatching pseudo population object summary\n")
+  cat("CausalGPS pseudo population object summary\n")
   cat_list <- function(input){
     cat(paste("   size: ", length(input),
               ", class: ", class(input),
@@ -116,4 +116,4 @@ summary.gpsm_pspop <- function(object, ...){
     cat_list(object$pseudo_pop[[item]])
     cat("\n")
   }
-}
+}
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-# GPSmatching
+# CausalGPS
 
 
 | Resource    |  Github Actions      |
@@ -19,8 +19,8 @@ An R package for implementing matching on generalized propensity scores with con
 
 ```r
 library("devtools")
-install_github("fasrc/GPSmatching")
-library("GPSmatching")
+install_github("fasrc/CausalGPS")
+library("CausalGPS")
 ```
 
 ## Usage
@@ -41,7 +41,10 @@ Input parameters:
 `running_appr`: running approach (base, parallel)  
 `covar_bl_method`: specified covariate balance method  
 `covar_bl_trs`: specified covariate balance threshold  
-`max_attempt`: maximum number of attempt to satisfy covariate balance  
+`max_attempt`: maximum number of attempt to satisfy covariate balance 
+`use_cov_transform`: If `TRUE`, uses internal transformers to achehive covariate balance.
+`transformers`: List of transformers (default: list("pow2","pow3")). Users can define a unary function and pass as transformer to the list.
+`trim_quantiles`: a vector of two indicating upper and lower trimming quantiles (default: c(0.01, 0.99)). 
 
 - Generating Pseudo Population
 
@@ -52,6 +55,7 @@ pseudo_pop <- gen_pseudo_pop(Y,
                              ci_appr = "matching",
                              running_appr = "base",
                              pred_model = "sl",
+                             gps_model = "parametric",
                              use_cov_transform = TRUE,
                              transformers = list("pow2", "pow3"),
                              sl_lib = c("m_xgboost","SL.earth","SL.gam",
@@ -61,6 +65,7 @@ pseudo_pop <- gen_pseudo_pop(Y,
                              nthread = 1,
                              covar_bl_method = "absolute",
                              covar_bl_trs = 0.1,
+                             trim_quantiles = c(0.01,0.99),
                              max_attempt = 1,
                              matching_fun = "matching_l1",
                              delta_n = 1,

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/articles/CausalGPS.html b/docs/articles/CausalGPS.html
diff --git a/docs/articles/contribution.html b/docs/articles/contribution.html
diff --git a/docs/articles/estimating_gps.html b/docs/articles/estimating_gps.html
diff --git a/docs/articles/faq.html b/docs/articles/faq.html
diff --git a/docs/articles/generate_synthetic_data.html b/docs/articles/generate_synthetic_data.html
diff --git a/docs/articles/generating_pseudo_population.html b/docs/articles/generating_pseudo_population.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/notes_on_sl_wrapper.html b/docs/articles/notes_on_sl_wrapper.html
diff --git a/docs/articles/outcome_models.html b/docs/articles/outcome_models.html
diff --git a/docs/articles/testing_the_package.html b/docs/articles/testing_the_package.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
-Original file line number
+Diff line change
@@ Expand Up / @@ -13,3 +13,4 @@ src/.DS_Store @@
     /doc/
     /Meta/
     src-i386
+    .DS_Store