updated

.Rbuildignore

@@ -0,0 +1,4 @@
+^mrbase\.oauth$
+^mrbase\.oauth2$
+^LICENSE\.md$
+^\.travis\.yml$

.travis.yml

@@ -0,0 +1,19 @@
+language: r
+r:
+  - release
+  - devel
+cache: packages
+
+r_github_packages:
+  - rondolab/MR-PRESSO
+  - mrcieu/MRInstruments
+  - mrcieu/ieugwasr
+  - mrcieu/MRInstruments
+  - WSpiller/RadialMR
+  - gqi/MRMix
+
+r_packages:
+  - covr
+
+after_success:
+  - Rscript -e 'library(covr); codecov()'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: TwoSampleMR
 Title: Two Sample MR functions and interface to MR Base database
-Version: 0.4.25
+Version: 1.0.0
 Authors@R: c(person("Gibran", "Hemani", email = "[email protected]",
                   role = c("aut", "cre")),
              person("Philip", "Haycock", email = "[email protected]",
@@ -15,7 +15,7 @@ Authors@R: c(person("Gibran", "Hemani", email = "[email protected]",
 Description: See title
 Depends:
     R (>= 3.1.0)
-Suggests:
+Imports:
     ggplot2,
     gridExtra,
     cowplot,
@@ -26,21 +26,27 @@ Suggests:
     markdown,
     gtable,
     rmarkdown,
-    MRInstruments,
     MendelianRandomization,
-    MRPRESSO,
     dplyr,
-    igraph,
     mr.raps,
-    RadialMR,
     psych,
     testthat,
-    randomForest
-Imports:
-    ieugwasr,
+    randomForest,
     meta,
-    data.table
-License: Artistic-2.0
+    data.table,
+    ieugwasr,
+    MRPRESSO,
+    MRInstruments,
+    RadialMR,
+    MRMix
+Remotes:
+    rondolab/MR-PRESSO,
+    mrcieu/MRInstruments,
+    mrcieu/ieugwasr,
+    mrcieu/MRInstruments,
+    WSpiller/RadialMR,
+    gqi/MRMix
+License: MIT + file LICENSE
 LazyData: true
 VignetteBuilder: knitr
 RoxygenNote: 6.1.1

R/forest_plot.R

@@ -48,11 +48,6 @@
 #' @param returnRobj = (logical) return the graph as an internal R object y/n?
 #'
 #' @return grid object giving the forest plot (or plot as pdf, and )
-#'
-#' @examples
-#' mr_forest_plot()
-#'
-
 mr_forest_plot_grouped <-
     function(name, eff_Col = "b", exposure_Name="exposure", outcome_Name="outcome", forest_Title = '', outfile_Name = 'annot_FP.pdf', left_Col_Names=c("Exposure", "Outcome"), left_Col_Titles = NULL, right_Col_Names = c("p", "Outcome.n.case", "Outcome.n.control", "Outcome.sample.size"), right_Col_Titles =
                  NULL, debug = FALSE,  log_ES = FALSE, decrease = TRUE,  returnRobj = TRUE, se_Col = "se") {

R/moe.R

@@ -180,7 +180,7 @@ get_rsq <- function(dat)
 #' @export
 #' @return List
 #' @examples
-#' 
+#' \dontrun{
 #' # Load libraries
 #' library(dplyr)
 #' library(randomForest)
@@ -204,6 +204,7 @@ get_rsq <- function(dat)
 #' # been sorted in order from most likely to least likely to 
 #' # be accurate, based on MOE prediction
 #' r[[1]]$estimates
+#'}
 mr_moe <- function(res, rf)
 {
 	require(dplyr)

R/steiger_filtering.R

@@ -18,6 +18,14 @@ steiger_filtering <- function(dat)
 
 steiger_filtering_internal <- function(dat)
 {
+	if(! "units.outcome" %in% names(dat))
+	{
+		dat$units.outcome <- NA
+	}
+	if(! "units.exposure" %in% names(dat))
+	{
+		dat$units.exposure <- NA
+	}
 	stopifnot(length(unique(dat$exposure)) == 1)
 	stopifnot(length(unique(dat$outcome)) == 1)
 	stopifnot(length(unique(dat$units.exposure)) == 1)
@@ -27,7 +35,7 @@ steiger_filtering_internal <- function(dat)
 	if(!"rsq.exposure" %in% names(dat))
 	{
 		dat$pval.exposure[dat$pval.exposure < 1e-300] <- 1e-300
-		if(dat$units.exposure[1] == "log odds")
+		if(compareNA(dat$units.exposure[1], "log odds"))
 		{
 			# message("Estimating rsq.exposure for binary trait")
 			# message("Ensure that beta.exposure, eaf.exposure, ncase.exposure, ncontrol.exposure are all specified with no missing values")
@@ -71,7 +79,7 @@ steiger_filtering_internal <- function(dat)
 	if(!"rsq.outcome" %in% names(dat))
 	{
 		dat$pval.outcome[dat$pval.outcome < 1e-300] <- 1e-300
-		if(dat$units.outcome[1] == "log odds")
+		if(compareNA(dat$units.outcome[1], "log odds"))
 		{
 			if(! "prevalence.outcome" %in% names(dat))
 			{
@@ -121,3 +129,9 @@ steiger_filtering_internal <- function(dat)
 	return(dat)
 }
 
+
+compareNA <- function(v1,v2) {
+    same <- (v1 == v2) | (is.na(v1) & is.na(v2))
+    same[is.na(same)] <- FALSE
+    return(same)
+}

README.md

@@ -1,6 +1,8 @@
 # Two Sample MR
 
-[![DOI](https://zenodo.org/badge/49515156.svg)](https://zenodo.org/badge/latestdoi/49515156)
+<!-- badges: start -->
+[![Travis build status](https://travis-ci.org/MRCIEU/TwoSampleMR.svg?branch=master)](https://travis-ci.org/MRCIEU/TwoSampleMR) [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental) [![DOI](https://zenodo.org/badge/49515156.svg)](https://zenodo.org/badge/latestdoi/49515156)
+<!-- badges: end -->
 
 Extended documentation is available here:
 

tests/testthat.R

@@ -0,0 +1,4 @@
+library(testthat)
+library(TwoSampleMR)
+
+test_check("TwoSampleMR")