On bug fix and small suggestions

.Rbuildignore

@@ -1,3 +1,4 @@
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^LICENSE\.md$
+^CITATION\.cff$

DESCRIPTION

@@ -1,15 +1,17 @@
 Package: mr.divw
-Type: Package
-Title: debiased inverse-variance weighted estimator for univariable and multivariable Mendelian randomization
+Title: debiased inverse-variance weighted estimator for univariable and
+    multivariable Mendelian randomization
 Version: 0.1.0
-Author: c(person("Ting", "Ye", , "tingye1@uw.edu", role = c("aut", "cre")),
-          person("Yinxiang", "Wu", , "wuyx@uw.edu", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0001-7806-6999")))
-Maintainer: The package maintainer <yourself@somewhere.net>
-Description: Perform causal effect estimation for summary-data Mendelian randomization using IVW, dIVW and MV-SRIVW estimators.
+Authors@R: c(
+    person("Ting", "Ye", , "tingye1@uw.edu", role = c("aut", "cre")),
+    person("Yinxiang", "Wu", , "wuyx@uw.edu", role = "aut",
+           comment = c(ORCID = "0000-0001-7806-6999"))
+  )
+Description: Perform causal effect estimation for summary-data Mendelian
+    randomization using IVW, dIVW and MV-SRIVW estimators.
 License: MIT + file LICENSE
+Depends: 
+    R (>= 3.5)
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
-Depends: 
-    R (>= 2.10)
+RoxygenNote: 7.3.3

R/globals.R

@@ -0,0 +1,8 @@
+utils::globalVariables(c(
+  "bmi.cad",
+  "beta.exposure",
+  "beta.outcome",
+  "se.exposure",
+  "se.outcome",
+  "pval.selection"
+  ))

R/mvmr.ivw.R

@@ -14,8 +14,10 @@
 #'
 #' @examples
 #' data("hdl_subfractions")
-#' # We are going to estimate the effect of S-HDL-P on the risk of CAS with adjustments of HDL, LDL, and TG levels
-#' beta.exposure <- hdl_subfractions$data[,c("gamma_exp1","gamma_exp2","gamma_exp3","gamma_exp4")] # corresponding to SNP effects on respectively  HDL, LDL, TG, and S-HDL-P
+#' # Estimate the effect of S-HDL-P on CAS risk, adjusting for HDL, LDL, and TG
+#' # Columns: SNP effects on HDL, LDL, TG, and S-HDL-P respectively
+#' beta.exposure <- hdl_subfractions$data[,
+#'   c("gamma_exp1","gamma_exp2","gamma_exp3","gamma_exp4")]
 #' se.exposure <- hdl_subfractions$data[,c("se_exp1","se_exp2","se_exp3","se_exp4")]
 #' beta.outcome <- hdl_subfractions$data$gamma_out1
 #' se.outcome <- hdl_subfractions$data$se_out1

R/mvmr.srivw.R

@@ -20,12 +20,15 @@
 #'
 #' @examples
 #' data("hdl_subfractions")
-#' # We are going to estimate the effect of S-HDL-P on the risk of CAS with adjustments of HDL, LDL, and TG levels
-#' beta.exposure <- hdl_subfractions$data[,c("gamma_exp1","gamma_exp2","gamma_exp3","gamma_exp4")] # corresponding to SNP effects on respectively  HDL, LDL, TG, and S-HDL-P
+#' # Estimate the effect of S-HDL-P on CAS risk, adjusting for HDL, LDL, and TG
+#' # Columns: SNP effects on HDL, LDL, TG, and S-HDL-P respectively
+#' beta.exposure <- hdl_subfractions$data[,
+#'   c("gamma_exp1","gamma_exp2","gamma_exp3","gamma_exp4")]
 #' se.exposure <- hdl_subfractions$data[,c("se_exp1","se_exp2","se_exp3","se_exp4")]
 #' beta.outcome <- hdl_subfractions$data$gamma_out1
 #' se.outcome <- hdl_subfractions$data$se_out1
-#' P <- hdl_subfractions$cor.mat[c(1:4,10),c(1:4,10)] # make sure the last index corresponds to the outcome
+#' # last index must correspond to the outcome
+#' P <- hdl_subfractions$cor.mat[c(1:4,10),c(1:4,10)]
 #' mvmr.srivw(beta.exposure = beta.exposure,
 #' se.exposure = se.exposure,
 #' beta.outcome = beta.outcome,

mr.divw.Rproj

@@ -18,3 +18,4 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace