Fix check + cleanup package

Author: mattlee821

.Rbuildignore

@@ -2,3 +2,6 @@
 ^\.Rproj\.user$
 ^LICENSE\.md$
 ^\.github$
+^docs$
+^_pkgdown\.yml$
+^functions\.Rcheck$

.gitignore

@@ -6,4 +6,7 @@
 rmd/imputation_test.html
 rmd/imputation_test_cache/
 rmd/imputation_test_files/
+vignettes/*.html
+vignettes/*_cache/
+vignettes/*_files/
 scripts/

DESCRIPTION

@@ -10,17 +10,25 @@ Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.3
+VignetteBuilder: knitr
 Imports:
   dplyr, forcats, ggplot2, tibble, tidyr, purrr,
   plyr,
   data.table,
-  here,
-  rmarkdown,
   stats,
   utils,
   rlang,
-  graphics,
-  tidyselect
+  survival,
+  ggforestplot,
+  cli,
+  gginnards,
+  ggtext,
+  glue,
+  ieugwasr,
+  patchwork,
+  scales,
+  ggrepel,
+  cowplot
 Suggests:
     stringr,
     tidyverse,
@@ -30,15 +38,10 @@ Suggests:
     ggstance,
     gwasvcf,
     genetics.binaRies,
-    survival,
     TwoSampleMR,
     wesanderson,
-    ggforestplot,
-    scales,
     calibrate,
-    cowplot,
     reshape2,
-    ggrepel,
     locuscomparer,
     haven,
     readstata13,
@@ -47,7 +50,7 @@ Suggests:
     doParallel,
     foreach,
     clusterProfiler,
-    biomaRt,checkmate,locusplotr,testthat (>= 3.0.0)
+    biomaRt,checkmate,locusplotr,testthat (>= 3.0.0),knitr,here,rmarkdown,tidyselect
 Remotes:
   NightingaleHealth/ggforestplot,
   MRCIEU/genetics.binaRies,

NAMESPACE

@@ -18,29 +18,21 @@ export(finemap_pval_LD)
 export(finimom_cs_table)
 export(forestplot)
 export(format_data)
-export(format_data2)
 export(get_ld_proxies)
 export(gg_locusplot)
 export(gg_regionplot)
-export(harmonise_data_sex)
 export(locuscomparer)
 export(manhattan)
+export(miamiplot)
 export(missing_EAF)
 export(model_test)
 export(mr_density_plot)
 export(mr_forest_plot)
 export(mr_funnel_plot)
-export(mr_heterogeneity_sex)
 export(mr_leaveoneout_plot)
-export(mr_leaveoneout_sex)
-export(mr_pleiotropy_test_sex)
 export(mr_scatter_plot)
-export(mr_sex)
-export(mr_singlesnp_sex)
 export(palette)
 export(proxy_search)
-export(proxy_search_DECODE)
-export(proxy_search_UKB)
 export(proxy_search_split)
 export(qqplot)
 export(read_file)

R/TwoSampleMR_functions.R

@@ -688,7 +688,7 @@ calculate_fstat_from_beta_se <- function(data, grouping_column) {
   fstat_mean_from_b_se <- data |>
     dplyr::group_by(!!rlang::sym(group_col_name)) |>
     dplyr::summarize(
-      mean_fstat_from_b_se = mean(fstat_from_b_se, na.rm = TRUE),
+      mean_fstat_from_b_se = mean(.data$fstat_from_b_se, na.rm = TRUE),
       .groups = "drop"
     )