here package used for better working directory management

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: retel
 Type: Package
 Title: Regularized Exponentially Tilted Empirical Likelihood
-Version: 0.0.0.9600
+Version: 0.0.0.9601
 Authors@R: c(
     person("Eunseop", "Kim", email = "markean@pm.me", 
             role = c("aut", "cre")),

inst/WORDLIST

@@ -3,6 +3,7 @@ CMD
 DMS
 SES
 Schennach
+WIP
 arXiv
 doi
 https

retel-paper/code/figures/figure1.R

@@ -32,7 +32,7 @@ lambda_RETEL <- function(par) {
 
 # Convex hull constraint satisfied at 1
 target <- lambda_RETEL(1)
-grid <- seq(from = 5, to = 20, length.out = 100)
+grid <- seq(from = 5, to = 20, length.out = 100L)
 approx <- vapply(round(2^grid), function(k) lambda_WETEL(1, k),
   FUN.VALUE = numeric(1L)
 )
@@ -68,7 +68,7 @@ ggplot(df) +
 
 # Convex hull constraint violated at 3
 target2 <- lambda_RETEL(-3)
-grid <- seq(from = 5, to = 20, length.out = 100)
+grid <- seq(from = 5, to = 20, length.out = 100L)
 approx2 <- vapply(round(2^grid), function(k) lambda_WETEL(-3, k),
   FUN.VALUE = numeric(1L)
 )

retel-paper/code/figures/figure2.R

@@ -6,7 +6,6 @@ library(retel)
 opts <- list("algorithm" = "NLOPT_LD_LBFGS", "xtol_rel" = 1e-06)
 
 # Data
-n <- 1
 x <- 0
 
 # Functions
@@ -15,7 +14,7 @@ f <- function(x, par) {
 }
 
 # Grid
-grid <- seq(from = -1, to = 1, length.out = 300)
+grid <- seq(from = -1, to = 1, length.out = 300L)
 f_keep_pc <- function(tau) {
   vapply(grid, function(k) {
     retel(f, x,

retel-paper/code/figures/figure3.R

@@ -3,9 +3,11 @@ library(cowplot)
 library(ggplot2)
 library(grid)
 library(gridExtra)
+suppressMessages(library(here))
+suppressMessages(here::i_am("code/figures/figure3.R"))
 
 # Data
-result <- readRDS("./simulations/mb/mb_1/n5s5.rds")
+result <- readRDS(here::here("simulations/mb/mb_1/n5s5.rds"))
 df <- as.data.frame(result)
 
 # RETEL_f

retel-paper/code/figures/supplement/figure1.R

@@ -3,20 +3,22 @@ library(cowplot)
 library(ggplot2)
 library(grid)
 library(gridExtra)
+suppressMessages(library(here))
+suppressMessages(here::i_am("code/figures/supplement/figure1.R"))
 
 
 ## Load data
 df_tau1_n5s1 <-
-  readRDS("./simulations/mb/mb_1/n5s1.rds") |>
+  readRDS(here::here("simulations/mb/mb_1/n5s1.rds")) |>
   as.data.frame()
 df_tau1_n20s1 <-
-  readRDS("./simulations/mb/mb_1/n20s1.rds") |>
+  readRDS(here::here("simulations/mb/mb_1/n20s1.rds")) |>
   as.data.frame()
 df_tau1_n50s1 <-
-  readRDS("./simulations/mb/mb_1/n50s1.rds") |>
+  readRDS(here::here("simulations/mb/mb_1/n50s1.rds")) |>
   as.data.frame()
 df_tau1_n100s1 <-
-  readRDS("./simulations/mb/mb_1/n100s1.rds") |>
+  readRDS(here::here("simulations/mb/mb_1/n100s1.rds")) |>
   as.data.frame()
 
 

retel-paper/code/figures/supplement/figure2.R

@@ -3,20 +3,22 @@ library(cowplot)
 library(ggplot2)
 library(grid)
 library(gridExtra)
+suppressMessages(library(here))
+suppressMessages(here::i_am("code/figures/supplement/figure2.R"))
 
 
 ## Load data
 df_tau1_n5s5 <-
-  readRDS("./simulations/mb/mb_1/n5s5.rds") |>
+  readRDS(here::here("simulations/mb/mb_1/n5s5.rds")) |>
   as.data.frame()
 df_tau1_n20s5 <-
-  readRDS("./simulations/mb/mb_1/n20s5.rds") |>
+  readRDS(here::here("simulations/mb/mb_1/n20s5.rds")) |>
   as.data.frame()
 df_tau1_n50s5 <-
-  readRDS("./simulations/mb/mb_1/n50s5.rds") |>
+  readRDS(here::here("simulations/mb/mb_1/n50s5.rds")) |>
   as.data.frame()
 df_tau1_n100s5 <-
-  readRDS("./simulations/mb/mb_1/n100s5.rds") |>
+  readRDS(here::here("simulations/mb/mb_1/n100s5.rds")) |>
   as.data.frame()
 
 

retel-paper/code/figures/supplement/figure3.R

@@ -3,20 +3,22 @@ library(cowplot)
 library(ggplot2)
 library(grid)
 library(gridExtra)
+suppressMessages(library(here))
+suppressMessages(here::i_am("code/figures/supplement/figure3.R"))
 
 
 ## Load data
 df_taulogn_n5s1 <-
-  readRDS("./simulations/mb/mb_logn/n5s1.rds") |>
+  readRDS(here::here("simulations/mb/mb_logn/n5s1.rds")) |>
   as.data.frame()
 df_taulogn_n20s1 <-
-  readRDS("./simulations/mb/mb_logn/n20s1.rds") |>
+  readRDS(here::here("simulations/mb/mb_logn/n20s1.rds")) |>
   as.data.frame()
 df_taulogn_n50s1 <-
-  readRDS("./simulations/mb/mb_logn/n50s1.rds") |>
+  readRDS(here::here("simulations/mb/mb_logn/n50s1.rds")) |>
   as.data.frame()
 df_taulogn_n100s1 <-
-  readRDS("./simulations/mb/mb_logn/n100s1.rds") |>
+  readRDS(here::here("simulations/mb/mb_logn/n100s1.rds")) |>
   as.data.frame()
 
 

retel-paper/code/figures/supplement/figure4.R

@@ -3,20 +3,22 @@ library(cowplot)
 library(ggplot2)
 library(grid)
 library(gridExtra)
+suppressMessages(library(here))
+suppressMessages(here::i_am("code/figures/supplement/figure4.R"))
 
 
 ## Load data
 df_taulogn_n5s5 <-
-  readRDS("./simulations/mb/mb_logn/n5s5.rds") |>
+  readRDS(here::here("simulations/mb/mb_logn/n5s5.rds")) |>
   as.data.frame()
 df_taulogn_n20s5 <-
-  readRDS("./simulations/mb/mb_logn/n20s5.rds") |>
+  readRDS(here::here("simulations/mb/mb_logn/n20s5.rds")) |>
   as.data.frame()
 df_taulogn_n50s5 <-
-  readRDS("./simulations/mb/mb_logn/n50s5.rds") |>
+  readRDS(here::here("simulations/mb/mb_logn/n50s5.rds")) |>
   as.data.frame()
 df_taulogn_n100s5 <-
-  readRDS("./simulations/mb/mb_logn/n100s5.rds") |>
+  readRDS(here::here("simulations/mb/mb_logn/n100s5.rds")) |>
   as.data.frame()
 
 

retel-paper/code/simulations/cr.R

@@ -11,7 +11,7 @@ library(retel)
 # Prior location
 l <- 0
 # Sample size
-n <- 5
+n <- 5L
 # Prior scale
 s <- 0.5
 
@@ -86,7 +86,7 @@ set.seed(847675)
 cl <- makeCluster(24L)
 registerDoParallel(cl)
 result <- foreach(
-  i = icount(S), .combine = "rbind", .inorder = F,
+  i = icount(S), .combine = "rbind", .inorder = FALSE,
   .packages = c("nloptr", "retel")
 ) %dorng% {
   # Sample data

retel-paper/code/simulations/mb.R

@@ -85,7 +85,7 @@ set.seed(847675)
 cl <- makeCluster(24L)
 registerDoParallel(cl)
 result <- foreach(
-  i = icount(S), .combine = "rbind", .inorder = F,
+  i = icount(S), .combine = "rbind", .inorder = FALSE,
   .packages = c("nloptr", "retel")
 ) %dorng% {
   # Sample theta from prior

retel-paper/renv.lock

@@ -709,6 +709,16 @@
       ],
       "Hash": "b29cf3031f49b04ab9c852c912547eef"
     },
+    "here": {
+      "Package": "here",
+      "Version": "1.0.1",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "rprojroot"
+      ],
+      "Hash": "24b224366f9c2e7534d2344d10d59211"
+    },
     "highr": {
       "Package": "highr",
       "Version": "0.10",