From e6a632495f06e4623357300e6d8d64eae127921e Mon Sep 17 00:00:00 2001
From: pratikunterwegs <pratikgupte16@gmail.com>
Date: Thu, 30 May 2024 15:05:42 +0100
Subject: [PATCH 1/2] Update renv to v1.0.7

---
 renv/activate.R | 43 +++++++++++++++++++++++++++++++------------
 1 file changed, 31 insertions(+), 12 deletions(-)

diff --git a/renv/activate.R b/renv/activate.R
index 9b2e7f1..d13f993 100644
--- a/renv/activate.R
+++ b/renv/activate.R
@@ -2,11 +2,13 @@
 local({
 
   # the requested version of renv
-  version <- "1.0.5"
+  version <- "1.0.7"
   attr(version, "sha") <- NULL
 
   # the project directory
-  project <- getwd()
+  project <- Sys.getenv("RENV_PROJECT")
+  if (!nzchar(project))
+    project <- getwd()
 
   # use start-up diagnostics if enabled
   diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
@@ -129,6 +131,21 @@ local({
   
   }
   
+  heredoc <- function(text, leave = 0) {
+  
+    # remove leading, trailing whitespace
+    trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text)
+  
+    # split into lines
+    lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]]
+  
+    # compute common indent
+    indent <- regexpr("[^[:space:]]", lines)
+    common <- min(setdiff(indent, -1L)) - leave
+    paste(substring(lines, common), collapse = "\n")
+  
+  }
+  
   startswith <- function(string, prefix) {
     substring(string, 1, nchar(prefix)) == prefix
   }
@@ -631,6 +648,9 @@ local({
   
     # if the user has requested an automatic prefix, generate it
     auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
+    if (is.na(auto) && getRversion() >= "4.4.0")
+      auto <- "TRUE"
+  
     if (auto %in% c("TRUE", "True", "true", "1"))
       return(renv_bootstrap_platform_prefix_auto())
   
@@ -822,24 +842,23 @@ local({
   
     # the loaded version of renv doesn't match the requested version;
     # give the user instructions on how to proceed
-    remote <- if (!is.null(description[["RemoteSha"]])) {
+    dev <- identical(description[["RemoteType"]], "github")
+    remote <- if (dev)
       paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
-    } else {
+    else
       paste("renv", description[["Version"]], sep = "@")
-    }
   
     # display both loaded version + sha if available
     friendly <- renv_bootstrap_version_friendly(
       version = description[["Version"]],
-      sha     = description[["RemoteSha"]]
+      sha     = if (dev) description[["RemoteSha"]]
     )
   
-    fmt <- paste(
-      "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.",
-      "- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.",
-      "- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
-      sep = "\n"
-    )
+    fmt <- heredoc("
+      renv %1$s was loaded from project library, but this project is configured to use renv %2$s.
+      - Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.
+      - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.
+    ")
     catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
   
     FALSE

From 21495907faaabbb83b0594d8ff2121d848003b1f Mon Sep 17 00:00:00 2001
From: pratikunterwegs <pratikgupte16@gmail.com>
Date: Thu, 30 May 2024 15:06:15 +0100
Subject: [PATCH 2/2] Update renv lockfile, WIP #50

---
 renv.lock | 688 +++++++++++++++++++++++++++---------------------------
 1 file changed, 340 insertions(+), 348 deletions(-)

diff --git a/renv.lock b/renv.lock
index 2079c83..ed7d28e 100644
--- a/renv.lock
+++ b/renv.lock
@@ -1,6 +1,6 @@
 {
   "R": {
-    "Version": "4.3.2",
+    "Version": "4.4.0",
     "Repositories": [
       {
         "Name": "CRAN",
@@ -11,47 +11,42 @@
   "Packages": {
     "BH": {
       "Package": "BH",
-      "Version": "1.81.0-1",
+      "Version": "1.84.0-0",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "68122010f01c4dcfbe58ce7112f2433d"
+      "Hash": "a8235afbcd6316e6e91433ea47661013"
     },
     "DBI": {
       "Package": "DBI",
-      "Version": "1.1.3",
+      "Version": "1.2.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "b2866e62bab9378c3cc9476a1954226b"
+      "Hash": "164809cd72e1d5160b4cb3aa57f510fe"
     },
     "EpiEstim": {
       "Package": "EpiEstim",
-      "Version": "2.4",
+      "Version": "2.2-4",
       "Source": "Repository",
-      "Repository": "https://mrc-ide.r-universe.dev",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
-        "abind",
         "coarseDataTools",
         "coda",
-        "distcrete",
-        "epitrix",
         "fitdistrplus",
-        "gghighlight",
         "ggplot2",
         "grDevices",
         "graphics",
         "gridExtra",
         "incidence",
-        "patchwork",
         "reshape2",
         "scales",
         "stats"
       ],
-      "Hash": "72f00b698770c640deb2f8dde261e560"
+      "Hash": "aeb8c10e5965a419755eb6dd42a3656d"
     },
     "EpiNow2": {
       "Package": "EpiNow2",
@@ -92,7 +87,7 @@
     },
     "MASS": {
       "Package": "MASS",
-      "Version": "7.3-58.1",
+      "Version": "7.3-60.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -103,13 +98,13 @@
         "stats",
         "utils"
       ],
-      "Hash": "762e1804143a332333c054759f89a706"
+      "Hash": "2f342c46163b0b54d7b64d1f798e2c78"
     },
     "MCMCpack": {
       "Package": "MCMCpack",
-      "Version": "1.6-3",
+      "Version": "1.7-0",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "MASS",
         "R",
@@ -123,11 +118,11 @@
         "stats",
         "utils"
       ],
-      "Hash": "520335edba1c95a90eec54d693727723"
+      "Hash": "225c857e115cf09e1804ff3e597fe555"
     },
     "Matrix": {
       "Package": "Matrix",
-      "Version": "1.6-5",
+      "Version": "1.7-0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -140,11 +135,11 @@
         "stats",
         "utils"
       ],
-      "Hash": "8c7115cd3a0e048bda2a7cd110549f7a"
+      "Hash": "1920b2f11133b12350024297d8a4ff4a"
     },
     "MatrixModels": {
       "Package": "MatrixModels",
-      "Version": "0.5-2",
+      "Version": "0.5-3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -153,11 +148,11 @@
         "methods",
         "stats"
       ],
-      "Hash": "26749bd5c7c4123dd23aeb9159be22d6"
+      "Hash": "0776bf7526869e0286b0463cb72fb211"
     },
     "QuickJSR": {
       "Package": "QuickJSR",
-      "Version": "1.0.6",
+      "Version": "1.1.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -165,7 +160,7 @@
         "Rcpp",
         "jsonlite"
       ],
-      "Hash": "6ded66fbe724abcec064fb15f626a0e4"
+      "Hash": "765d4f4bcec02ed0663d4de3db23f6e5"
     },
     "R.methodsS3": {
       "Package": "R.methodsS3",
@@ -180,16 +175,16 @@
     },
     "R.oo": {
       "Package": "R.oo",
-      "Version": "1.25.0",
+      "Version": "1.26.0",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "R.methodsS3",
         "methods",
         "utils"
       ],
-      "Hash": "a0900a114f4f0194cf4aa8cd4a700681"
+      "Hash": "4fed809e53ddb5407b3da3d0f572e591"
     },
     "R.utils": {
       "Package": "R.utils",
@@ -228,28 +223,27 @@
     },
     "Rcpp": {
       "Package": "Rcpp",
-      "Version": "1.0.11",
+      "Version": "1.0.12",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "methods",
         "utils"
       ],
-      "Hash": "ae6cbbe1492f4de79c45fce06f967ce8"
+      "Hash": "5ea2700d21e038ace58269ecdbeb9ec0"
     },
     "RcppEigen": {
       "Package": "RcppEigen",
-      "Version": "0.3.3.9.3",
+      "Version": "0.3.4.0.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
-        "Matrix",
         "R",
         "Rcpp",
         "stats",
         "utils"
       ],
-      "Hash": "1e035db628cefb315c571202d70202fe"
+      "Hash": "df49e3306f232ec28f1604e36a202847"
     },
     "RcppParallel": {
       "Package": "RcppParallel",
@@ -263,9 +257,9 @@
     },
     "SparseM": {
       "Package": "SparseM",
-      "Version": "1.81",
+      "Version": "1.82",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "graphics",
@@ -273,11 +267,11 @@
         "stats",
         "utils"
       ],
-      "Hash": "2042cd9759cc89a453c4aefef0ce9aae"
+      "Hash": "d9654aa07d133ba02190ad518a653931"
     },
     "StanHeaders": {
       "Package": "StanHeaders",
-      "Version": "2.26.28",
+      "Version": "2.32.9",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -285,7 +279,7 @@
         "RcppEigen",
         "RcppParallel"
       ],
-      "Hash": "35b5aee9ec9507aca2e021997a9e557e"
+      "Hash": "affbfba7203fd83b6594362f1355c25b"
     },
     "abind": {
       "Package": "abind",
@@ -342,13 +336,13 @@
     },
     "backports": {
       "Package": "backports",
-      "Version": "1.4.1",
+      "Version": "1.5.0",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "c39fbec8a30d23e721980b8afb31984c"
+      "Hash": "e1e1b9d75c37401117b636b7ae50827a"
     },
     "base64enc": {
       "Package": "base64enc",
@@ -398,7 +392,7 @@
     },
     "boot": {
       "Package": "boot",
-      "Version": "1.3-28",
+      "Version": "1.3-30",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -406,25 +400,27 @@
         "graphics",
         "stats"
       ],
-      "Hash": "0baa960e3b49c6176a4f42addcbacc59"
+      "Hash": "96abeed416a286d4a0f52e550b612343"
     },
     "brio": {
       "Package": "brio",
-      "Version": "1.1.3",
+      "Version": "1.1.5",
       "Source": "Repository",
-      "Repository": "RSPM",
-      "Hash": "976cf154dfb043c012d87cddd8bca363"
+      "Repository": "CRAN",
+      "Requirements": [
+        "R"
+      ],
+      "Hash": "c1ee497a6d999947c2c224ae46799b1a"
     },
     "broom": {
       "Package": "broom",
-      "Version": "1.0.5",
+      "Version": "1.0.6",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "backports",
         "dplyr",
-        "ellipsis",
         "generics",
         "glue",
         "lifecycle",
@@ -434,42 +430,44 @@
         "tibble",
         "tidyr"
       ],
-      "Hash": "fd25391c3c4f6ecf0fa95f1e6d15378c"
+      "Hash": "a4652c36d1f8abfc3ddf4774f768c934"
     },
     "bslib": {
       "Package": "bslib",
-      "Version": "0.5.1",
+      "Version": "0.7.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "base64enc",
         "cachem",
+        "fastmap",
         "grDevices",
         "htmltools",
         "jquerylib",
         "jsonlite",
+        "lifecycle",
         "memoise",
         "mime",
         "rlang",
         "sass"
       ],
-      "Hash": "283015ddfbb9d7bf15ea9f0b5698f0d9"
+      "Hash": "8644cc53f43828f19133548195d7e59e"
     },
     "cachem": {
       "Package": "cachem",
-      "Version": "1.0.8",
+      "Version": "1.1.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "fastmap",
         "rlang"
       ],
-      "Hash": "c35768291560ce302c0a6589f92e837d"
+      "Hash": "cd9a672193789068eb5a2aad65a0dedf"
     },
     "callr": {
       "Package": "callr",
-      "Version": "3.7.3",
+      "Version": "3.7.6",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -478,7 +476,7 @@
         "processx",
         "utils"
       ],
-      "Hash": "9b2191ede20fa29828139b9900922e51"
+      "Hash": "d7e13f49c19103ece9e58ad2d83a7354"
     },
     "cellranger": {
       "Package": "cellranger",
@@ -495,25 +493,18 @@
     "cfr": {
       "Package": "cfr",
       "Version": "0.1.0",
-      "Source": "GitHub",
-      "RemoteType": "github",
-      "Remotes": "epiverse-trace/epiparameter",
-      "RemoteHost": "api.github.com",
-      "RemoteRepo": "cfr",
-      "RemoteUsername": "epiverse-trace",
-      "RemotePkgRef": "epiverse-trace/cfr",
-      "RemoteRef": "HEAD",
-      "RemoteSha": "2b6171acd0e3abf68d3a6e67f1895aaef0d87671",
+      "Source": "Repository",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "checkmate",
         "stats"
       ],
-      "Hash": "e8d04bfdbf150dfecc4be7e6d3e90893"
+      "Hash": "ad7c5fc8ff8a86b3c973e09aaf36864f"
     },
     "checkmate": {
       "Package": "checkmate",
-      "Version": "2.2.0",
+      "Version": "2.3.1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
@@ -521,7 +512,7 @@
         "backports",
         "utils"
       ],
-      "Hash": "ca9c113196136f4a9ca9ce6079c2c99e"
+      "Hash": "c01cab1cb0f9125211a6fc99d540e315"
     },
     "ciTools": {
       "Package": "ciTools",
@@ -544,14 +535,14 @@
     },
     "cli": {
       "Package": "cli",
-      "Version": "3.6.1",
+      "Version": "3.6.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "89e6d8219950eac806ae0c489052048a"
+      "Hash": "1216ac65ac55ec0058a6f75d7ca0fd52"
     },
     "clipr": {
       "Package": "clipr",
@@ -579,24 +570,24 @@
     },
     "coda": {
       "Package": "coda",
-      "Version": "0.19-4",
+      "Version": "0.19-4.1",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "lattice"
       ],
-      "Hash": "24b6d006b8b2343876cf230687546932"
+      "Hash": "af436915c590afc6fffc3ce3a5be1569"
     },
     "codetools": {
       "Package": "codetools",
-      "Version": "0.2-18",
+      "Version": "0.2-20",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "019388fc48e48b3da0d3a76ff94608a8"
+      "Hash": "61e097f35917d342622f21cdc79c256e"
     },
     "colorspace": {
       "Package": "colorspace",
@@ -627,19 +618,19 @@
     },
     "countrycode": {
       "Package": "countrycode",
-      "Version": "1.5.0",
+      "Version": "1.6.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "bbc5ab5258e5ddf38f2cd2c5a7afa860"
+      "Hash": "08b7058813f13c7a1bb294fea9045e3a"
     },
     "covidregionaldata": {
       "Package": "covidregionaldata",
       "Version": "0.9.3",
       "Source": "Repository",
-      "Repository": "https://epiforecasts.r-universe.dev",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "R6",
@@ -663,13 +654,13 @@
     },
     "cpp11": {
       "Package": "cpp11",
-      "Version": "0.4.6",
+      "Version": "0.4.7",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "707fae4bbf73697ec8d85f9d7076c061"
+      "Hash": "5a295d7d963cc5035284dcdbaf334f4e"
     },
     "crayon": {
       "Package": "crayon",
@@ -685,30 +676,30 @@
     },
     "curl": {
       "Package": "curl",
-      "Version": "5.0.2",
+      "Version": "5.2.1",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "511bacbfa153a15251166b463b4da4f9"
+      "Hash": "411ca2c03b1ce5f548345d2fc2685f7a"
     },
     "data.table": {
       "Package": "data.table",
-      "Version": "1.14.8",
+      "Version": "1.15.4",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "methods"
       ],
-      "Hash": "b4c06e554f33344e044ccd7fdca750a9"
+      "Hash": "8ee9ac56ef633d0c7cab8b2ca87d683e"
     },
     "dbplyr": {
       "Package": "dbplyr",
-      "Version": "2.3.3",
+      "Version": "2.5.0",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "DBI",
         "R",
@@ -730,21 +721,20 @@
         "vctrs",
         "withr"
       ],
-      "Hash": "d6fd1b1440c1cacc6623aaa4e9fe352b"
+      "Hash": "39b2e002522bfd258039ee4e889e0fd1"
     },
     "desc": {
       "Package": "desc",
-      "Version": "1.4.2",
+      "Version": "1.4.3",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "R6",
         "cli",
-        "rprojroot",
         "utils"
       ],
-      "Hash": "6b9602c7ebbe87101a9c8edb6e8b6d21"
+      "Hash": "99b79fcbd6c4d1ce087f5c5c758b384f"
     },
     "diffobj": {
       "Package": "diffobj",
@@ -763,14 +753,14 @@
     },
     "digest": {
       "Package": "digest",
-      "Version": "0.6.33",
+      "Version": "0.6.35",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "b18a9cf3c003977b0cc49d5e76ebe48d"
+      "Hash": "698ece7ba5a4fa4559e3d537e7ec3d31"
     },
     "distcrete": {
       "Package": "distcrete",
@@ -781,39 +771,35 @@
     },
     "distributional": {
       "Package": "distributional",
-      "Version": "0.3.2",
+      "Version": "0.4.0",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
-        "digest",
-        "farver",
         "generics",
-        "ggplot2",
         "lifecycle",
         "numDeriv",
         "rlang",
-        "scales",
         "stats",
         "utils",
         "vctrs"
       ],
-      "Hash": "0a94c3c917918a1c90f4609171ff41b6"
+      "Hash": "3bad76869f2257ea4fd00a3c08c2bcce"
     },
     "dotCall64": {
       "Package": "dotCall64",
-      "Version": "1.0-2",
+      "Version": "1.1-1",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R"
       ],
-      "Hash": "6aa9e277302190b6c618af042d904bdf"
+      "Hash": "80f374ef8500fcdc5d84a0345b837227"
     },
     "dplyr": {
       "Package": "dplyr",
-      "Version": "1.1.3",
+      "Version": "1.1.4",
       "Source": "Repository",
-      "Repository": "RSPM",
+      "Repository": "CRAN",
       "Requirements": [
         "R",
         "R6",
@@ -830,7 +816,7 @@
         "utils",
         "vctrs"
       ],
-      "Hash": "e85ffbebaad5f70e1a2e2ef4302b4949"
+      "Hash": "fedd9d00c2944ff00a0e2696ccf048ec"
     },
     "dtplyr": {
       "Package": "dtplyr",
@@ -851,27 +837,11 @@
       ],
       "Hash": "54ed3ea01b11e81a86544faaecfef8e2"
     },
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