lint for code factor

nickbrazeau · Dec 20, 2024 · a8ebac9 · a8ebac9
1 parent 4c7e7e0
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Showing 13 changed files with 83 additions and 39 deletions.
diff --git a/data-raw/IBD_simulation_data.R b/data-raw/IBD_simulation_data.R
@@ -62,11 +62,11 @@ sim_IBDIBD <- function(demesize, distmat, rate, Ft) {
   ) %>%
     magrittr::set_colnames(c("deme1", "deme2", "geodist"))
   # individuals to long
-  inds <- 1:cumsum(demesize)[length(demesize)]
+  inds <- seq_len(cumsum(demesize)[length(demesize)])
   # trackers for demes
-  d1 <- tibble::tibble(smpl1 = inds, deme1 = as.factor(rep(1:length(demesize), demesize)),
+  d1 <- tibble::tibble(smpl1 = inds, deme1 = as.factor(rep(seq_len(length(demesize)), demesize)),
                        demesize1 = rep(demesize, demesize))
-  d2 <- tibble::tibble(smpl2 = inds, deme2 = as.factor(rep(1:length(demesize), demesize)),
+  d2 <- tibble::tibble(smpl2 = inds, deme2 = as.factor(rep(seq_len(length(demesize)), demesize)),
                        demesize2 = rep(demesize, demesize))
   # combinations and joins
   combinds <- tibble::as_tibble(t(combn(inds, 2)), .name_repair = "minimal") %>%
@@ -77,35 +77,33 @@ sim_IBDIBD <- function(demesize, distmat, rate, Ft) {
 
   # function for drawing mean IBD based iso by dist
   draw_mean_Ftibd <- function(demesize1, demesize2, geodist, rate, Ft) {
-    ret <- 1/(demesize1 + demesize2) * (1 - pexp(geodist, rate)) +
+    1/(demesize1 + demesize2) * (1 - pexp(geodist, rate)) +
       ( (1 - 1/(demesize1 + demesize2)) *  (1 - pexp(geodist, rate)) * Ft )
-    return(ret)
   }
   combinds$mft <- purrr::pmap_dbl(combinds[,c("demesize1", "demesize2", "geodist")],
                                   draw_mean_Ftibd,
                                   rate = rate, Ft = Ft)
 
   # draw value of realized IBD from mean distribution
   draw_realized_ibdibd <- function(mft) {
-    ribdibd <- rnorm_interval(mean = mft, sd = mft * (1-mft),
-                              a = 0, b = 1)
-    return(ribdibd)
+    rnorm_interval(mean = mft, sd = mft * (1-mft),
+                   a = 0, b = 1)
   }
 
   # tidy up and out
-  combinds <- combinds %>%
+  combinds %>%
     dplyr::mutate(gendist = purrr::map_dbl(mft, draw_realized_ibdibd)) %>%
     dplyr::select(c("smpl1", "smpl2", "deme1", "deme2", "gendist", "geodist"))
-  return(combinds)
+
 
 }
 
 # Deme A and B are close but A is very far from C, while B is closer (eg a right triangle)
 set.seed(48)
 IBD_simulation_data <- sim_IBDIBD(demesize = c(3,3,4), distmat = matrix(c(0,500,1000,
-                                                             500,0,750,
-                                                             100,750,0), nrow = 3),
-                     rate = 1e-3, Ft = 0.3)
+                                                                          500,0,750,
+                                                                          100,750,0), nrow = 3),
+                                  rate = 1e-3, Ft = 0.3)
 
 # drop within deme
 IBD_simulation_data <- IBD_simulation_data[IBD_simulation_data$geodist > 0, ]

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/installation.html b/docs/articles/installation.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -1,8 +1,8 @@
-pandoc: '2.18'
-pkgdown: 2.0.5
+pandoc: 2.19.2
+pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   installation: installation.html
-  runmod: runmod.html
-last_built: 2022-08-10T05:33Z
+  runvanillamod: runvanillamod.html
+last_built: 2024-12-20T01:15Z
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/pipe.html b/docs/reference/pipe.html
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
@@ -18,25 +18,52 @@
   <url>
     <loc>/articles/runmod.html</loc>
   </url>
+  <url>
+    <loc>/articles/runvanillamod.html</loc>
+  </url>
   <url>
     <loc>/authors.html</loc>
   </url>
+  <url>
+    <loc>/design_engineering.html</loc>
+  </url>
   <url>
     <loc>/index.html</loc>
   </url>
   <url>
     <loc>/news/index.html</loc>
   </url>
+  <url>
+    <loc>/reference/IBD_simulation_data.html</loc>
+  </url>
   <url>
     <loc>/reference/deme_inbreeding_spcoef.html</loc>
   </url>
+  <url>
+    <loc>/reference/deme_inbreeding_spcoef_vanilla.html</loc>
+  </url>
   <url>
     <loc>/reference/discent_sim_dat.html</loc>
   </url>
   <url>
     <loc>/reference/index.html</loc>
   </url>
+  <url>
+    <loc>/reference/is.vanillaDISCresult.html</loc>
+  </url>
   <url>
     <loc>/reference/pipe.html</loc>
   </url>
+  <url>
+    <loc>/reference/print.vanillaDISCresult.html</loc>
+  </url>
+  <url>
+    <loc>/reference/summary.vanillaDISCresult.html</loc>
+  </url>
+  <url>
+    <loc>/reference/tidyout.html</loc>
+  </url>
+  <url>
+    <loc>/reference/tidyout.vanillaDISCresult.html</loc>
+  </url>
 </urlset>