fix mathjax

update rounding strategy

Author: aravind-j

R/LEAV.R

@@ -19,8 +19,8 @@
 #'
 #' For accessions in a collection compute the Length of Encoded Attribute Values
 #' (LEAV) information measure from qualitative and quantitative trait data
-#' \insertCite{wallace_information_1968,balakrishnan_Strategies_2001,balakrishnan_Strategies_2001a,balakrishnan_Strategies_2003}{LEAVcore}
-#' \loadmathjax.
+#' \insertCite{wallace_information_1968,balakrishnan_Strategies_2001,balakrishnan_Strategies_2001a,balakrishnan_Strategies_2003}{LEAVcore}.
+#' \loadmathjax
 #'
 #' For each accession \mjseqn{s} in the collection, the message length
 #' \mjseqn{F_{s}} to optimally encode all the \mjseqn{d} traits/descriptors is
@@ -101,7 +101,7 @@
 #' freq_list <- lapply(qual, function(x) {
 #'   prop <-  prop.adj(cassava_EC[, x], method = "sqrt")
 #'   size.count <- ceiling(size * length(x))
-#'   round.to.target(prop * size.count)
+#'   round_to_target(prop * size.count)
 #' })
 #' names(freq_list) <- qual
 #'

R/LEAVcore.R

@@ -31,7 +31,7 @@ LEAVcore <- function(data, names,
     fqout <- prop * size.count
     fq_overall <- summary(data[, x])
     fqout <- ifelse(fqout > fq_overall, fq_overall, fqout)
-    fqout <- round.to.target(fqout)
+    fqout <- round_to_target(fqout)
     return(fqout)
   })
   names(freq1) <- qualitative
@@ -99,7 +99,7 @@ LEAVcore <- function(data, names,
   freq <- lapply(qualitative, function(x) {
     prop <-  prop.adj(data[, x], method = prop.adj)
     fqout <- prop * nrow(data)
-    # fqout <- round.to.target(fqout)
+    # fqout <- round_to_target(fqout)
     return(fqout)
   })
   names(freq) <- qualitative
@@ -117,7 +117,8 @@ LEAVcore <- function(data, names,
 
   ## Estimate LEAV ----
   LEAVdf <- LEAV(data = data, names = names,
-                 quantitative = quantitative, qualitative = qualitative,
+                 quantitative = quantitative,
+                 qualitative = qualitative,
                  adj = FALSE,
                  freq = freq, mean = mean, sd = sd, e = e)
 
@@ -139,7 +140,7 @@ LEAVcore <- function(data, names,
 
 }
 
-round.to.target <- function(x, target = round(sum(x))) {
+round_to_target <- function(x, target = round(sum(x))) {
 
   while(sum(round(x)) - target > 0) {
     i <- which.min(ifelse(x %% 1 < 0.5, 1, x %% 1))
@@ -151,3 +152,17 @@ round.to.target <- function(x, target = round(sum(x))) {
   }
   round(x)
 }
+
+# Hamilton rounding
+# largest remainder method
+round_preserve_sum <- function(x, target = round(sum(x))) {
+  y <- floor(x)
+  deficit <- target - sum(y)
+
+  if(deficit > 0) {
+    idx <- order(x - y, decreasing = TRUE)[1:deficit]
+    y[idx] <- y[idx] + 1
+  }
+
+  y
+}

R/inflen.qual.R

@@ -19,8 +19,8 @@
 #'
 #' The function \code{inflen.qual} computes the length of information code that
 #' can indicate the possession of a descriptor state of a qualitative trait
-#' \insertCite{wallace_information_1968,balakrishnan_Strategies_2001,balakrishnan_Strategies_2001a,balakrishnan_Strategies_2003}{LEAVcore}
-#' \loadmathjax.
+#' \insertCite{wallace_information_1968,balakrishnan_Strategies_2001,balakrishnan_Strategies_2001a,balakrishnan_Strategies_2003}{LEAVcore}.
+#' \loadmathjax
 #'
 #' For each qualitative trait/descriptor \mjseqn{d} the probability of
 #' occurrence of a descriptor state \mjseqn{m} in the in a subset \mjseqn{t} is

R/inflen.quant.R

@@ -19,8 +19,8 @@
 #'
 #' The function \code{inflen.quant} computes the length of information code that
 #' can indicate the possession of a specific value by a quantitative trait
-#' \insertCite{wallace_information_1968,balakrishnan_Strategies_2001,balakrishnan_Strategies_2001a,balakrishnan_Strategies_2003}{LEAVcore}
-#' \loadmathjax.
+#' \insertCite{wallace_information_1968,balakrishnan_Strategies_2001,balakrishnan_Strategies_2001a,balakrishnan_Strategies_2003}{LEAVcore}.
+#' \loadmathjax
 #'
 #' For each quantitative trait \mjseqn{d}, it is assumed that it is normally
 #' distributed within subset \mjseqn{t} with mean \mjseqn{\mu_{d,t}} and the

_pkgdown.yml

@@ -1,6 +1,7 @@
 template:
   bootstrap: 5
   light-switch: yes
+  math-rendering: mathjax
   bslib:
     base_font:
       google: Fira Sans