Fix bugs in endemic_channel function

R/endemic_channel.R

@@ -68,9 +68,8 @@ endemic_channel <- function(incidence_historic, observations = NULL,
       "`observations` must be numeric and positive" =
         (is.numeric(observations) &&
           all(observations >= 0)),
-      "`observations` size doesn't correspond to incidence interval" =
-        ((incidence_historic$interval == "1 week" &
-          length(observations) == 52))
+      "`observations` size is larger than the epidemiological year" =
+        (length(observations) <= 52)
     )
   }
 

R/utils.R

@@ -213,8 +213,8 @@ geometric_mean <- function(x, method = c(
     w_positive <- length(x_positive) / n_x
     x_negative <- x[x < 0]
     w_negative <- length(x_negative) / n_x
-    gm_positive <- exp(sum(log(x_positive)) / n_x)
-    gm_negative <- -1 * exp(sum(log(abs(x_negative))) / n_x)
+    gm_positive <- exp(sum(log(x_positive)))
+    gm_negative <- -1 * exp(sum(log(abs(x_negative))))
     gm <- w_positive * gm_positive + w_negative * gm_negative
   } else if (method == "optimized") {
     # The formula is:
@@ -309,7 +309,7 @@ geometric_sd <- function(x, method = c(
 
   if (method == "positive") {
     stopifnot("`x` includes zero or negative values,
-              check the geom_mean methods" = any(x <= 0))
+              check the geom_mean methods" = any(x > 0))
     gsd <- stats::sd((log(x)))
   } else if (method == "shifted") {
     x_shifted <- x + shift

inst/WORDLIST

@@ -6,6 +6,7 @@ Codecov
 ColOpenData
 Cordovez
 DIVIPOLA
+DOI
 De
 DOI
 Epimodelac