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Merged
Pakillo merged 2 commits into from
Feb 19, 2026
Merged

Canopy_service_test #36

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f2b2e0d
Update canopy_service_test.R
aliciamontesinos Feb 19, 2026
77200f3
Fix typos and improve vector initialization
Pakillo Feb 19, 2026
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29 changes: 15 additions & 14 deletions R/canopy_service_test.R
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Original file line number Diff line number Diff line change
@@ -1,21 +1,23 @@
#' Title
#' Identifies wheather a species acts as depressing, enhancing or neutral
#' @description
#' Tests whether a canopy species has a depressing, enhancing or neutral
#' effect on recruitment in general (i.e., at the community level) compared
#' to the "Open", independently considering all the recruit species together.
#'
#' @param int_data
#' @param cover_data
#'
#' @returns
#' @inheritParams check_interactions
#' @inheritParams check_cover
#'
#'
#' @returns Data frame with the same variables provided by the function
#' [int_significance()] but without distinguishing between recruit species.
#'
#' @export
#'
#' @examples
#' canopy_service_test(Amoladeras_int, Amoladeras_cover)
#'
#' #como canopy_service_test_UNI pero sin quitar especies de reclutas
#que no tienen cover ( solo las canopy que no tienen cover)
#sustituimos pre_associndex_UNISITE_UNI por
#associndex(int_data,cover_data, expand="yes", rm_sp_no_cover="onlycanopy")
#calcula para cada especie de nodriza, si alberga bajo su copa una mayor (o menor)
# densidad de reclutas (de cualquier especie) que la esperada en funcion del area que ocupa.
#The input data are two files: the field data containing interactions and species cover
#'

canopy_service_test <- function(int_data,cover_data){

df<-associndex(int_data,cover_data, expand="yes", rm_sp_no_cover="onlycanopy")
Expand All @@ -42,7 +44,7 @@ canopy_service_test <- function(int_data,cover_data){

testability <- c()
for(i in 1:n_tests) {
testability[i] <- binom.test(df$Ftot[i], df$Ftot[i], df$extreme_p[i], alternative ="two.sided")$p.value
testability[i] <- stats::binom.test(df$Ftot[i], df$Ftot[i], df$extreme_p[i], alternative ="two.sided")$p.value
}
df$testability <- testability

Expand Down Expand Up @@ -86,4 +88,3 @@ canopy_service_test <- function(int_data,cover_data){
df <- df[ , !(names(df) %in% drops)]
return(df)
}

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