Added the as.alienData function with help file written in roxygen2 (#2)

* Added the as.alienData function with help file written in roxygen2

* CamelCase functions

* restore Bartomeus data file in R/

* Fixing issue with weight_sd and weight_mean functions

* removin weight_mean and weigthed_sd, already present in stats - close  #17

* Rebuild package and add new clean target in makefile

* fixinx syntax issues

* code review; fix minor issues/syntax errors

* Set mandatory idObs object in as.alienData() #21

* cleaning up data format

* removing ressourceConsumer matrix

* Details on roxygen documentation

* Add data consistency among interacPair and idObs #21

* set build interac matrix #21

* Add interacSp and interacInd from interacPair

* finish to reference interacSp and interacInd with idObs #21

* check consistency among traitSp and traitInd with idObs #21

* imp. coOcc methods: inferred or not; last checks on out objects; make sure coOcc rownames and colnames reffered to idObs

* make sure siteEnv are referenced in idObs #21

* build doc of as.alienData function

* Push last edits on as.alienData function

* set traitSp and traitInd as long format

* fixing functions errors

* Fixing last issue with res

* building docs; and close #21

* Add data and test it

* Add comments on as.alienData posible enhancements

* set Nacho's comments in issue #12

* set bartomeus in data folder

* init as.alienData test

* init test on integrity #18

* cover unit tests as.alienData() - issue #18

* add unit tests to data structure issue #18

Makefile

@@ -1,19 +1,14 @@
 rfun := $(wildcard R/*.R)
 rman := $(wildcard man/)
 rtes := $(wildcard tests/testthat/*.R)
-rdm = README.Rmd
-md = README.md
 chk = record_updates.txt
 rscr = pkg2date.R
 
 
-all: $(md) $(chk)
-
-$(md): $(rdm)
-	Rscript --no-site-file  --no-init-file $(rscr) 0
+all: $(chk)
 
 $(chk): $(rfun) $(rtes) $(rman)
 	Rscript --no-site-file  --no-init-file $(rscr) 1
 
 clean:
-	rm -rf man/* NAMESPACES
+	rm -rf man/* NAMESPACE

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(as.alienData)
 export(binomialToJags)
 export(estNichPars)
 export(extractBayesReg)
@@ -22,3 +23,4 @@ export(predNicheProb)
 export(residualsNicheProb)
 export(simTraitMatch)
 importFrom(magrittr,"%>%")
+importFrom(stats,sd)

R/Bartomeus.R → R/data.R

@@ -14,8 +14,7 @@
 #' @docType data
 #' @keywords datasets
 #' @author Ignasi Bartomeus
-#' @name Bartomeus
-#' @usage data(Bartomeus)
+#' @name bartomeus
+#' @usage data(bartomeus)
 #' @format A data frame with X variables
-#' @export
-# 'Bartomeus'
+"bartomeus"

pkg2date.R

@@ -30,11 +30,11 @@ if (!as.numeric(args[1])) {
   decor()
   ## load the package
   cat("##-- loading ........\n")
-  devtools::load_all(".")
+  devtools::load_all()
   decor()
   ## document the package
   cat("##-- documenting ....\n")
-  devtools::document(".")
+  devtools::document()
   decor()
   ## testing the code
   cat("##-- testing ........\n")

tests/testthat/test-alienData.R

@@ -0,0 +1,42 @@
+context("alienData function")
+
+load('./argsAlienData.RData')
+out <- as.alienData(idObs=idObs,interactPair=interactPair,traitSp=traitSp,traitInd=traitInd,verbose=FALSE)
+
+test_that("check data structure", {
+  expect_is(out, "alienData")
+  # Even if items from the list are NULL, all items have to be returned
+  expect_equal(names(out),c("idObs","interactSp","interactInd","coOcc","coAbund","siteEnv","traitSp","traitInd","phylo"))
+})
+
+test_that("check data integrity", {
+
+  # Generate fake data for idObs
+  len <- 3
+  sites <- sample(paste("site",letters[1:3],sep="_"),len,replace=TRUE) # 3 sites
+  sp <- paste0("sp",sample(1:len,len,replace=TRUE)) # 3 species
+  ind <- 1:len # 3 individus
+  idObs <- data.frame(idSite=sites,idTime=rep(NA,len),idSp=sp, idInd=ind,stringsAsFactors=FALSE)
+
+  interactPair <-  data.frame(idTo=c("1","sp1"),idFrom=c("1","2"),strength=c(NA,NA),verbose=FALSE,stringsAsFactors=FALSE)
+  expect_error(as.alienData(idObs=idObs, interactPair=interactPair,verbose=FALSE),"'idTo' values belongs to 'idSp' and 'idInd' in 'idObs'. Interaction can't be at the species AND individual levels")
+
+  interactPair <-  data.frame(idTo=c("1","2"),idFrom=c("sp1","2"),strength=c(NA,NA),verbose=FALSE,stringsAsFactors=FALSE)
+  expect_error(as.alienData(idObs=idObs, interactPair=interactPair,verbose=FALSE),"'idFrom' values belongs to 'idSp' and 'idInd' in 'idObs'. Interaction can't be at the species AND individual levels")
+
+  interactPair <- data.frame(idTo="sp4",idFrom="sp1",strength=NA,stringsAsFactors=FALSE)
+  expect_error(as.alienData(idObs=idObs, interactPair=interactPair,verbose=FALSE),"Some species ids in 'idTo' are not in 'idObs'")
+
+  interactPair <-  data.frame(idTo="4",idFrom="1",strength=NA,stringsAsFactors=FALSE)
+  expect_error(as.alienData(idObs=idObs, interactPair=interactPair,verbose=FALSE),"Some individus ids in 'idTo' are not in 'idObs'")
+
+  interactPair <- data.frame(idTo="sp1",idFrom="sp4",strength=NA,stringsAsFactors=FALSE)
+  expect_error(as.alienData(idObs=idObs, interactPair=interactPair,verbose=FALSE),"Some species ids in 'idFrom' are not in 'idObs'")
+
+  interactPair <-  data.frame(idTo="1",idFrom="4",strength=NA,stringsAsFactors=FALSE)
+  expect_error(as.alienData(idObs=idObs, interactPair=interactPair,verbose=FALSE),"Some individus ids in 'idFrom' are not in 'idObs'")
+
+  interactPair <-  data.frame(idTo=c("2","2","3"),idFrom=c("2","2","2"),strength=c(NA,NA,NA),verbose=FALSE,stringsAsFactors=FALSE)
+  expect_error(as.alienData(idObs=idObs, interactPair=interactPair,verbose=FALSE),"Some 'idFrom' and 'idTo' are duplicated")
+
+})