merging with master

DESCRIPTION

@@ -1,4 +1,4 @@
-Package: alienR
+Package: alien
 Type: Package
 Title: Comparative analysis of interaction inference methods
 Version: 0.0.1
@@ -31,7 +31,7 @@ Imports:
 SystemRequirements: none, one or more of JAGS (>= 4.0.0; (http://mcmc-jags.sourceforge.net))
 NeedsCompilation: no
 License: MIT
-BugReports: https://github.com/TheoreticalEcosystemEcology/alienR/issues
+BugReports: https://github.com/TheoreticalEcosystemEcology/alien/issues
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 5.0.1

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

R/predNicheProb.R

@@ -13,7 +13,7 @@
 #' The next elements are as many predicted interaction as replicates.
 #'
 #' @note
-#' See more here: https://github.com/ibartomeus/trait_match
+#' See more here: \url{https://github.com/ibartomeus/trait_match}
 #'
 #' @author
 #' Dominique Gravel and Ignasi Bartomeus
@@ -35,5 +35,5 @@ predNicheProb <- function(pars, Tlevel1, Tlevel2, replicates = 100) {
     for (i in 1:replicates + 1) {
         out[[i]] <- rbinom(length(Tlevel1), size = 1, prob = pLM)
     }
-    out
+    return(out)
 }

README.md

@@ -3,7 +3,7 @@ Status
 
 **Early development** **Version**: 0.0.1
 
-[![Travis](https://travis-ci.org/TheoreticalEcosystemEcology/alienR.svg?branch=master)](https://travis-ci.org/TheoreticalEcosystemEcology/alienR) [![Build status](https://ci.appveyor.com/api/projects/status/sk3sbvusvcyy0at0?svg=true)](https://ci.appveyor.com/project/TheoreticalEcosystemEcology/alienR/build/1.0.7) [![codecov](https://codecov.io/gh/TheoreticalEcosystemEcology/alienR/branch/master/graphs/badge.svg)](https://codecov.io/gh/KevCaz/recruitR)
+[![Travis](https://travis-ci.org/TheoreticalEcosystemEcology/alienR.svg?branch=master)](https://travis-ci.org/TheoreticalEcosystemEcology/alienR) [![Build status](https://ci.appveyor.com/api/projects/status/sk3sbvusvcyy0at0?svg=true)](https://ci.appveyor.com/project/TheoreticalEcosystemEcology/alienR/build/1.0.7) [![codecov](https://codecov.io/gh/TheoreticalEcosystemEcology/alien/branch/master/graph/badge.svg)](https://codecov.io/gh/TheoreticalEcosystemEcology/alien)
 
 ALIEN: The aim of the package is to predict All Links In Ecological Networks
 ----------------------------------------------------------------------------
@@ -17,7 +17,7 @@ Incoming content
     -   binomial
     -   poisson
     -   RF
--   Indirect matching centrality (latent \~ traits) (DG)
+-   Indirect matching centrality (latent ~ traits) (DG)
 -   Niche binary (DG)
 -   Niche probabilistic (DG)
 -   iEat recommend (DB)
@@ -28,6 +28,9 @@ Incoming content
 -   4th corner (GB)
 -   Ben's magic (BW)
 -   Ives' phylo (GB)
+-   Permutation methods (GB)
+    -   C-scores
+    -   V-ratio
 
 **Deadline:** Package ready by Christmas
 
@@ -75,7 +78,7 @@ devtools::test()
 All of the previous steps can be done with:
 
 ``` bash
-cd path/to/alienR
+cd path/to/alien
 make
 ```
 
@@ -89,7 +92,7 @@ Contribute to this package
 -   `git fetch` / `git pull` before you do anything else
 -   new branches must be made from `master` -- if not, you are responsible for rebasing
 -   good commit messages are 72 chars on the first line and explain what has been done in the imperative tone. A good rule of thumb is that if you say "If merged, this commit will" before the commit message, it should be a sentence. A good commit message is: `add informations about development practices`. A bad commit message is `CONTRIBUTING changes`
--   if the branching complexity of your function is \> 3 (number of nested for / if / while), rewrite
+-   if the branching complexity of your function is > 3 (number of nested for / if / while), rewrite
 
 ### Styleguide
 
@@ -100,9 +103,9 @@ Contribute to this package
 -   all `roxygen2` flags (e.g. @param etc.) are to be set up.
 -   R extension file has to be written in capital letter (e.g `fitBayesReg.R`)
 
-Have a look at [<http://adv-r.had.co.nz/Style.html>](http://adv-r.had.co.nz/Style.html)
+Have a look at <http://adv-r.had.co.nz/Style.html>
 
-For further details on namespaces: [<http://r-pkgs.had.co.nz/namespace.html>](http://r-pkgs.had.co.nz/namespace.html)
+For further details on namespaces: <http://r-pkgs.had.co.nz/namespace.html>
 
 License
 -------

tests/Testthat.R

@@ -1,2 +1,2 @@
 library(testthat)
-test_check("alienR")
+test_check("alien")

tests/testthat/test-models.R

@@ -1,5 +1,6 @@
 context("Models")
 
+## 2B improved
 test_that("integrated model works", {
     out <- integratedModel(pars = c(1,1,1,1),
                             Tlevel1 = rnorm(10),
@@ -20,6 +21,7 @@ test_that("integrated model works", {
 #   expect_equal(TRUE, TRUE)#is.numeric(out))
 # })
 
+## 2B improved
 test_that("neutral model works", {
   out <- neutralModel(pars = NULL,
                           Tlevel1 = rnorm(10),
@@ -28,3 +30,11 @@ test_that("neutral model works", {
                           sd_Tlevel1 = 1)
   expect_equal(TRUE, is.numeric(out))
 })
+
+
+test_that("residuals computation for the niche model works", {
+  out <- residualsNicheProb(pars = c(1,1,1,1),
+                          Tlevel1 = rnorm(10),
+                          Tlevel2 = rnorm(10))
+  expect_equal(TRUE, is.numeric(out))
+})

vignettes/BayesTutorial.Rmd

@@ -6,16 +6,16 @@ output: html_document
 ---
 
 #Aim
-A short tutorial explaining the different options for fitting hierarchical bayesian models for species interactions using the package alienR
+A short tutorial explaining the different options for fitting hierarchical bayesian models for species interactions using the package alien
 
 ```{r}
-library(alienR)
+library(alien)
 library(ggplot2)
 library(knitr)
 opts_chunk$set(warning=F,message=F)
 
 #source scripts because I can't seem to understand how roxygen generates functions to the package! To delete once we understand how paths are handled in package creation
-s<-sapply(list.files("C:/Users/Ben/Documents/alienR/R",pattern=".R",full.names = T),source)
+s<-sapply(list.files("C:/Users/Ben/Documents/alien/R",pattern=".R",full.names = T),source)
 ```
 
 # Simulate data
@@ -68,7 +68,7 @@ ggplot(sumframe,aes(x=as.factor(I),y=J,fill=lower)) + geom_tile() + scale_fill_c
 If we want the distributions, instead of a summary we can plot the posterior predictions directly. For the sake of plotting, lets look at just one node.
 
 ```{r}
-justB<-predframe %>% filter(I=="b") 
+justB<-predframe %>% filter(I=="b")
 ggplot(data=justB,aes(x=J,y=value)) + geom_boxplot(fill="black") + labs(y="Probability of interaction") + ggtitle("For Species B in the higher level") + theme_bw()
 ```
 
@@ -107,7 +107,7 @@ ggplot(sumframe,aes(x=as.factor(I),y=J,fill=lower)) + geom_tile() + scale_fill_c
 Create the same boxplot as in the intercept model
 
 ```{r}
-justB<-predframe2 %>% filter(I=="b") 
+justB<-predframe2 %>% filter(I=="b")
 ggplot(data=justB,aes(x=J,y=value)) + geom_boxplot(fill="black") + labs(y="Probability of interaction") + ggtitle("For Species B in the higher level") + theme_bw()
 ```
 
@@ -135,4 +135,4 @@ allstats<-rbind_all(list(intercept_stats,binomial_stats))
 ggplot(allstats,aes(x=nstat)) + geom_density(alpha=0.6,aes(fill=Model)) + facet_wrap(~Metric,scales='free',nrow=1) + theme_bw()  + labs(x="value")
 ```
 
-Same data, different model, different network statistics! Models matter.
+Same data, different model, different network statistics! Models matter.