Merge pull request #5 from nicholasjclark/development

Merging development to master for 1.0.3 release

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: MRFcov
 Type: Package
 Title: Markov Random Fields with additional covariates 
-Version: 1.0.2
-Date/Publication: 2018-01-08
+Version: 1.0.3
+Date/Publication: 2018-17-05
 URL: https://github.com/nicholasjclark/MRFcov
 Authors@R: c(
     person("Nicholas J", "Clark", email = "[email protected]", role = c("aut", "cre")),
@@ -13,7 +13,7 @@ Description: Approximate node interaction parameters of undirected Markov Random
     graphs. Models can incorporate additional covariates, allowing users to estimate
     how interactions between nodes in the graph are predicted to change across
     covariate gradients.
-Depends: R (>= 3.3.3), penalized
+Depends: R (>= 3.3.3), penalized, glmnet
 Imports: purrr,
     parallel,
     plyr,

NAMESPACE

@@ -4,16 +4,16 @@ export(MRFcov)
 export(bootstrap_MRF)
 export(comp_rosalia_MRF)
 export(countzero)
-export(cv_MRF)
 export(cv_MRF_diag)
-export(getMRF_adjacency_cont)
-export(getMRF_adjacency_factor)
+export(cv_MRF_diag_rep)
 export(plotMRF_hm)
 export(plotMRF_hm_cont)
 export(plotMRF_hm_factor)
 export(plotMRF_net_cont)
 export(predict_MRF)
+export(predict_MRFnetworks)
 export(prep_MRF_covariates)
+import(glmnet)
 import(penalized)
 importFrom(magrittr,"%>%")
 importFrom(parallel,clusterEvalQ)

R/Bird.parasites.R

@@ -14,5 +14,8 @@
 #'   \item{scale.prop.zos}{scaled numeric variable representing relative abundance
 #'   of \emph{Zosterops} host species}
 #' }
+#' @references Clark, N.J., Wells, K., Dimitrov, D. & Clegg, S.M. (2016)
+#' Co-infections and environmental conditions drive the distributions of blood
+#' parasites in wild birds. Journal of Animal Ecology, 85, 1461-1470.
 #' @source \url{http://dx.doi.org/10.5061/dryad.pp6k4}
 "Bird.parasites"

R/Dipping.survey.R

@@ -51,5 +51,7 @@
 #'   \item{dipping_round6}{model matrix variable for the factor \emph{dipping_round}, round 6. The
 #'   base contrast level for this variable is round 2}
 #' }
+#' @references Golding, N., Nunn, M.A. & Purse, B.V. (2015) Identifying biotic interactions
+#' which drive the spatial distribution of a mosquito community. Parasites & Vectors, 8, 367
 #' @source \url{https://doi.org/10.6084/m9.figshare.1420528.v1}
 "Dipping.survey"

R/comp_rosalia_MRF.R

@@ -11,8 +11,8 @@
 #'@param rosalia_mod A fitted \code{\link[rosalia]{rosalia}} model
 #'@return A \code{list} of two objects:
 #'\itemize{
-#'    \item \code{Positive_predictive_value}: The positive predictive value
-#'    \item \code{Negative_predictive_value}: The negative predictive value
+#'    \item \code{Positive_interactions}: The positive predictive value
+#'    \item \code{Negative_interactions}: The negative predictive value
 #'    }
 #'
 #'@seealso \code{\link{MRFcov}}, \code{\link[rosalia]{rosalia}}
@@ -46,6 +46,6 @@ pos.pred <- sum(true.pos, na.rm = TRUE)/
 
 neg.pred <- sum(true.neg, na.rm = TRUE)/
                 (sum(true.neg, na.rm = TRUE) + sum(missed.neg, na.rm = TRUE))
-return(list(Positive_predictive_value = pos.pred,
-            Negative_predictive_value = neg.pred))
+return(list(Positive_interactions = pos.pred,
+            Negative_interactions = neg.pred))
 }