Fix to properly import stats and permute packages.

These have been added in ROxygen importFrom statements, and the NAMESPACE was rebuilt.  Closes issue #69.

NAMESPACE

@@ -10,3 +10,10 @@ export(rate_change_interval)
 export(synchrony)
 export(turnover)
 export(variance_ratio)
+importFrom(permute,shuffleSeries)
+importFrom(stats,aggregate)
+importFrom(stats,as.formula)
+importFrom(stats,coef)
+importFrom(stats,confint)
+importFrom(stats,sd)
+importFrom(stats,var)

R/community_stability.R

@@ -25,6 +25,7 @@
 #'                      time.var = "year", 
 #'                      abundance.var = "abundance",
 #'                      replicate.var = "subplot") # across all subplots
+#' @importFrom stats aggregate as.formula sd
 #' @export
 
 community_stability <- function(df, time.var,

R/rate_change.R

@@ -41,6 +41,7 @@
 #'              species.var = "species",
 #'              abundance.var = "abundance",
 #'              replicate.var = "subplot") # across all subplots
+#' @importFrom stats coef
 #' @export
 rate_change <- function(df, time.var, 
                         species.var, 

R/synchrony.R

@@ -46,6 +46,7 @@
 #'              replicate.var = "subplot", 
 #'              metric="Gross") # With Gross et al. (2014) metric.
 #' }
+#' @importFrom stats aggregate as.formula sd
 #' @export
 synchrony <- function(df, time.var, 
                       species.var, 

R/temporal_torus_translation.R

@@ -28,6 +28,7 @@
 #' Hallett, Lauren M., Joanna S. Hsu, Elsa E. Cleland, Scott L. Collins, Timothy L. Dickson, Emily C. Farrer, Laureano A. Gherardi, et al. "Biotic Mechanisms of Community Stability Shift along a Precipitation Gradient." Ecology 95, no. 6 (2014): 1693-1700.
 #'
 #' Harms, Kyle E., Richard Condit, Stephen P. Hubbell, and Robin B. Foster. "Habitat Associations of Trees and Shrubs in a 50-Ha Neotropical Forest Plot." Journal of Ecology 89, no. 6 (2001): 947-59.
+#' @importFrom stats confint
 #' @export
 cyclic_shift <- function(df, time.var,
                          species.var,
@@ -148,6 +149,7 @@ confint.cyclic_shift <- function(object,
 #'
 #' @param comdat A community dataframe
 #' @return rand.comdat A randomized community dataframe
+#' @importFrom permute shuffleSeries
 shuffle_community <- function(comdat){
 
   # create empty matrix with same number of rows, columns as comdat

R/utilities.R

@@ -94,6 +94,7 @@ check_multispp <- function(df, species.var, replicate.var){
 
 #' Utility function to stop calculations if the species never change in a replicate
 #' @param comdat A community dataframe
+#' @importFrom stats var
 check_sppvar <- function(comdat){
   sppvar <- sum(apply(comdat, 2, var))
   if(sppvar == 0)

R/variance_ratio.R

@@ -52,6 +52,7 @@
 #'
 #'  Schluter, Dolph. (1984) "A Variance Test for Detecting Species Associations,
 #'  with Some Example Applications." Ecology 65, no. 3: 998-1005. doi:10.2307/1938071.
+#' @importFrom stats aggregate confint
 #' @export
 #' @examples
 #'  data(knz_001d)