Merge pull request #10 from SCCWRP/TT

Tt

Author: fawda123

DESCRIPTION

@@ -35,27 +35,19 @@ Authors@R: c(
     email = "VanSickle.John@epa.gov"
     )
   )
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.1
 Collate: 
     'ASCI.R'
     'STE.R'
     'allscr.R'
     'class-asci.R'
     'asci-methods.R'
     'chkinp.R'
-    'demo_algae_sitedata.R'
     'demo_algae_tax.R'
-    'diatom_rf_oe.R'
     'getids.R'
     'globalVariables.R'
-    'hybrid_rf_oe.R'
-    'oefun.R'
-    'oelkup.R'
-    'pmmi_calcmetrics.R'
-    'pmmifun.R'
-    'pmmilkup.R'
+    'mmi_calmetrics.R'
+    'mmifun.R'
+    'mmilkup.R'
     'rarify.R'
-    'rf_out_top.R'
-    'rfpred.r'
-    'sba_rf_oe.R'
-    'sitcat.R'
+    'score_metric.R'

NAMESPACE

@@ -1,26 +1,20 @@
 # Generated by roxygen2: do not edit by hand
 
 export(ASCI)
-export(Supp1_OE)
 export(Supp1_mmi)
-export(Supp2_OE)
 export(chkinp)
 export(getids)
-export(oefun)
-export(perf)
-export(pmmi_calcmetrics)
-export(pmmifun)
+export(mmi_calcmetrics)
+export(mmifun)
 export(rarify)
-export(rfpred)
+export(score_metric)
 export(scores)
 import(purrr)
-import(randomForest)
 import(tibble)
 importFrom(dplyr,arrange)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,filter)
 importFrom(dplyr,group_by)
-importFrom(dplyr,inner_join)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,rename)
@@ -43,7 +37,6 @@ importFrom(stats,sd)
 importFrom(stats,t.test)
 importFrom(stats,var)
 importFrom(tibble,enframe)
-importFrom(tibble,rownames_to_column)
 importFrom(tidyr,gather)
 importFrom(tidyr,nest)
 importFrom(tidyr,separate)

R/ASCI.R

@@ -1,16 +1,16 @@
 #' Score samples using the ASCI tool
 #'
 #' @param taxain \code{data.frame} for input taxonomy data
-#' @param sitein \code{data.frame} for input site data
 #' @param tax chr string indicating output to return from a specific taxa, must one to many of \code{'diatoms'}, \code{'sba'}, or \code{'hybrid'}, defaults to all
-#' @param ... additional arguments passed to other funcions, e.g., \code{\link{rfpred}}
+#' @param ... additional arguments passed to other funcions
 #' 
 #' @details 
-#' Two indices for three taxonomy types are scored, pMMI and O/E for diatoms, soft-bodied algae, and hybrid. This function combines output from the \code{\link{pmmifun}} and \code{\link{oefun}} functions in a user-friendly format.
+#' One index for three taxonomy types are scored, MMI for diatoms, soft-bodied algae, and hybrid. 
+#' This function outputs the reulsts of \code{\link{mmifun}} functions in a user-friendly format.
 #' 
 #' @return 
 #' A \code{\link{asci}} object with specific methods.  See the examples for accessing.
-#' 
+#'
 #' @export
 #' 
 #' @importFrom dplyr bind_rows mutate select
@@ -19,120 +19,55 @@
 #' @import purrr
 #' @import tibble
 #' 
-#' @seealso  \code{\link{pmmifun}}, \code{\link{oefun}}
+#' @seealso  \code{\link{mmifun}}
 #' 
 #' @examples 
-#' results <- ASCI(demo_algae_tax, demo_algae_sitedata)
+#' results <- ASCI(demo_algae_tax)
 #' scores(results)
 #' Supp1_mmi(results)
-#' Supp1_OE(results)
-#' Supp2_OE(results)
-ASCI <- function(taxain, sitein, tax = c('diatoms', 'sba', 'hybrid'), ...){
-  
-  ## sanity checks
+ASCI <- function(taxain, tax = c('diatoms', 'sba', 'hybrid'), ...){
 
   # check tax argument
   if(any(!tax %in% c('diatoms', 'sba', 'hybrid')))
     stop('tax must match diatoms, sba, and/or hybrid')
 
   # run all other checks, get output if passed
-  dat <- chkinp(taxain, sitein)
+  dat <- chkinp(taxain)
 
-  ##
-  # individual output
+  # mmi
+  mmind <- mmifun(dat, ...)
 
-  # oe
-  oeind <- oefun(dat$taxa, dat$site, ...)
-  
-  # pmmi
-  pmmind <- pmmifun(dat$taxa, dat$site, ...)
-    
   ##
   # main output (scores)
-
-  # oe
-  oescr <- oeind %>% 
-    map(function(x){
-      
-      x$OE_scores %>% 
-        select(SampleID, O, E, OoverE, OoverE_Percentile) %>% 
-        gather('met', 'val', -SampleID)
-      
-      }) %>% 
-    enframe('taxa') %>% 
-    unnest
-    
-  # pmmi
-  pmmiscr <- pmmind %>% 
+  mmiscr <- mmind %>% 
     map(~ .x$MMI_scores) %>% 
     map(gather, 'met', 'val', -SampleID) %>% 
     enframe('taxa') %>% 
-    unnest
-
-  # combine scrs, long format
-  scr <- bind_rows(oescr, pmmiscr) %>% 
-    spread(met, val) %>% 
-    select(taxa, SampleID, MMI, MMI_Percentile, O, E, OoverE, OoverE_Percentile)
+    unnest %>% 
+    spread(met, val)
 
   ##
   # supplementary info
-
-  # pmmi
-  Supp1_mmi <- pmmind %>% 
+  Supp1_mmi <- mmind %>% 
     map(~ .x$MMI_supp) %>% 
     map(gather, 'Metric', 'Value', -SampleID) %>% 
     enframe('taxa') %>% 
     unnest
 
-  # oe capture probs
-  Supp1_OE <- oeind %>% 
-    map(~ .x$Capture_Probs) %>% 
-    enframe('taxa') %>% 
-    unnest
-  
-  # oe group occurrence probs
-  Supp2_OE <- oeind %>% 
-    map(~ .x$Group_Occurrence_Probs) %>% 
-    map(gather, 'pGroup', 'Prob', -SampleID) %>% 
-    enframe('taxa') %>% 
-    unnest
-  
-  # oe null
-  null_OE <- oeind %>% 
-    map(function(x){
-      
-      x$OE_scores %>% 
-        select(SampleID, Onull, Enull, OoverE.null) %>% 
-        gather('met', 'val', -SampleID)
-      
-    }) %>% 
-    enframe('taxa') %>% 
-    unnest
-  
   # subset taxa if needed
   if(length(tax) < 3){
 
-    scr <- scr %>% 
+    mmiscr <- mmiscr %>% 
       filter(taxa %in% tax)
 
     Supp1_mmi <- Supp1_mmi %>% 
       filter(taxa %in% tax)
 
-    Supp1_OE <- Supp1_OE %>% 
-      filter(taxa %in% tax)
-    
-    Supp2_OE <- Supp2_OE %>% 
-      filter(taxa %in% tax)
-    
-    null_OE <- null_OE %>% 
-      filter(taxa %in% tax)
-    
   }
-    
+  
   ##
   # create asci class output
-  out <- asci(scores = scr, Supp1_mmi = Supp1_mmi, Supp1_OE = Supp1_OE, 
-             Supp2_OE = Supp2_OE, null_OE = null_OE, taxa = tax)
+  out <- asci(scores = mmiscr, Supp1_mmi = Supp1_mmi, taxa = tax)
 
   return(out)
 

R/STE.R

@@ -5,7 +5,7 @@
 #'  
 #' @format A \code{\link[base]{data.frame}} of taxonomic lookup data used for verifying species names in sample data, 4961 rows and five columns.
 #'
-#' @details The object is used internally in \code{\link{oefun}} and \code{\link{pmmifun}}.
+#' @details The object is used internally in \code{\link{mmifun}}.
 #' 
 #' @examples 
 #' data(STE)