Merge pull request #90 from lawinslow/master

mda.lakes cleanup

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: mda.lakes
 Type: Package
 Title: Tools for combining models, data, and processing for lakes
-Version: 3.0.4
+Version: 4.1.2
 Date: 2015-12-03
 Author: Luke Winslow, Jordan Read
 Maintainer: Luke Winslow <lwinslow@usgs.gov>
@@ -15,7 +15,8 @@ Imports:
     httr,
     rLakeAnalyzer (>= 1.5),
     insol,
-    plyr
+    plyr,
+    accelerometry
 Enhances: geoknife
 Description: More about what it does (maybe more than one line)
 License: LICENSE file

NAMESPACE

@@ -5,12 +5,10 @@ export(area_light_temp_threshold)
 export(area_light_threshold)
 export(area_temp_threshold)
 export(calc_mod_obs_metric)
+export(calc_stratified_periods)
 export(calc_toha)
 export(calc_toha_stats)
-export(chained.habitat.calc)
-export(chained.habitat.calc.kevin)
 export(comb_output_table)
-export(continuous.habitat.calc)
 export(create_irr_day_cycle)
 export(driver_add_burnin_years)
 export(driver_add_rain)
@@ -37,26 +35,20 @@ export(getZmean)
 export(get_driver_index)
 export(get_driver_path)
 export(get_ice_onoff)
-export(get_wtr_chained)
+export(hansen_habitat_calc)
 export(interp_hypso)
-export(load_gdp_file)
-export(met_check_download_gdp)
-export(met_drivers_start_gdp)
-export(met_from_hostetler)
-export(met_from_nldas)
+export(necsc_thermal_metrics_core)
 export(opti_thermal_habitat)
 export(populate_base_lake_nml)
-export(prep_run_chained_glm)
-export(prep_run_chained_glm_kd)
 export(prep_run_glm_kd)
 export(sens_seasonal_site)
 export(set_driver_url)
-export(write_error_log)
 import(GLMr)
 import(glmtools)
 import(lakeattributes)
+import(lubridate)
 import(rLakeAnalyzer)
-import(stringr)
+importFrom(accelerometry,rle2)
 importFrom(insol,JD)
 importFrom(insol,insolation)
 importFrom(insol,normalvector)

R/calc_stratified_periods.R

@@ -0,0 +1,49 @@
+#' @title Calculate all stratified periods based on temp threshold
+#' 
+#' @param surfT data.frame with two columns, datetime and surface temperature
+#' @param botT data.frame with two columns, datetime and bottom temperature (must be same nrow as surfT)
+#' @param temp_thresh Threshold to define stratified in deg C (default = 1)
+#' @param force_positive Is only warm stratified periods to be considered (drop winter when 0 is above 4 deg water, default TRUE)
+#' 
+#' @description 
+#' A function to calculate 
+#' 
+#' @importFrom accelerometry rle2
+#' 
+#' @export
+calc_stratified_periods = function(surfT, botT, temp_thresh = 1, force_positive = TRUE){
+
+
+	##assume they are data.frames to start
+	datetime = surfT[,1]
+	surfT = surfT[,2]
+	botT = botT[,2]
+
+
+	if(length(botT) != length(surfT)){
+		stop('botT and surfT must be the same length or number of rows')
+	}
+
+	t_diff = surfT - botT
+	if(force_positive){
+		t_diff[t_diff < 0] = 0 #force only warm stratification
+	}else{
+		t_diff = abs(t_diff) #use both warm and cold stratification
+	}
+
+
+	periods = rle2(as.numeric(t_diff >= temp_thresh), indices = TRUE)
+
+	strat_periods = as.data.frame(periods[periods[,'values'] == 1, ,drop=FALSE])
+	strat_periods$values = NULL
+
+	#if no strat periods were found, just return empty data.frame
+	if(nrow(strat_periods) == 0){
+		return(strat_periods)
+	}
+
+	strat_periods$onset = datetime[strat_periods$starts]
+	strat_periods$breakdown = datetime[strat_periods$stops]
+
+	return(strat_periods)
+}