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Merge pull request #85 from lawinslow/master
updating upstream
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,69 +1,69 @@ | ||
| #source("Libraries/GLM.functions.R") | ||
| #require(rGLM) | ||
| lyrDz <<- 0.25 | ||
| #year <- '2009' | ||
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| calc.strat.days <- function(WBIC,year,min.duration=30,mix.diff=1.0,all.days=1:365){ | ||
| # min.duration is in TIME UNITS | ||
| # mix diff is °C | ||
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| folder <- paste("../supporting files/10-06Final/WBIC_",WBIC,'/',sep='') | ||
| file <- paste('output',year,'.nc4',sep='') | ||
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| # does the file exist? | ||
| if (file %in% list.files(path = paste(folder))){ | ||
| cat('WBIC ');cat(WBIC); cat(' processing.') | ||
| GLMnc <- getGLMnc(file,folder=folder) | ||
| cat('.') | ||
| temp.surf <- getTempGLMnc(GLMnc,lyrDz,ref='surface',z.out=0) | ||
| temp.bot <- getTempGLMnc(GLMnc,lyrDz,ref='bottom',z.out=0) | ||
| nc_close(GLMnc) | ||
| is.strat <- (temp.surf[,2]-temp.bot[,2]>mix.diff) # is boolean vector | ||
| strat.DoY <- as.numeric(strftime(temp.surf[,1], format = "%j")) | ||
| # get rid of days that aren't stratified | ||
| strat.DoY <- strat.DoY[is.strat] | ||
| is.strat <- (all.days %in% strat.DoY) | ||
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| return(is.strat) | ||
| } else { | ||
| return(vector(length=length(all.days))) | ||
| } | ||
| } | ||
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| get.lakes <- function(year){ | ||
| # if doing more than a few years, this should be stripped for just one column and kept in memory (future) | ||
| dat<-read.delim('../supporting files/omg.huge.output.tsv',header = TRUE, sep = "\t") | ||
| # get rid of all rows that don't match the year | ||
| use.idx <- which(dat$year==year & !is.na(dat$dateOver8.9)) | ||
| dat <- dat[use.idx,] | ||
| lake.ids <- as.character(dat$lakeid) | ||
| return(lake.ids) | ||
| } | ||
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| call.lakes <- function(year){ | ||
| file.out <- paste("../supporting files/is.strat_",year,'.tsv',sep='') | ||
| lake.ids <- get.lakes(year=year) | ||
| num.lakes <- length(lake.ids) | ||
| all.days=1:365 | ||
| strat.count <- vector(length=length(all.days)) | ||
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| for (j in 1:num.lakes){ | ||
| WBIC = lake.ids[j] | ||
| strat.count <- calc.strat.days(WBIC,year,all.days=all.days)+strat.count | ||
| cat('.\n') | ||
| } | ||
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| write.out <- data.frame(DoY=all.days,strat.count=strat.count) | ||
| # need to name the columns | ||
| col.names <- names(write.out) | ||
| col.names <- c("DoY",paste("strat.count.",num.lakes,sep='')) | ||
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| names(write.out) <- col.names | ||
| write.table(x=write.out,file=file.out,sep='\t',col.names=TRUE,quote=FALSE,row.names = FALSE) | ||
| } | ||
| #call.lakes(1998) | ||
| #source("Libraries/GLM.functions.R") | ||
| #require(rGLM) | ||
| lyrDz <<- 0.25 | ||
| #year <- '2009' | ||
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|
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| calc.strat.days <- function(WBIC,year,min.duration=30,mix.diff=1.0,all.days=1:365){ | ||
| # min.duration is in TIME UNITS | ||
| # mix diff is °C | ||
|
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||
| folder <- paste("../supporting files/10-06Final/WBIC_",WBIC,'/',sep='') | ||
| file <- paste('output',year,'.nc4',sep='') | ||
|
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| # does the file exist? | ||
| if (file %in% list.files(path = paste(folder))){ | ||
| cat('WBIC ');cat(WBIC); cat(' processing.') | ||
| GLMnc <- getGLMnc(file,folder=folder) | ||
| cat('.') | ||
| temp.surf <- getTempGLMnc(GLMnc,lyrDz,ref='surface',z.out=0) | ||
| temp.bot <- getTempGLMnc(GLMnc,lyrDz,ref='bottom',z.out=0) | ||
| nc_close(GLMnc) | ||
| is.strat <- (temp.surf[,2]-temp.bot[,2]>mix.diff) # is boolean vector | ||
| strat.DoY <- as.numeric(strftime(temp.surf[,1], format = "%j")) | ||
| # get rid of days that aren't stratified | ||
| strat.DoY <- strat.DoY[is.strat] | ||
| is.strat <- (all.days %in% strat.DoY) | ||
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| return(is.strat) | ||
| } else { | ||
| return(vector(length=length(all.days))) | ||
| } | ||
| } | ||
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||
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| get.lakes <- function(year){ | ||
| # if doing more than a few years, this should be stripped for just one column and kept in memory (future) | ||
| dat<-read.delim('../supporting files/omg.huge.output.tsv',header = TRUE, sep = "\t") | ||
| # get rid of all rows that don't match the year | ||
| use.idx <- which(dat$year==year & !is.na(dat$dateOver8.9)) | ||
| dat <- dat[use.idx,] | ||
| lake.ids <- as.character(dat$lakeid) | ||
| return(lake.ids) | ||
| } | ||
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| call.lakes <- function(year){ | ||
| file.out <- paste("../supporting files/is.strat_",year,'.tsv',sep='') | ||
| lake.ids <- get.lakes(year=year) | ||
| num.lakes <- length(lake.ids) | ||
| all.days=1:365 | ||
| strat.count <- vector(length=length(all.days)) | ||
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| for (j in 1:num.lakes){ | ||
| WBIC = lake.ids[j] | ||
| strat.count <- calc.strat.days(WBIC,year,all.days=all.days)+strat.count | ||
| cat('.\n') | ||
| } | ||
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| write.out <- data.frame(DoY=all.days,strat.count=strat.count) | ||
| # need to name the columns | ||
| col.names <- names(write.out) | ||
| col.names <- c("DoY",paste("strat.count.",num.lakes,sep='')) | ||
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| names(write.out) <- col.names | ||
| write.table(x=write.out,file=file.out,sep='\t',col.names=TRUE,quote=FALSE,row.names = FALSE) | ||
| } | ||
| #call.lakes(1998) | ||
| #call.lakes(1996) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,47 @@ | ||
| #' @title Calculate limno metrics for lots of lakes | ||
| #' | ||
| #' @description | ||
| #' Calculte aggregate metrics from a data frame with modeled and observed data. | ||
| #' Metric options include all available rLakeAnalyzer metrics | ||
| #' | ||
| #' @seealso \code{\link[glmtools]{compare_to_field}} | ||
| #' | ||
| #' | ||
| #' | ||
| #' @export | ||
| calc_mod_obs_metric = function(mod_obs_df, metric){ | ||
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| #for each lake | ||
| uids = unique(mod_obs_df$site_id) | ||
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| all_out = data.frame() | ||
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| for(lid in uids){ | ||
| lake_data = subset(mod_obs_df, site_id == lid) | ||
| lake_data$site_id = NULL | ||
| bathy = getBathy(strsplit(lid, '_')[[1]][2]) | ||
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| lake_data = ddply(lake_data, 'DateTime', function(df){ | ||
| if(nrow(na.omit(df)) >= 5){ | ||
| return(na.omit(df)) | ||
| }else{ | ||
| return(data.frame()) | ||
| } | ||
| }) | ||
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| #run compare to field | ||
| calc_metric = glmtools:::.compare_to_field(lake_data, bthA=bathy$areas, bthD=bathy$depths, metric=metric, as_value=TRUE) | ||
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| if(nrow(calc_metric) > 0){ | ||
| calc_metric$site_id = lid | ||
| #merge metrics together | ||
| all_out = rbind(all_out, calc_metric) | ||
| } | ||
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| } | ||
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| #output | ||
| return(all_out) | ||
|
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| } |
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