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Merge pull request #92 from lawinslow/master
Code for dataset RC1
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,68 @@ | ||
| #' @title Summary stats for Notaro | ||
| #' | ||
| #' @param nc.file path to nc file | ||
| #' | ||
| #' @return data.frame with summary statistics | ||
| #' | ||
| #' | ||
| #' @import tidyr | ||
| #' @import lubridate | ||
| #' | ||
| #' @export | ||
| summarize_notaro = function(nc.file){ | ||
| library(glmtools) | ||
| exclude.vars <- c("extc_coef", "salt", "precip", "wind") | ||
| var.names <- as.character(sim_vars(nc.file)$name) | ||
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| lake.data = lapply(var.names[!var.names %in% exclude.vars], function(x) summarize_var_notaro(nc.file, x)) | ||
| df.data <- data.frame() | ||
| for (i in 1:length(lake.data)){ | ||
| df.data <- rbind(df.data, lake.data[[i]]) | ||
| } | ||
| return(df.data) | ||
| } | ||
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| # for the 1D vars, get depths and summarize, for annual scale | ||
| summarize_var_notaro <- function(nc.file, var.name){ | ||
| library(dplyr) | ||
| library(tidyr) | ||
| library(lubridate) | ||
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| unit <- sim_var_units(nc.file, var.name) | ||
| is.1D <- glmtools:::.is_heatmap(nc.file, var.name) | ||
| value.name <- sprintf('%s%s', var.name, ifelse(unit=='', '',paste0(' (',unit,')'))) | ||
| if (is.1D){ | ||
| rename_depths <- function(depths){ | ||
| unlist(lapply(strsplit(depths, '[_]'), function(x) sprintf('%s_%s', round(eval(parse(text=head(tail(x,2),1))), digits = 2), tail(x,1)))) | ||
| } | ||
| get_depth <- function(names){ | ||
| as.numeric(unname(unlist(sapply(names, function(x) strsplit(x,'[_]')[[1]][1])))) | ||
| } | ||
| get_stat <- function(names){ | ||
| unname(unlist(sapply(names, function(x) strsplit(x,'[_]')[[1]][2]))) | ||
| } | ||
| var <- get_var(nc.file, var.name, reference='surface') %>% | ||
| mutate(base.date=as.POSIXct(paste0(lubridate::year(DateTime),'-01-01')), tz='UTC') %>% | ||
| mutate(doy=as.numeric(DateTime-base.date)/86400+1) %>% | ||
| select(-DateTime, -tz, -base.date) %>% select(doy, everything()) %>% group_by(doy) %>% | ||
| summarize_each(c('mean','sd')) %>% | ||
| setNames(c('doy',rename_depths(names(.)[-1L]))) %>% gather(key = doy) %>% | ||
| setNames(c('doy','depth_stat','value')) %>% | ||
| mutate(depth=get_depth(depth_stat), statistic=get_stat(depth_stat), variable=value.name) %>% | ||
| select(doy, depth, statistic, value, variable) %>% | ||
| filter(doy < 366) | ||
| } else { | ||
| var <- get_var(nc.file, var.name)%>% | ||
| mutate(base.date=as.POSIXct(paste0(lubridate::year(DateTime),'-01-01')), tz='UTC') %>% | ||
| mutate(doy=as.numeric(DateTime-base.date)/86400+1) %>% select_('doy', var.name) %>% group_by(doy) %>% | ||
| summarize_each(c('mean','sd')) %>% gather(key = doy) %>% | ||
| setNames(c('doy','statistic','value')) %>% | ||
| mutate(depth=NA, variable=value.name) %>% | ||
| select(doy, depth, statistic, value, variable) %>% | ||
| filter(doy < 366) | ||
| } | ||
|
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| return(var) | ||
| } | ||
|
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