Nothing
## ----setup, include=FALSE------------------------------------------------
knitr::opts_chunk$set(echo = TRUE, message = FALSE, warning = FALSE, eval = FALSE)
## ------------------------------------------------------------------------
# require(tidyverse)
# # county level data of fertilizer application.
# #Source: https://www.sciencebase.gov/catalog/item/5851b2d1e4b0f99207c4f238
# raw_data = read_csv("../data-raw/CNTY_FERT_1987-2012.csv")
# #summary(raw_data)
#
# # County summary from US census bureau.
# # Source: https://www.census.gov/geo/maps-data/data/gazetteer2010.html
# county_raw = read.table("../data-raw/Gaz_counties_national.txt", sep = "\t", header=TRUE)
#
# # read in data, extracted from coverage in ArcGIS.
# n45_64 <- read.table("../data-raw/cty_fert0.n45-64.txt", sep = ",", header = T)
# n65_85 <- read.table("../data-raw/cty_fert0.n65-85.txt", sep = ",", header = T)
# p45_64 <- read.table("../data-raw/cty_fert0.p45-64.txt", sep = ",", header = T)
# p65_85 <- read.table("../data-raw/cty_fert0.p65-85.txt", sep = ",", header = T)
# # merge nitrogen and P data together.
# n45_85 = inner_join(n45_64, n65_85, by = c("FIPS","STATE","Rowid_"))
# p45_85 = inner_join(p45_64, p65_85, by = c("FIPS","STATE","Rowid_"))
#
## ------------------------------------------------------------------------
# # clean nitroge and phosphorus data.
# nitrogen_1985 = n45_85 %>%
# select(-Rowid_) %>% # remove irrelavent info.
# # add leading zeros for FIPS to make it 5 digits.
# mutate(FIPS = str_pad(FIPS, 5, pad = "0")) %>%
# gather(Year_temp, Quantity, Y45:Y85) %>%
# mutate(Fertilizer = rep("N", length(.$Quantity)),
# Farm.Type = rep("farm", length(.$Quantity)),
# Year = paste("19",str_sub(Year_temp, start = 2),sep = "")
# ) %>%
# select(-Year_temp)
#
# phosphorus_1985 = p45_85 %>%
# select(-Rowid_) %>% # remove irrelavent info.
# mutate(FIPS = str_pad(FIPS, 5, pad = "0")) %>%
# gather(Year_temp, Quantity, Y45:Y85) %>%
# mutate(Fertilizer = rep("P", length(.$Quantity)),
# Farm.Type = rep("farm", length(.$Quantity)),
# Year = paste("19",str_sub(Year_temp, start = 2),sep = "")
# ) %>%
# select(-Year_temp)
# # clean dataset for data before 1985
# clean_data_1985 = rbind(phosphorus_1985, nitrogen_1985)
## ------------------------------------------------------------------------
# # remove duplicates in county data.
# county_data = county_raw %>%
# distinct(GEOID, .keep_all = TRUE) %>%
# # select certin columns.
# select(GEOID, ALAND, AWATER,INTPTLAT, INTPTLONG) %>%
# mutate(FIPSno = GEOID) %>%
# select(-GEOID)
#
# # combine county data with county level fertilizer data.
# county_summary = left_join(raw_data,county_data, by = "FIPSno")
#
# clean_data = county_summary %>%
# # remove some columns with FIPS numbers.
# select(-c(FIPS_st, FIPS_co,FIPSno)) %>%
# # wide to long dataset.
# gather(Fert.Type, Quantity, farmN1987:nonfP2012) %>%
# # separate the fert.type into three columns: farm type, fertilizer, year.
# mutate(Year = str_sub(Fert.Type, start = -4),
# Fertilizer = str_sub(Fert.Type, start = -5, end = -5),
# Farm.Type = str_sub(Fert.Type, start = 1, end = 4)
# ) %>%
# # repalce nonf into nonfarm
# mutate(Farm.Type = ifelse(Farm.Type == "nonf", "nonfarm", "farm")) %>%
# # remove Fert.Type
# select(-Fert.Type)
#
# # extract county summaries info from clean data.
# cnty_summary_1985 = county_summary %>%
# select(FIPS,State, County, ALAND, AWATER, INTPTLAT, INTPTLONG) %>%
# right_join(clean_data_1985, by = "FIPS")
#
# # add data from 1945.
# clean_data = rbind(clean_data, cnty_summary_1985) %>%
# rename(Nutrient = Fertilizer) %>% # renam Fertilizer to nutrient.
# mutate(Input.Type = rep("Fertilizer")) # add a colume as fertilizer, compared with Manure.
## ------------------------------------------------------------------------
# # read in manure data from 1982 to 1997.
# cnty_manure_97 = read_csv("../data-raw/cnty_manure_82-97.csv")
# cnty_manure_summary = cnty_manure_97 %>%
# select(-c(State, County)) %>%
# gather(dummy, Quantity, N_1982:P_1997) %>% # dummy is a temporay column.
# mutate(Farm.Type = rep("farm", length(.$FIPS)),
# Input.Type = rep("Manure", length(.$FIPS))) %>%
# separate(dummy, c("Nutrient", "Year"), sep = "_")
## ------------------------------------------------------------------------
# # read in manure data.
# cnty_manure_02 = read_csv("../data-raw/cnty_manure_2002.csv")
# cnty_manure_07 = read_csv("../data-raw/cnty_manure_2007.csv")
# cnty_manure_12 = read_csv("../data-raw/cnty_manure_2012.csv")
#
# cnty_manure_02_12 = rbind(cnty_manure_02, cnty_manure_07, cnty_manure_12) %>%
# select(-c(State, County)) %>%
# gather(Nutrient, Quantity, N:P) %>%
# mutate(Farm.Type = rep("farm", length(.$FIPS)),
# Input.Type = rep("Manure", length(.$FIPS)))
## ----sava_data, eval=FALSE-----------------------------------------------
#
# # connect manure data.
# cnty_manure_summary = rbind(cnty_manure_summary,cnty_manure_02_12)
#
# cnty_manure_all = county_summary %>%
# select(FIPS,State, County, ALAND, AWATER, INTPTLAT, INTPTLONG) %>%
# right_join(cnty_manure_summary, by = "FIPS")
#
# clean_data = rbind(clean_data, cnty_manure_all)
#
# # NOT RUN
# # save cleaned data into .rda format.
# save(clean_data, file = "../data/usfertilizer_county.rda")
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