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OlooOloo
Oloo
authored and
Oloo
committed
clean up and build
1 parent 47a1068 commit 8579d48

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Lines changed: 191 additions & 176 deletions

‎DESCRIPTION‎

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Package: cleaned
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Title: Comprehensive Livestock Environmental Assessment for Improved Nutrition, a Secured Environment, and Sustainable Development along Livestock and Fish Value Chains
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Version: 0.4.0
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Date: 2022-01-19
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Version: 0.5.0
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Date: 2023-08-09
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Authors@R: c(person("Stephen", "Oloo",
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email = "oloostephen08@gmail.com",
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role = c("aut", "cre"),
@@ -42,5 +42,5 @@ Suggests:
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testthat,
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spelling
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Language: en-US
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RoxygenNote: 7.1.2
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RoxygenNote: 7.2.3
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VignetteBuilder: knitr

‎R/biomass_calculation.R‎

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#'
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#' @description It computes biomass.
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#'
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#' @param para A JSON file
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#' @param para A JSON file containing user inputs
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#'
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#' @param land_required A dataframe computed using the `land_requirement` function
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#' @param land_required A list computed using the `land_requirement` function
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#'
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#' @return dataframe
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#'

‎R/differences.R‎

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#'
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#' @examples
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#' \dontrun{
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#' data(mufindi)
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#' data(para)
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#' data(ghg_para)
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#' feed_basket_quality <- feed_quality(mufindi)
18-
#' energy_required <- energy_requirement(mufindi,feed_basket_quality)
19-
#' land_required <- land_requirement(feed_basket_quality, energy_required, mufindi)
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#' soil_erosion <- soil_health(mufindi, land_required)
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#' water_required <- water_requirement(mufindi,land_required)
22-
#' nitrogen_balance <- n_balance(mufindi, land_required, soil_erosion)
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#' livestock_productivity <- land_productivity(mufindi)
24-
#' biomass <- biomass_calculation(mufindi, land_required)
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#' feed_basket_quality <- feed_quality(para)
18+
#' energy_required <- energy_requirement(para,feed_basket_quality)
19+
#' land_required <- land_requirement(feed_basket_quality, energy_required, para)
20+
#' soil_erosion <- soil_health(para, land_required)
21+
#' water_required <- water_requirement(para,land_required)
22+
#' nitrogen_balance <- n_balance(para, land_required, soil_erosion)
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#' livestock_productivity <- land_productivity(para)
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#' biomass <- biomass_calculation(para, land_required)
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#' soil_carbon <- soil_organic_carbon(para, land_required, biomass)
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#' ghg_emissions <- ghg_emission(mufindi,energy_required,ghg_para,land_required,nitrogen_balance)
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#' combineOutputs(feed_basket_quality,energy_required,land_required,soil_erosion,water_required,
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#' nitrogen_balance,livestock_productivity,biomass,soil_carbon,ghg_emissions)
29-
#' calculate_differences(...)
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#' ghg_emissions <- ghg_emission(para,energy_required,ghg_para,land_required,nitrogen_balance)
27+
#' combineOutputs(para,feed_basket_quality,energy_required,land_required,soil_erosion,water_required,
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#' nitrogen_balance,livestock_productivity,biomass,soil_carbon,ghg_emissions,filePath)
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#' calculate_differences(outFile,...)
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#' }
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#'
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#' @export
@@ -142,6 +142,7 @@ calculate_differences <- function(outFile,...){
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erosion_t_soil_per_kg_protein,
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ghg_emission_t_co2_eq_per_year,
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ghg_emission_t_co2_eq_per_ha_per_year,
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ghg_emission_t_co2_eq_per_kg_fpcm,
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ghg_emission_t_co2_eq_per_kg_meat,
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ghg_emission_t_co2_eq_per_kg_protein,
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percent_precipitation_used_for_feed_production,

‎R/energy_requirement.R‎

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#' @description It calculates energy requirement. Compute this after
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#' the `feed_quality` function
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#'
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#' @param para A JSON file
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#' @param para A JSON file containing user inputs
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#'
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#' @param feed_basket_quality A dataframe computed using the `feed_quality` function
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#'

‎R/feed_quality.R‎

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#'
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#' @description It computes feed quality
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#'
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#' @param para A list
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#' @param para A JSON file containing user inputs
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#'
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#' @importFrom dplyr mutate_at bind_rows
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#'

‎R/ghg_emission.R‎

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#'
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#' @description It computes greenhouse gas emissions.
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#'
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#' @param para A JSON file
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#' @param para A JSON file containing user inputs
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#'
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#' @param ghg_ipcc_data A JSON file
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#' @param ghg_ipcc_data A JSON file containing IpCC coeficients
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#'
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#' @param land_required A dataframe computed using the `land_requirement` function
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#' @param land_required A list computed using the `land_requirement` function
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#'
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#' @param energy_required A list computed using the `energy_required` function
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#'

‎R/land_requirement.R‎

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#'
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#' @description It compute land requirements
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#'
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#' @param para A JSON file
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#' @param para A JSON file containing user inputs
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#'
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#' @param feed_basket_quality A dataframe computed using the `feed_quality` function
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#'
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#' @param energy_required A list computed using the `energy_required` function
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#'
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#' @return dataframe
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#' @return list
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#'
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#' @importFrom dplyr summarise mutate filter left_join %>% mutate_if
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#'

‎R/merge_outputs.R‎

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#' @title JSON output
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#'
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#' @param para A JSON file containing user inputs
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#'
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#' @description It generates a JSON file of all CLEANED model computation.
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#'
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#' @param feed_basket_quality A dataframe computed using the `feed_quality` function
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#'
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#' @param soil_erosion A dataframe computed using the `soil_health` function
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#'
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#' @param land_required A dataframe computed using the `land_requirement` function
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#' @param land_required A list computed using the `land_requirement` function
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#'
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#' @param energy_required A list computed using the `energy_required` function
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#'
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#' @param water_required A dataframe computed using the `water_required` function
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#' @param water_required A list computed using the `water_required` function
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#'
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#' @param nitrogen_balance A dataframe computed using the `n_balance` function
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#'
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#'
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#' @param soil_carbon A dataframe computed using the `soil_organic_carbon` function
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#'
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#' @param ghg_emission A dataframe computed using the `n_balance` ghg_emission
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#' @param ghg_emission A list computed using the `n_balance` ghg_emission
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#'
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#' @param filePath A path to where the JSON is to be saved
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#'
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#' @return saved JSON file
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#'
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#' @importFrom jsonlite toJSON
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#'
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#' @examples
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#' \dontrun{
31-
#' data(mufindi)
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#' data(para)
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#' data(ghg_para)
33-
#' feed_basket_quality <- feed_quality(mufindi)
34-
#' energy_required <- energy_requirement(mufindi,feed_basket_quality)
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#' land_required <- land_requirement(feed_basket_quality, energy_required, mufindi)
36-
#' soil_erosion <- soil_health(mufindi, land_required)
37-
#' water_required <- water_requirement(mufindi,land_required)
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#' nitrogen_balance <- n_balance(mufindi, land_required, soil_erosion)
39-
#' livestock_productivity <- land_productivity(mufindi, energy_required)
40-
#' biomass <- biomass_calculation(mufindi, land_required)
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#' feed_basket_quality <- feed_quality(para)
38+
#' energy_required <- energy_requirement(para,feed_basket_quality)
39+
#' land_required <- land_requirement(feed_basket_quality, energy_required, para)
40+
#' soil_erosion <- soil_health(para, land_required)
41+
#' water_required <- water_requirement(para,land_required)
42+
#' nitrogen_balance <- n_balance(para, land_required, soil_erosion)
43+
#' livestock_productivity <- land_productivity(para, energy_required)
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#' biomass <- biomass_calculation(para, land_required)
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#' soil_carbon <- soil_organic_carbon(para, land_required, biomass)
42-
#' ghg_emission <- ghg_emission(mufindi,energy_required,ghg_para,land_required,nitrogen_balance)
43-
#' combineOutputs(feed_basket_quality,energy_required,land_required,soil_erosion,water_required,
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#' nitrogen_balance,livestock_productivity,biomass,soil_carbon,ghg_emission)
46+
#' ghg_emission <- ghg_emission(para,energy_required,ghg_para,land_required,nitrogen_balance)
47+
#' combineOutputs(para,feed_basket_quality,energy_required,land_required,soil_erosion,water_required,
48+
#' nitrogen_balance,livestock_productivity,biomass,soil_carbon,ghg_emission,filePath)
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#' }
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#'
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#' @export

‎R/nitrogen_balance.R‎

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#'
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#' @description It computes nitrogen balance
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#'
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#' @param para A JSON file
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#' @param para A JSON file containing user inputs
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#'
7-
#' @param land_required A dataframe computed using the `land_requirement` function
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#' @param land_required A list computed using the `land_requirement` function
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#'
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#' @param soil_erosion A dataframe computed using the `soil_health` function
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#'

‎R/plotting.R‎

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#'
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#' @description It plots all results
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#'
5-
#' @param scenarios_all A dataframe computed using the `differences` function
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#' @param outFile Path to the new comparison output json computed using the `differences` function
6+
#'
7+
#' @param oDir directory where the plots are to be saved
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#'
79
#' @importFrom dplyr %>%
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#'
911
#' @examples
1012
#' \dontrun{
1113
#' data(mufindi)
1214
#' data(ghg_para)
13-
#' feed_basket_quality <- feed_quality(mufindi)
14-
#' energy_required <- energy_requirement(mufindi,feed_basket_quality)
15-
#' land_required <- land_requirement(feed_basket_quality, energy_required, mufindi)
16-
#' soil_erosion <- soil_health(mufindi, land_required)
17-
#' water_required <- water_requirement(mufindi,land_required)
18-
#' nitrogen_balance <- n_balance(mufindi, land_required, soil_erosion)
19-
#' livestock_productivity <- land_productivity(mufindi)
20-
#' biomass <- biomass_calculation(mufindi, land_required)
15+
#' feed_basket_quality <- feed_quality(para)
16+
#' energy_required <- energy_requirement(para,feed_basket_quality)
17+
#' land_required <- land_requirement(feed_basket_quality, energy_required, para)
18+
#' soil_erosion <- soil_health(para, land_required)
19+
#' water_required <- water_requirement(para,land_required)
20+
#' nitrogen_balance <- n_balance(para, land_required, soil_erosion)
21+
#' livestock_productivity <- land_productivity(para)
22+
#' biomass <- biomass_calculation(para, land_required)
2123
#' soil_carbon <- soil_organic_carbon(para, land_required, biomass)
22-
#' ghg_emissions <- ghg_emission(mufindi,energy_required,ghg_para,land_required,nitrogen_balance)
23-
#' combineOutputs(feed_basket_quality,energy_required,land_required,soil_erosion,water_required,
24-
#' nitrogen_balance,livestock_productivity,economics,biomass,soil_carbon,ghg_emissions)
25-
#' calculate_differences(iDir)
26-
#' clean_plotting(outFile)
24+
#' ghg_emissions <- ghg_emission(para,energy_required,ghg_para,land_required,nitrogen_balance)
25+
#' combineOutputs(para,feed_basket_quality,energy_required,land_required,soil_erosion,water_required,
26+
#' nitrogen_balance,livestock_productivity,economics,biomass,soil_carbon,ghg_emissions,filePath)
27+
#' calculate_differences(outFile,...)
28+
#' clean_plotting(outFile,oDir)
2729
#' }
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#'
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#' @export
@@ -53,85 +55,87 @@ clean_plotting <- function(outFile,oDir){
5355
}else if(tt == "total_protein_produced_kg_per_year"){
5456
title = "Total protein (kg/yr)"
5557
}else if (tt == "total_tlu"){
56-
title = "Soil leaching (%)"
58+
title = "Tropical Livestock Unit"
5759
}else if (tt == "total_land_requirement_ha"){
58-
title = "Erosion (t soil/yr)"
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title = "Land required (ha/yr)"
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}else if (tt == "total_land_requirement_ha_per_kg_fpcm"){
60-
title = "Erosion (t soil/ha/yr)"
62+
title = "Land required (ha/kg FPCM)"
6163
}else if (tt == "total_land_requirement_ha_per_kg_meat"){
62-
title = "Erosion (kg soil/ kg FPCM)"
64+
title = "Land required (ha/kg meat)"
6365
}else if (tt == "total_land_requirement_ha_per_kg_protein"){
64-
title = "Land required (ha/yr)"
66+
title = "Land required (ha/kg protein)"
6567
}else if (tt == "total_land_requirement_ha_per_tlu"){
66-
title = "Land required (ha/MT FPCM)"
68+
title = "Land required (ha/TLU)"
6769
}else if (tt == "total_n_balance_kg_n_per_year"){
68-
title = "GHG (t CO2eq/ha)"
70+
title = "N balance (kg N/yr)"
6971
}else if (tt == "percent_area_mining"){
70-
title = "GHG (t CO2eq/ha/yr)"
72+
title = "Soil mining (%)"
7173
}else if (tt == "percent_area_leaching"){
72-
title = "GHG (CO2eq/kg milk)"
74+
title = "Soil leaching (%)"
7375
}else if (tt == "n_balance_kg_n_per_ha_per_year"){
74-
title = "GHG (CO2eq/kg meat)"
76+
title = "N balance (kg N/ha/yr)"
7577
}else if (tt == "n_balance_kg_n_per_kg_fpcm"){
76-
title = "GHG (CO2eq/kg protein)"
78+
title = "N balance (kg N/kg FPCM)"
7779
}else if (tt == "n_balance_kg_n_per_kg_meat"){
78-
title = "% Precipitation use for feed production"
80+
title = "N balance (kg N/kg meat)"
7981
}else if (tt == "n_balance_kg_n_per_kg_protein"){
80-
title = "Water (m3/yr)"
82+
title = "N balance (kg N/kg protein)"
8183
}else if (tt == "erosion_t_soil_year"){
82-
title = "Water (m3/ha)"
84+
title = "Erosion (t soil/yr)"
8385
}else if (tt == "erosion_t_soil_per_ha_per_year"){
84-
title = "Water (m3/kg FPCM)"
86+
title = "Erosion (t soil/ha/yr)"
8587
}else if (tt == "erosion_t_soil_per_kg_fpcm"){
86-
title = "Water (m3/kg meat)"
88+
title = "Erosion (t soil/kg FPCM)"
8789
}else if (tt == "erosion_t_soil_per_kg_meat"){
88-
title = "Water (m3/kg meat)"
90+
title = "Erosion (t soil/kg meat)"
8991
}else if (tt == "erosion_t_soil_per_kg_protein"){
90-
title = "Water (m3/kg meat)"
92+
title = "Erosion (t soil/kg protein)"
9193
}else if (tt == "ghg_emission_t_co2_eq_per_year"){
92-
title = "Water (m3/kg meat)"
94+
title = "GHG (t CO2eq/yr)"
9395
}else if (tt == "ghg_emission_t_co2_eq_per_ha_per_year"){
94-
title = "Water (m3/kg meat)"
96+
title = "GHG (t CO2eq/ha/yr)"
97+
}else if (tt == "ghg_emission_t_co2_eq_per_kg_fpcm"){
98+
title = "GHG (CO2eq/kg FPCM)"
9599
}else if (tt == "ghg_emission_t_co2_eq_per_kg_meat"){
96-
title = "Water (m3/kg meat)"
100+
title = "GHG (CO2eq/kg meat)"
97101
}else if (tt == "ghg_emission_t_co2_eq_per_kg_protein"){
98-
title = "Water (m3/kg meat)"
102+
title = "GHG (CO2eq/kg protein)"
99103
}else if (tt == "percent_precipitation_used_for_feed_production"){
100-
title = "Water (m3/kg meat)"
104+
title = "% Precipitation use for feed production"
101105
}else if (tt == "total_water_use_m3"){
102-
title = "Water (m3/kg meat)"
106+
title = "Water use (m3/yr)"
103107
}else if (tt == "total_water_use_m3_per_ha"){
104-
title = "Water (m3/kg meat)"
108+
title = "Water use (m3/ha)"
105109
}else if (tt == "total_water_use_m3_per_kg_fpcm"){
106-
title = "Water (m3/kg meat)"
110+
title = "Water use (m3/kg FPCM)"
107111
}else if (tt == "total_water_use_m3_per_kg_meat"){
108-
title = "Water (m3/kg meat)"
112+
title = "Water use (m3/kg meat)"
109113
}else if (tt == "total_water_use_m3_per_kg_protein"){
110-
title = "Water (m3/kg meat)"
114+
title = "Water (m3/kg protein)"
111115
}else if (tt == "carbon_stock_change_t_co2eq_per_year"){
112-
title = "Water (m3/kg meat)"
116+
title = "Carbon stock changes (t CO2eq/yr)"
113117
}else if (tt == "carbon_stock_change_t_co2eq_per_ha_per_year"){
114-
title = "Water (m3/kg meat)"
118+
title = "Carbon stock changes (t CO2eq/ha/yr)"
115119
}else if (tt == "carbon_stock_change_t_co2eq_per_fpcm"){
116-
title = "Water (m3/kg meat)"
120+
title = "Carbon stock changes (t CO2eq/kg FPCM)"
117121
}else if (tt == "carbon_stock_change_t_co2eq_per_meat"){
118-
title = "Water (m3/kg meat)"
122+
title = "Carbon stock changes (t CO2eq/kg meat)"
119123
}else if (tt == "carbon_stock_change_t_co2eq_per_protein"){
120-
title = "Water (m3/kg meat)"
124+
title = "Carbon stock changes (t CO2eq/kg protein)"
121125
}else if (tt == "total_milk_produced_energy_kcal_per_year"){
122-
title = "Water (m3/kg meat)"
126+
title = "Energy (kcal/kg FPCM)"
123127
}else if (tt == "total_meat_produced_energy_kcal_per_year"){
124-
title = "Water (m3/kg meat)"
128+
title = "Energy (kcal/kg meat)"
125129
}else if (tt == "total_milk_produced_ame_days_per_year"){
126-
title = "Water (m3/kg meat)"
130+
title = "AME (days/kg FPCM)"
127131
}else if (tt == "total_meat_produced_ame_days_per_year"){
128-
title = "Water (m3/kg meat)"
132+
title = "AME (days/kg meat)"
129133
}else if (tt == "total_carbon_balance_per_fpcm"){
130-
title = "Water (m3/kg meat)"
134+
title = "Carbon balance (t CO2eq/kg FPCM)"
131135
}else if (tt == "total_carbon_balance_per_meat"){
132-
title = "Water (m3/kg meat)"
136+
title = "Carbon balance (t CO2eq/kg meat)"
133137
}else if (tt == "total_carbon_balance_per_protein"){
134-
title = "Water (m3/kg protein)"
138+
title = "Carbon balance (t CO2eq/kg protein)"
135139
}else{
136140
NA
137141
}

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