updates updates updates

DESCRIPTION

@@ -11,13 +11,13 @@ Authors@R: c(
     person("Hayley", "Kaminski", ,"hayley.kaminski@des.qld.gov.au",
     role = "aut"))
 Description: Contains functions which can be used to calculate Pesticide Risk Metric 
-    values in aquatic envrionments from concentrations of multiple pesticides with known species sensitive 
+    values in aquatic environments from concentrations of multiple pesticides with known species sensitive 
     distributions (SSDs). Pesticides provided by this package have all be validated
     however if the user has their own pesticides with SSD values they can append them
     to the pesticide_info table to include them in estimates.
-License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
+License: GPL (>= 3)
 RoxygenNote: 7.3.1
 Imports: 
     dplyr,

R/Gamma_Formula.R

@@ -1,13 +1,13 @@
 #' Gamma CDF Equation Formula
 #'
 #' @param concentration The vector of concentration values for a selected pesticide,
-#'  that has a gamma shaped species sensitivity distribution,
+#'  that has a Gamma shaped species sensitivity distribution,
 #'  to run the equation on.
-#' @param shape_location The k/shape value for the gamma equation for the selected pesticide.
+#' @param shape_location The k/shape value for the Gamma equation for the selected pesticide.
 #' These can be found in the "pesticide_info" data frame provided in this package.
 #' If you are including other pesticides you will need to append them with their
 #'  respective distribution variables to the "pesticide_info" table.
-#' @param scale The scale/theta value for the gamma equation for the selected pesticide.
+#' @param scale The scale/theta value for the Gamma equation for the selected pesticide.
 #' These can be found in the "pesticide_info" data frame provided in this package.
 #' If you are including other pesticides you will need to append them with their
 #'  respective distribution variables to the "pesticide_info" table.

R/Log_Gumbel_Formula.R

@@ -1,13 +1,13 @@
 #' Log Gumbel CDF Equation Formula
 #'
 #' @param concentration The vector of concentration values for a selected pesticide,
-#' that has a log gumbel shaped species sensitivity distribution,
+#' that has a Log Gumbel shaped species sensitivity distribution,
 #' to run the equation on.
-#' @param shape_location The mu/location value for the log gumbel equation for the selected pesticide.
+#' @param shape_location The mu/location value for the Log Gumbel equation for the selected pesticide.
 #' These can be found in the "pesticide_info" data frame provided in this package.
 #' If you are including other pesticides you will need to append them with their
 #' respective distribution variables to the "pesticide_info" table.
-#' @param scale The beta/scale value for the log gumbel equation for the selected pesticide.
+#' @param scale The beta/scale value for the Log Gumbel equation for the selected pesticide.
 #' These can be found in the "pesticide_info" data frame provided in this package.
 #' If you are including other pesticides you will need to append them with their
 #' respective distribution variables to the "pesticide_info" table.

R/Log_Logistic_Formula.R

@@ -1,13 +1,13 @@
 #' Log Logistic Formula
 #'
 #' @param concentration The vector of concentration values for a selected pesticide,
-#' that has a log logistic shaped species sensitivity distribution,
+#' that has a Log Logistic shaped species sensitivity distribution,
 #' to run the equation on.
-#' @param scale The log logistic alpha/scale value for the selected pesticide.
+#' @param scale The Log Logistic alpha/scale value for the selected pesticide.
 #' These can be found in the "pesticide_info" data frame provided in this package.
 #' If you are including other pesticides you will need to append them with their
 #' respective distribution variables to the "pesticide_info" table.
-#' @param shape_location The log logistic beta/shape value for the selected pesticide.
+#' @param shape_location The Log Logistic beta/shape value for the selected pesticide.
 #' These can be found in the "pesticide_info" data frame provided in this package.
 #' If you are including other pesticides you will need to append them with their
 #' respective distribution variables to the "pesticide_info" table.

R/Log_Logistic_Log_Logistic_Formula.R

@@ -3,19 +3,19 @@
 #' @param concentration The vector of concentration values for a selected pesticide,
 #' that has a Log Logistic Log Logistic shaped species sensitivity distribution,
 #' to run the equation on.
-#' @param scale The alpha/scale value for the first log logistic equation for the selected pesticide.
+#' @param scale The alpha/scale value for the first Log Logistic equation for the selected pesticide.
 #' These can be found in the "pesticide_info" data frame provided in this package.
 #' If you are including other pesticides you will need to append them with their
 #' respective distribution variables to the "pesticide_info" table.
-#' @param shape_location The beta/shape value for the first log logistic equation for the selected pesticide.
+#' @param shape_location The beta/shape value for the first Log Logistic equation for the selected pesticide.
 #' These can be found in the "pesticide_info" data frame provided in this package.
 #' If you are including other pesticides you will need to append them with their
 #' respective distribution variables to the "pesticide_info" table.
-#' @param scale_2 The alpha/scale value for the second log logistic equation for the selected pesticide.
+#' @param scale_2 The alpha/scale value for the second Log Logistic equation for the selected pesticide.
 #' These can be found in the "pesticide_info" data frame provided in this package.
 #' If you are including other pesticides you will need to append them with their
 #' respective distribution variables to the "pesticide_info" table.
-#' @param shape_location_2 The beta/shape value for the second log logistic equation for the selected pesticide.
+#' @param shape_location_2 The beta/shape value for the second Log Logistic equation for the selected pesticide.
 #' These can be found in the "pesticide_info" data frame provided in this package.
 #' If you are including other pesticides you will need to append them with their
 #' respective distribution variables to the "pesticide_info" table.

R/Log_Normal_Formula.R

@@ -1,13 +1,13 @@
 #' Log-Normal CDF Equation Formula
 #'
 #' @param concentration The vector of concentration values for a selected pesticide,
-#' that has a log normal shaped species sensitivity distribution,
+#' that has a Log Normal shaped species sensitivity distribution,
 #' to run the equation on.
-#' @param shape_location The mu/location value for the log normal equation for the selected pesticide.
+#' @param shape_location The mu/location value for the Log Normal equation for the selected pesticide.
 #' These can be found in the "pesticide_info" data frame provided in this package.
 #' If you are including other pesticides you will need to append them with their
 #' respective distribution variables to the "pesticide_info" table.
-#' @param scale The sigma/scale value for the log normal equation for the selected pesticide.
+#' @param scale The sigma/scale value for the Log Normal equation for the selected pesticide.
 #' These can be found in the "pesticide_info" data frame provided in this package.
 #' If you are including other pesticides you will need to append them with their
 #' respective distribution variables to the "pesticide_info" table.

R/Log_Normal_Log_Normal_Formula.R

@@ -1,21 +1,21 @@
 #' Log-Normal Log-Normal (double curve) CDF Equation Formula
 #'
 #' @param concentration The vector of concentration values for a selected pesticide,
-#' that has a log normal log normal species sensitivity distribution,
+#' that has a Log Normal Log Normal species sensitivity distribution,
 #' to run the equation on.
-#' @param shape_location The mu/shape value for the first log normal equation for the selected pesticide.
+#' @param shape_location The mu/shape value for the first Log Normal equation for the selected pesticide.
 #' These can be found in the "pesticide_info" data frame provided in this package.
 #' If you are including other pesticides you will need to append them with their
 #' respective distribution variables to the "pesticide_info" table.
-#' @param scale The sigma/scale value for the first log normal equation for the selected pesticide.
+#' @param scale The sigma/scale value for the first Log Normal equation for the selected pesticide.
 #' These can be found in the "pesticide_info" data frame provided in this package.
 #' If you are including other pesticides you will need to append them with their
 #' respective distribution variables to the "pesticide_info" table.
-#' @param shape_location_2 The mu/shape value for the second log normal equation for the selected pesticide.
+#' @param shape_location_2 The mu/shape value for the second Log Normal equation for the selected pesticide.
 #' These can be found in the "pesticide_info" data frame provided in this package.
 #' If you are including other pesticides you will need to append them with their
 #'  respective distribution variables to the "pesticide_info" table.
-#' @param scale_2 The sigma/scale value for the second log normal equation for the selected pesticide.
+#' @param scale_2 The sigma/scale value for the second Log Normal equation for the selected pesticide.
 #' These can be found in the "pesticide_info" data frame provided in this package.
 #' If you are including other pesticides you will need to append them with their
 #' respective distribution variables to the "pesticide_info" table.

R/add_your_own_pesticide.R

@@ -11,7 +11,7 @@
 #' @param scales A vector of scale values (if applicable, else put NA)
 #' @param scale_2s A vector of secondary scale values (if applicable, else put NA)
 #' @param weights A vector of weight values (if applicable, else put NA)
-#' @param pesticide_info A dataset to add pesticides too
+#' @param pesticide_info A data set to add pesticides too
 #'
 #' @return A data frame
 #' @export

README.Rmd

@@ -18,7 +18,7 @@ knitr::opts_chunk$set(
 <!-- badges: start -->
 <!-- badges: end -->
 
-This package provides code for estimating combined toxicity of measured pesticides using their Species Sensitivity Distributions (SSDs) in a multi-substance potentially affected fraction approach. The resulting value is a estimate of the percentage of species impacted by the measured pesticides, a value which is referred to in this package as the **Pesticide Risk Metric (PRM)**. This is based on the the Queensland Department of Environment and Science Water Quality & Investigation's [method](https://www.publications.qld.gov.au/dataset/method-development-pesticide-risk-metric-baseline-condition-of-waterways-to-gbr/resource/c65858f9-d7ba-4aef-aa4f-e148f950220f) used in the Reef 2050 Water Quality Improvement Plan, with the main difference being the ability to add different pesticides to be measured provided they have one of the following SSD distributions:
+This package provides code for estimating the combined toxicity of measured pesticides using their Species Sensitivity Distributions (SSDs) in a multi-substance, potentially affected fraction approach. The resulting value is an estimate of the percentage of species impacted by the measured pesticides; a value which is referred to in this package as the **Pesticide Risk Metric (PRM)**. This is based on the Queensland Department of Environment and Science Water Quality & Investigation's [method](https://www.publications.qld.gov.au/dataset/method-development-pesticide-risk-metric-baseline-condition-of-waterways-to-gbr/resource/c65858f9-d7ba-4aef-aa4f-e148f950220f) used in the Reef 2050 Water Quality Improvement Plan. The main difference is the ability to add different pesticides to be measured provided they have one of the following SSD distributions:
 
 * Burr_Type_III
 * Gamma

README.md

@@ -6,16 +6,16 @@
 <!-- badges: start -->
 <!-- badges: end -->
 
-This package provides code for estimating combined toxicity of measured
-pesticides using their Species Sensitivity Distributions (SSDs) in a
-multi-substance potentially affected fraction approach. The resulting
-value is a estimate of the percentage of species impacted by the
-measured pesticides, a value which is referred to in this package as the
-**Pesticide Risk Metric (PRM)**. This is based on the the Queensland
+This package provides code for estimating the combined toxicity of
+measured pesticides using their Species Sensitivity Distributions (SSDs)
+in a multi-substance, potentially affected fraction approach. The
+resulting value is an estimate of the percentage of species impacted by
+the measured pesticides; a value which is referred to in this package as
+the **Pesticide Risk Metric (PRM)**. This is based on the Queensland
 Department of Environment and Science Water Quality & Investigation’s
 [method](https://www.publications.qld.gov.au/dataset/method-development-pesticide-risk-metric-baseline-condition-of-waterways-to-gbr/resource/c65858f9-d7ba-4aef-aa4f-e148f950220f)
-used in the Reef 2050 Water Quality Improvement Plan, with the main
-difference being the ability to add different pesticides to be measured
+used in the Reef 2050 Water Quality Improvement Plan. The main
+difference is the ability to add different pesticides to be measured
 provided they have one of the following SSD distributions:
 
 - Burr_Type_III
@@ -119,11 +119,11 @@ head(Canto_wet_season_Total_PRM)
 #> # A tibble: 6 × 3
 #>   `Site Name`    `Sampling Year` `Total PRM`
 #>   <chr>          <chr>                 <dbl>
-#> 1 Celestial City 2017-2018             21.1 
-#> 2 Mt Lunar       2017-2018              5.97
+#> 1 Celestial City 2017-2018             21.0 
+#> 2 Mt Lunar       2017-2018              5.98
 #> 3 Violet Town    2017-2018             37.5 
-#> 4 Celestial City 2018-2019             16.8 
-#> 5 Mt Lunar       2018-2019              3.92
+#> 4 Celestial City 2018-2019             16.9 
+#> 5 Mt Lunar       2018-2019              3.94
 #> 6 Violet Town    2018-2019             31.2
 ```
 

data-raw/Canto_pesticides.R

@@ -1,4 +1,4 @@
-## code to prepare `Canto_pesticides` dataset goes here
+## code to prepare `Canto_pesticides` data set goes here
 library(vroom)
 library(dplyr)
 

data-raw/pesticide_info.R

@@ -1,4 +1,4 @@
-## code to prepare `pesticide_Info` dataset goes here
+## code to prepare `pesticide_Info` data set goes here
 pesticide_info <- read.csv("~/GitHub/pesticide_info_OG22.csv")
 pesticide_info <- pesticide_info %>% select(-1)
 #usethis::use_data(pesticide_info, overwrite = TRUE)