diff --git a/R/fimsframe.R b/R/fimsframe.R index 6d33dd97..9331344d 100644 --- a/R/fimsframe.R +++ b/R/fimsframe.R @@ -41,81 +41,163 @@ setClass( # is it problematic to set the generic for data? not sure... # but it will not work without set generic # can't call this data because there is already a generic + +#' Get the data to be used in the model +#' +#' @param x A FIMSFrame object containing all the data used in +#' the model. +#' @return +#' A dataframe of all data in the model. +#' @rdname get_data setGeneric("get_data", function(x) standardGeneric("get_data")) +#' @rdname get_data setMethod("get_data", "FIMSFrame", function(x) x@data) +#' @rdname get_data setMethod( "get_data", "data.frame", function(x) FIMSFrame(x)@data ) -# example: so we can call fleets(obj) instead of obj@fleets +#' Get the fleets to be used in the model +#' +#' @param x A FIMSFrame object containing fleets in the model. +#' @return +#' A vector of all fleets in the model. +#' @rdname fleets setGeneric("fleets", function(x) standardGeneric("fleets")) +#' @rdname fleets setMethod("fleets", "FIMSFrame", function(x) x@fleets) +#' @rdname fleets setMethod( "fleets", "data.frame", function(x) FIMSFrame(x)@fleets ) +#' Get the number of years to be used in the model +#' +#' @param x A FIMSFrame object containing the number of years. +#' @return +#' An integer value of the number of years in the model. +#' @rdname n_years setGeneric("n_years", function(x) standardGeneric("n_years")) +#' @rdname n_years setMethod("n_years", "FIMSFrame", function(x) x@n_years) +#' @rdname n_years setMethod( "n_years", "data.frame", function(x) FIMSFrame(x)@n_years ) +#' Get the first year used in the model +#' +#' @param x A FIMSFrame object containing the first year of the model. +#' @return +#' An integer value of the first year in the model. +#' @rdname start_year setGeneric("start_year", function(x) standardGeneric("start_year")) +#' @rdname start_year setMethod("start_year", "FIMSFrame", function(x) x@start_year) +#' @rdname start_year setMethod( "start_year", "data.frame", function(x) FIMSFrame(x)@start_year ) +#' Get the last year used in the model +#' +#' @param x A FIMSFrame object containing the last year of the model. +#' @return +#' An integer value of the last year in the model. +#' @rdname end_year setGeneric("end_year", function(x) standardGeneric("end_year")) +#' @rdname end_year setMethod("end_year", "FIMSFrame", function(x) x@end_year) +#' @rdname end_year setMethod( "end_year", "data.frame", function(x) FIMSFrame(x)@end_year ) +#' Get the ages used in the model +#' +#' @param x A FIMSFrame object containing the ages in the model. +#' @return +#' A vector of the ages in the model. +#' @rdname ages setGeneric("ages", function(x) standardGeneric("ages")) +#' @rdname ages setMethod("ages", "FIMSFrame", function(x) x@ages) +#' @rdname ages setMethod( "ages", "data.frame", function(x) FIMSFrame(x)@ages ) +#' Get the number of ages used in the model +#' +#' @param x A FIMSFrame object containing the ages in the model. +#' @return +#' An integer value of the number of ages in the model. +#' @rdname n_ages setGeneric("n_ages", function(x) standardGeneric("n_ages")) +#' @rdname n_ages setMethod("n_ages", "FIMSFrame", function(x) x@n_ages) +#' @rdname n_ages setMethod( "n_ages", "data.frame", function(x) FIMSFrame(x)@n_ages ) +#' Get the lengths used in the model +#' +#' @param x A FIMSFrame object containing the lengths in the model. +#' @return +#' A vector of the lengths in the model. +#' @rdname get_lengths setGeneric("get_lengths", function(x) standardGeneric("get_lengths")) +#' @rdname get_lengths setMethod("get_lengths", "FIMSFrame", function(x) x@lengths) +#' @rdname get_lengths setMethod( "get_lengths", "data.frame", function(x) FIMSFrame(x)@lengths ) +#' Get the number of lengths used in the model +#' +#' @param x A FIMSFrame object containing the lengths in the model. +#' @return +#' An integer value of the number of lengths in the model. +#' @rdname n_lengths setGeneric("n_lengths", function(x) standardGeneric("n_lengths")) +#' @rdname n_lengths setMethod("n_lengths", "FIMSFrame", function(x) x@n_lengths) +#' @rdname n_lengths setMethod( "n_lengths", "data.frame", function(x) FIMSFrame(x)@n_lengths ) +#' Get the weight at age data used in the model +#' +#' @param x A FIMSFrame object containing the weight at age data +#' in the model. +#' @return +#' A dataframe of weight at age data used in the model. +#' @rdname weight_at_age setGeneric("weight_at_age", function(x) standardGeneric("weight_at_age")) +#' @rdname weight_at_age setMethod("weight_at_age", "FIMSFrame", function(x) x@weight_at_age) +#' @rdname weight_at_age setMethod( "weight_at_age", "data.frame", @@ -128,7 +210,11 @@ setMethod( #' Get the weight at age data to be used in the model #' -#' @param x The object containing weight at age data. +#' @param x A FIMSFrame object containing weight at age data. +#' @return +#' A vector of weight at age data. The order of the vector is the order +#' the data frame was in before this function was called because it is just +#' extracting a column. #' @export #' @rdname m_weight_at_age setGeneric("m_weight_at_age", function(x) standardGeneric("m_weight_at_age")) @@ -155,14 +241,16 @@ setMethod("m_ages", "FIMSFrame", function(x) { #' Get the landings data to be used in the model #' -#' @param x The object containing landings. +#' @param x A FIMSFrame object containing landings. +#' @return +#' A vector of landings data. The order of the vector is the order +#' the data frame was in before this function was called because it is just +#' extracting a column. #' @export +#' @rdname m_landings setGeneric("m_landings", function(x) standardGeneric("m_landings")) - -#' Get the landings data to be used in the model -#' -#' @param x The FIMSFrame object containing landings. #' @export +#' @rdname m_landings setMethod( "m_landings", "FIMSFrame", function(x) { @@ -176,16 +264,19 @@ setMethod( #' Get the index data to be used in the model #' -#' @param x The object containing index. -#' @param fleet_name The name of the fleet for the index data. +#' @param x A FIMSFrame object containing index data. +#' @param fleet_name A string providing the name of the fleet for which you +#' want the index data. Technically, you can pass it a +#' vector of strings but it is more common to pass it a single string. +#' @return +#' A vector of index data. The order of the vector is the order +#' the data frame was in before this function was called because it is just +#' extracting a column. #' @export +#' @rdname m_index setGeneric("m_index", function(x, fleet_name) standardGeneric("m_index")) - -#' Get the index data to be used in the model -#' -#' @param x The FIMSFrame object containing index. -#' @param fleet_name The name of the fleet for the index data. #' @export +#' @rdname m_index setMethod( "m_index", "FIMSFrame", function(x, fleet_name) { @@ -201,17 +292,19 @@ setMethod( #' Get the age-composition data to be used in the model #' -#' @param x The object containing the age-composition data. -#' @param fleet_name The name of the fleet for the age-composition data. +#' @param x A FIMSFrame object containing age-composition data. +#' @param fleet_name A string providing the name of the fleet for which you +#' want the age-composition data. Technically, you can pass it a +#' vector of strings but it is more common to pass it a single string. +#' @return +#' A vector of age-composition data. The order of the vector is the order +#' the data frame was in before this function was called because it is just +#' extracting a column. #' @export +#' @rdname m_agecomp setGeneric("m_agecomp", function(x, fleet_name) standardGeneric("m_agecomp")) -# Should we add name as an argument here? - -#' Get the age-composition data data to be used in the model -#' -#' @param x The FIMSFrame containing age-composition data. -#' @param fleet_name The name of the fleet for the age-composition data. #' @export +#' @rdname m_agecomp setMethod( "m_agecomp", "FIMSFrame", function(x, fleet_name) {