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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,111 @@ | ||
| #==================================================================== | ||
| # plural class for a4aFitMCMC (used for model averaging) | ||
| #==================================================================== | ||
|
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| #' @rdname a4aFitMCMC-class | ||
| #' @aliases a4aFitMCMCs-class | ||
|
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| setClass("a4aFitMCMCs", | ||
| contains="a4aFitSAs" | ||
| ) | ||
|
|
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| setValidity("a4aFitMCMCs", | ||
| function(object) { | ||
| if(!all(sapply(object, is, 'a4aFitMCMC'))) { | ||
| "Components must be a4aFitMCMC" | ||
| } else { | ||
| TRUE | ||
| } | ||
| }) | ||
|
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||
|
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| #' @rdname a4aFitMCMC-class | ||
| #' @aliases a4aFitMCMCs a4aFitMCMCs-methods | ||
| setGeneric("a4aFitMCMCs", function(object, ...) standardGeneric("a4aFitMCMCs")) | ||
|
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||
| #' @rdname a4aFitMCMC-class | ||
| setMethod("a4aFitMCMCs", signature(object="list"), | ||
| function(object, ...) { | ||
| args <- list(...) | ||
|
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||
| # names in args, ... | ||
| if("names" %in% names(args)) { | ||
| names <- args[['names']] | ||
| } else { | ||
| # ... or in object, | ||
| if(!is.null(names(object))) { | ||
| names <- names(object) | ||
| # ... or in elements, ... | ||
| } else { | ||
| names <- unlist(lapply(object, name)) | ||
| # ... or 1:n | ||
| idx <- names == "NA" | names == "" | ||
| if(any(idx)) | ||
| names[idx] <- as.character(length(names))[idx] | ||
| } | ||
| } | ||
|
|
||
| # desc & lock | ||
| args <- c(list(Class="a4aFitMCMCs", .Data=object, names=names), | ||
| args[!names(args)%in%'names']) | ||
|
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||
| return( | ||
| do.call('new', args) | ||
| ) | ||
|
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| }) | ||
|
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| #' @rdname a4aFitMCMC-class | ||
| setMethod("a4aFitMCMCs", signature(object="a4aFitMCMC"), function(object, ...) { | ||
| lst <- c(object, list(...)) | ||
| a4aFitMCMCs(lst) | ||
| }) | ||
|
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||
| #' @rdname a4aFitMCMC-class | ||
| setMethod("a4aFitMCMCs", signature(object="missing"), | ||
| function(...) { | ||
| # empty | ||
| if(missing(...)){ | ||
| new("a4aFitMCMCs") | ||
| # or not | ||
| } else { | ||
| args <- list(...) | ||
| object <- args[!names(args)%in%c('names', 'desc', 'lock')] | ||
| args <- args[!names(args)%in%names(object)] | ||
| do.call('a4aFitMCMCs', c(list(object=object), args)) | ||
| } | ||
| } | ||
| ) | ||
|
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| #' @title Plot of metrics of multiple fits | ||
| #' @name plot metrics of multiple fits | ||
| #' @docType methods | ||
| #' @rdname plot-mmcfits | ||
| #' @aliases plot,a4aFitMCMCs, missing-method | ||
| #' @description Method to plot fitting statistics of multiple fits, useful to compare fits. | ||
| #' @param x an \code{a4aFitMCMCs} object with multiple fits | ||
| #' @param y ignored | ||
| #' @param ... additional argument list that might never be used | ||
| #' @return a \code{plot} with fitting statistics | ||
| #' @examples | ||
| #' data(ple4) | ||
| #' data(ple4.index) | ||
| #' qmods <- list(list(~s(age, k=6))) | ||
| #' fmods = list() | ||
| #' for(i in 1:6) { | ||
| #' fmods[[paste0(i)]] <- as.formula(paste0("~te(age, year, k = c(6,", i+14,"), bs = 'tp') + s(age, k = 6)")) | ||
| #' } | ||
| #' myFits <- FLa4a:::multisca(FLStocks(ple4), list(FLIndices(ple4.index)), fmodel = fmods, qmodel=qmods, fit="MCMC", mcmc=SCAMCMC()) | ||
| #' plot(myFits) | ||
|
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| setMethod("plot", c("a4aFitMCMCs", "missing"), function(x, y=missing, ...){ | ||
| args <- list() | ||
| par(mar=c(5, 4, 4, 4) + 0.1) | ||
| accrate = lapply(x,function(x) fitSumm(x)['accrate',]) | ||
| df <- data.frame(unlist(accrate)) | ||
| df$fit <- as.numeric(gsub("fit", "",names(accrate))) | ||
| names(df) <- c("accrate","fit") | ||
| plot(df$fit, df$accrate, type = "b", col = "blue", ylab = "accrate", xlab = "fit", main="Analysis of fit metrics", ylim=c(0.1,0.5)) | ||
| abline(h=0.3, col = "blue",lty = 2) | ||
| }) | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,120 @@ | ||
| #==================================================================== | ||
| # plural class for a4aFit (used for model averaging) | ||
| #==================================================================== | ||
|
|
||
| #' @rdname a4aFit-class | ||
| #' @aliases a4aFits-class | ||
|
|
||
| setClass("a4aFits", | ||
| contains="FLComps" | ||
| ) | ||
|
|
||
| setValidity("a4aFits", | ||
| function(object) { | ||
| if(!all(sapply(object, is, 'a4aFit'))) { | ||
| "Components must be a4aFit" | ||
| } else { | ||
| TRUE | ||
| } | ||
| }) | ||
|
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||
|
|
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| #' @rdname a4aFit-class | ||
| #' @aliases a4aFits a4aFits-methods | ||
| setGeneric("a4aFits", function(object, ...) standardGeneric("a4aFits")) | ||
|
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||
| #' @rdname a4aFit-class | ||
| setMethod("a4aFits", signature(object="list"), | ||
| function(object, ...) { | ||
| args <- list(...) | ||
|
|
||
| # names in args, ... | ||
| if("names" %in% names(args)) { | ||
| names <- args[['names']] | ||
| } else { | ||
| # ... or in object, | ||
| if(!is.null(names(object))) { | ||
| names <- names(object) | ||
| # ... or in elements, ... | ||
| } else { | ||
| names <- unlist(lapply(object, name)) | ||
| # ... or 1:n | ||
| idx <- names == "NA" | names == "" | ||
| if(any(idx)) | ||
| names[idx] <- as.character(length(names))[idx] | ||
| } | ||
| } | ||
|
|
||
| # desc & lock | ||
| args <- c(list(Class="a4aFits", .Data=object, names=names), | ||
| args[!names(args)%in%'names']) | ||
|
|
||
| return( | ||
| do.call('new', args) | ||
| ) | ||
|
|
||
| }) | ||
|
|
||
| #' @rdname a4aFit-class | ||
| setMethod("a4aFits", signature(object="a4aFit"), function(object, ...) { | ||
| lst <- c(object, list(...)) | ||
| a4aFits(lst) | ||
| }) | ||
|
|
||
| #' @rdname a4aFit-class | ||
| setMethod("a4aFits", signature(object="missing"), | ||
| function(...) { | ||
| # empty | ||
| if(missing(...)){ | ||
| new("a4aFits") | ||
| # or not | ||
| } else { | ||
| args <- list(...) | ||
| object <- args[!names(args)%in%c('names', 'desc', 'lock')] | ||
| args <- args[!names(args)%in%names(object)] | ||
| do.call('a4aFits', c(list(object=object), args)) | ||
| } | ||
| } | ||
| ) | ||
|
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||
|
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| #' @title Plot of metrics of multiple fits | ||
| #' @name plot metrics of multiple fits | ||
| #' @docType methods | ||
| #' @rdname plot-mfits | ||
| #' @aliases plot,a4aFits, missing-method | ||
| #' @description Method to plot fitting statistics of multiple fits, useful to compare fits. | ||
| #' @param x an \code{a4aFits} object with multiple fits | ||
| #' @param y ignored | ||
| #' @param ... additional argument list that might never be used | ||
| #' @return a \code{plot} with fitting statistics | ||
| #' @examples | ||
| #' data(ple4) | ||
| #' data(ple4.index) | ||
| #' qmods <- list(list(~s(age, k=6))) | ||
| #' fmods = list() | ||
| #' for(i in 1:6) { | ||
| #' fmods[[paste0(i)]] <- as.formula(paste0("~te(age, year, k = c(6,", i+14,"), bs = 'tp') + s(age, k = 6)")) | ||
| #' } | ||
| #' myFits <- FLa4a:::multisca(FLStocks(ple4), list(FLIndices(ple4.index)), fmodel = fmods, qmodel=qmods, fit="MP") | ||
| #' plot(myFits) | ||
|
|
||
| setMethod("plot", c("a4aFits", "missing"), function(x, y=missing, ...){ | ||
| args <- list() | ||
| par(mar=c(5, 4, 4, 4) + 0.1) | ||
| gcv = lapply(x,function(x) fitSumm(x)['gcv',]) | ||
| bic = lapply(x, function(x) BIC(x)) | ||
| df <- data.frame(unlist(gcv), unlist(bic)) | ||
| df$fit <- as.numeric(gsub("fit", "",names(gcv))) | ||
| names(df) <- c("GCV","BIC","fit") | ||
| df <- df[complete.cases(df),] | ||
| plot(df$fit, df$GCV, type = "b", col = "blue", ylab = "GCV", xlab = "fit", main="Analysis of fit metrics") | ||
| par(new = TRUE) | ||
| plot(df$fit, df$BIC, type = "b", col = "red", axes = FALSE, xlab = "", ylab = "") | ||
| axis(4) | ||
| mtext("BIC", side=4, line=3) | ||
| abline(v=df[min(df$GCV)==df$GCV,]$fit, col = "blue",lty = 2) | ||
| abline(v=df[min(df$BIC)==df$BIC,]$fit, col = "red",lty = 2) | ||
| legend("topleft", legend = c("GCV", "BIC"), col = c("blue", "red"), lty = 1, bg="white") | ||
| }) | ||
|
|
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