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tokamitokami
committedFeb 29, 2024
updates to pass cran tests
1 parent 70c8b54 commit 5fd7070

21 files changed

+37
-23
lines changed
 

‎DESCRIPTION

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@@ -31,7 +31,7 @@ NeedsCompilation: no
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BugReports: https://github.com/tokami/TropFishR/issues
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URL: https://github.com/tokami/TropFishR
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Encoding: UTF-8
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RoxygenNote: 7.1.1
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RoxygenNote: 7.3.1
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Suggests:
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graphics,
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grDevices,

‎R/Bhattacharya.R

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@@ -69,6 +69,8 @@
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Bhattacharya <- function(param, n_rnorm = 1000, savePlots = FALSE){
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72+
if(interactive()){
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res <- param
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if("midLengths" %in% names(res) == TRUE){
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midLengths <- as.character(res$midLengths)
@@ -444,4 +446,9 @@ Bhattacharya <- function(param, n_rnorm = 1000, savePlots = FALSE){
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plot(ret)
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return(ret)
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}
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}else{
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writeLines("Interactive session needed for Bhattacharya.")
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return(NULL)
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}
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}

‎R/ELEFAN.R

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@@ -95,7 +95,8 @@
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#' lfq = alba, method = "cross",
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#' Linf_fix = 10,
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#' K_range = round(exp(seq(from = log(0.1), to = log(2), length.out = 50)),2),
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#' cross.date = alba$dates[3], cross.midLength = alba$midLengths[4]
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#' cross.date = alba$dates[3], cross.midLength = alba$midLengths[4],
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#' plot = FALSE
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#' )
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#' fit4$Rn_max; unlist(fit4$par)
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#' plot(fit4); points(alba$dates[3], alba$midLengths[4], col=2, cex=2, lwd=2)
@@ -261,7 +262,7 @@ ELEFAN <- function(lfq, Linf_fix = NA, Linf_range = NA,
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}
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if(!hide.progressbar){
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if(!hide.progressbar && interactive()){
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nlk <- prod(dim(ESP_list_L))
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pb <- txtProgressBar(min=1, max=nlk, style=3)
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counter <- 1
@@ -316,7 +317,7 @@ ELEFAN <- function(lfq, Linf_fix = NA, Linf_range = NA,
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}
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# update counter and progress bar
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if(!hide.progressbar){
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if(!hide.progressbar && interactive()){
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setTxtProgressBar(pb, counter)
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counter <- counter + 1
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}

‎R/ELEFAN_GA.R

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@@ -313,7 +313,7 @@ ELEFAN_GA <- function(lfq,
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if(plot){
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plot(lfq, Fname = "rcounts")
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Lt <- lfqFitCurves(lfq, par = lfq$pars, draw=TRUE)
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Lt <- lfqFitCurves(lfq, par = lfq$par, draw=TRUE)
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}
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return(lfq)
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}

‎R/ELEFAN_SA.R

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@@ -357,7 +357,7 @@ ELEFAN_SA <- function(lfq,
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if(plot){
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plot(res, Fname = "rcounts")
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Lt <- lfqFitCurves(res, par = res$pars, draw=TRUE)
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Lt <- lfqFitCurves(res, par = res$par, draw=TRUE)
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}
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return(res)
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}

‎R/alba.R

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@@ -2,7 +2,6 @@
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#'
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#' @title Length-frequency data of the clam Abra alba
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#'
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#'
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#' @description Length-frequency data of the clam Abra alba as presented
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#' by Brey et al. (1988). Includes 7 approximately bi-monthly samplings of
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#' A. alba binned into 14 length classes. The data is of class "lfq", which

‎R/catchCurve.R

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@@ -382,7 +382,8 @@ catchCurve <- function(param,
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cutterList <- vector("list", reg_num)
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#identify plot
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if(is.null(reg_int) & !auto){
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if(is.null(reg_int) & !auto){
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if(interactive()){
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writeLines("Please choose the minimum and maximum point in the graph \nto include for the regression line!")
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flush.console()
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for(I in 1:reg_num){
@@ -417,6 +418,11 @@ catchCurve <- function(param,
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cutterList[[I]] <- cutter
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}
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}else{
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writeLines("Either start an interactive session to choose points, use reg_int to define the points for the regression analysis or use auto=TRUE.")
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return(NULL)
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}
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}
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‎R/plot.Bhattacharya.R

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@@ -10,7 +10,7 @@
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#' lines should be created
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#'
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#' @examples
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#' \donttest{
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#' \dontrun{
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#' data(synLFQ1)
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#' output <- Bhattacharya(param = synLFQ1)
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#' plot(output)

‎R/powell_wetherall.R

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@@ -135,6 +135,7 @@ powell_wetherall <- function(param, catch_columns = NA,
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#identify plot
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if(is.null(reg_int)){
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if(interactive()){
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repeat{
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writeLines("Please choose the minimum and maximum point in the \ngraph to include for the regression line!")
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flush.console()
@@ -162,6 +163,11 @@ powell_wetherall <- function(param, catch_columns = NA,
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break
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}
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}
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}else{
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writeLines("Please specify reg_int or choose points for the regression analysis in an interactive session.")
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return(NULL)
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}
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}
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if(!is.null(reg_int)){
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cutter <- reg_int

‎R/predict_mod.R

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@@ -359,7 +359,7 @@ predict_mod <- function(param, type, FM_change = NA,
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list_Es <- vector("list", length(Lc))
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# show progress bar only if the loop has more than 1 runs
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if (!hide.progressbar) {
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if (!hide.progressbar && interactive()) {
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nlk <- length(Lc)
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if(nlk > 1){
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pb <- txtProgressBar(min=1, max=nlk, style=3)
@@ -501,7 +501,7 @@ predict_mod <- function(param, type, FM_change = NA,
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list_Es[[i]] <- df_loop_Es
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# update counter and progress bar
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if (!hide.progressbar) {
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if (!hide.progressbar && interactive()) {
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if(nlk > 1){
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setTxtProgressBar(pb, counter)
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counter <- counter + 1
@@ -920,7 +920,7 @@ predict_mod <- function(param, type, FM_change = NA,
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pred.FM_Lc_com_res_loopSSB_list <- vector("list",length(FM_Lc_com_mat.list))
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pred.FM_Lc_com_res_loopSPR_list <- vector("list",length(FM_Lc_com_mat.list))
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if (!hide.progressbar) {
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if (!hide.progressbar && interactive()) {
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nlk <- prod(length(FM_Lc_com_mat.list),dim(FM_Lc_com_mat.list[[1]])[2])
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pb <- txtProgressBar(min=1, max=nlk, style=3)
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counter <- 1
@@ -939,7 +939,7 @@ predict_mod <- function(param, type, FM_change = NA,
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pred.FM_Lc_com_res_loop1_list[[x22]] <- res2$totals
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# update counter and progress bar
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if (!hide.progressbar) {
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if (!hide.progressbar && interactive()) {
943943
setTxtProgressBar(pb, counter)
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counter <- counter + 1
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}

‎R/synLFQ1.R

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@@ -2,7 +2,6 @@
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#'
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#' @title Synthetic length-frequency data I
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#'
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#'
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#' @description Synthetic length-frequency data as provided in Sparre & Venema (1998).
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#' Can be used to apply the function \code{\link[TropFishR]{Bhattacharya}} or
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#' \code{\link[TropFishR]{ELEFAN}}.

‎R/synLFQ2.R

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@@ -2,7 +2,6 @@
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#'
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#' @title Synthetic length frequency data II
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#'
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#'
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#' @description Synthetic length frequency data from Sparre & Venema (1998). Can be used
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#' for the estimation of the instantaneous total mortality rate (Z) by means
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#' of \code{\link{Z_BevertonHolt}}.

‎R/synLFQ3.R

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#'
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#' @title Synthetic length frequency data III
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#'
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#'
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#' @description Synthetic length frequency data from Sparre & Venema (1998). Can be
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#' used for the estimation of the instantaneous total mortality rate (Z) by means
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#' of \code{\link{Z_BevertonHolt}}.

‎R/synLFQ4.R

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#'
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#' @title Synthetic length-frequency data IV (with seasonal oscillation)
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#'
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#'
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#' @description Synthetic length-frequency data as generated by the function
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#' \code{lfqGen} from the \emph{fishdynr} package (Taylor 2016). Can be used by
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#' \code{\link[TropFishR]{ELEFAN}} or \code{\link[TropFishR]{ELEFAN_SA}}.

‎R/synLFQ5.R

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#'
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#' @title Synthetic length-frequency data V (without seasonal oscillation)
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#'
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#'
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#' @description Synthetic length-frequency data as generated by the function
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#' \code{lfqGen} from the \emph{fishdynr} package (Taylor 2016). Can be used by
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#' \code{\link[TropFishR]{ELEFAN}} or \code{\link[TropFishR]{ELEFAN_SA}}.

‎R/synLFQ6.R

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@@ -2,7 +2,6 @@
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#'
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#' @title Synthetic length-frequency data VI (without seasonal oscillation)
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#'
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#'
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#' @description Synthetic length-frequency data as generated by the function
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#' \code{lfqGen} from the \emph{fishdynr} package (Taylor 2016). Can be used by
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#' \code{\link[TropFishR]{ELEFAN}} or \code{\link[TropFishR]{ELEFAN_SA}}.

‎R/synLFQ7.R

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#'
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#' @title Synthetic length-frequency data VII with seasonal oscillation
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#'
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#'
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#' @description Synthetic length-frequency data as generated by the function
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#' \code{lfqGen} from the \emph{fishdynr} package (Taylor 2016). Can be used by
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#' \code{\link[TropFishR]{ELEFAN}}, \code{\link[TropFishR]{ELEFAN_SA}}, or

‎R/synLFQ8.R

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#'
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#' @title Synthetic length-frequency data VIII with variable harvest rate
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#'
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#'
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#' @description Synthetic length-frequency data as generated by the
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#' function \code{virtualPop2} from the \emph{fishdynr} package
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#' (Taylor and Mildenberger, 2018). Can be used by

‎man/ELEFAN.Rd

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‎man/growth_length_age.Rd

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‎man/plot.Bhattacharya.Rd

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