added quarto to vignette

.Rhistory

@@ -1,148 +1,3 @@
-dat2list
-old_dir <- getwd()
-# Document function below that is used to run the SPM code
-dirname <- "examples/atka"
-setwd(dirname)
-args=""
-system(paste("spm",args))
-read.csv("spm_detail.csv"))
-read.csv("spm_detail.csv")
-(tibble::tibble(read.csv("spm_detail.csv"))
-)
-source("~/_mymods/afsc-assessments/spmR/R/runSPM.R")
-source("~/_mymods/afsc-assessments/spmR/R/runSPM.R")
-source("~/_mymods/afsc-assessments/spmR/R/runSPM.R")
-# Document function below that is used to run the SPM code
-dirname <- "examples/atka"
-source("~/_mymods/afsc-assessments/spmR/R/runSPM.R")
-source("~/_mymods/afsc-assessments/spmR/R/runSPM.R")
-View(runSPM)
-# Document function below that is used to run the SPM code
-runSPM("examples/atka")
-source("~/_mymods/afsc-assessments/spmR/R/runSPM.R")
-source("~/_mymods/afsc-assessments/spmR/R/runSPM.R")
-# Document function below that is used to run the SPM code
-runSPM("examples/atka")
-source("~/_mymods/afsc-assessments/spmR/R/runSPM.R")
-getwd()
-setwd(old_dir)
-getwd()
-# Document function below that is used to run the SPM code
-runSPM("examples/atka")
-# Document function below that is used to run the SPM code
-runSPM("examples/atka")
-setwd(old_dir)
-getwd()
-# Document function below that is used to run the SPM code
-runSPM("examples/atka")
-source("~/_mymods/afsc-assessments/spmR/R/runSPM.R")
-setwd(old_dir)
-getwd()
-dirname
-setwd(dirname)
-setwd(old_dir)
-# Document function below that is used to run the SPM code
-runSPM("examples/atka")
-source("~/_mymods/afsc-assessments/spmR/R/runSPM.R")
-# Document function below that is used to run the SPM code
-runSPM("examples/atka")
-source("~/_mymods/afsc-assessments/spmR/R/runSPM.R")
-# Document function below that is used to run the SPM code
-runSPM("examples/atka")
-source("~/_mymods/afsc-assessments/spmR/R/runSPM.R")
-getwd
-getwd()
-setwd(old_dir)
-source("~/_mymods/afsc-assessments/spmR/R/runSPM.R")
-# Document function below that is used to run the SPM code
-runSPM("examples/atka")
-library(spmR)
-df <-
-runSPM("examples/atka")
-df
-p1<- df %>% filter(Alternative==2,SSB<500) %>% ggplot(aes(x=SSB,y=F)) + geom_point(color="salmon",alpha=.2) + theme_few()
-library(tidyverse)
-library(patchwork)
-p1<- df %>% filter(Alternative==2,SSB<500) %>% ggplot(aes(x=SSB,y=F)) + geom_point(color="salmon",alpha=.2) + theme_few()
-library(ggthemes)
-p1<- df %>% filter(Alternative==2,SSB<500) %>% ggplot(aes(x=SSB,y=F)) + geom_point(color="salmon",alpha=.2) + theme_few()
-p2<- df %>% filter(Alternative==2,SSB<500) %>% ggplot(aes(x=SSB,y=ABC)) + geom_point(alpha=.2,color="blue") + theme_few()
-p3<- df %>% filter(Alternative==2,SSB<500) %>% ggplot(aes(x=log(SSB),y=log(Rec)/log(SSB))) + geom_point(alpha=.2,color="green",size=.5) + geom_smooth() + theme_few()
-p1/p2/p3
-p1<- df %>% filter(Alternative==2,) %>% ggplot(aes(x=SSB,y=F)) + geom_point(color="salmon",alpha=.2) + theme_few()
-p1/p2/p3
-p2<- df %>% filter(Alternative==2) %>% ggplot(aes(x=SSB,y=ABC)) + geom_point(alpha=.2,color="blue") + theme_few()
-p3<- df %>% filter(Alternative==2) %>% ggplot(aes(x=log(SSB),y=log(Rec)/log(SSB))) + geom_point(alpha=.2,color="green",size=.5) + geom_smooth() + theme_few()
-p1/p2/p3
-pdt <- df
-pdt$Alternative <- as.factor(pdt$Alternative)
-names(pdt)
-pt <- pdt%>%filter(Yr>2021,Alternative==2) %>% group_by(Yr,Alternative) %>% summarise(Catch=mean(Catch),ABC=mean(ABC),OFL=mean(OFL),SSB=median(SSB) ,lb=quantile(SSB,.2) ,ub=quantile(SSB,.8) )
-pt
-ggplot(pt,aes(x=Yr,y=SSB,fill=Alternative)) + geom_line() + mytheme + ylim(c(0,340000)) + geom_ribbon(aes(ymin=lb,ymax=ub,fill=Alternative),alpha=0.25) + labs(y="Spawning biomass (kt)",x="Year") + scale_x_continuous(breaks=seq(2022,2035,2))
-mytheme<-theme_few()
-ggplot(pt,aes(x=Yr,y=SSB,fill=Alternative)) + geom_line() + mytheme + ylim(c(0,340000)) + geom_ribbon(aes(ymin=lb,ymax=ub,fill=Alternative),alpha=0.25) + labs(y="Spawning biomass (kt)",x="Year") + scale_x_continuous(breaks=seq(2022,2035,2))
-c1 <- ggplot(pt,aes(x=Yr,y=Catch,color=Alternative,size=1.)) + geom_line(size=1.5) + mytheme + labs(y="Catch (kt)",x="Year") + scale_x_continuous(breaks=seq(2015,2032,2))
-c1 <- c1 + geom_line(aes(x=Yr,y=ABC),size=1)
-#c1 <- c1 + geom_line(data=pt[as.numeric(Alternative)==2,.(Yr,ABC)],aes(x=Yr,y=ABC))
-c1
-pt[as.numeric(Alternative)==2,.(Yr,ABC)]
-pt <- pdt[Yr>2018,.(Catch=mean(Catch),ABC=mean(ABC),OFL=mean(OFL)),.(Yr,Alternative)]
-pt
-ggplot(pt,aes(x=Yr,y=OFL,color=Alternative)) + geom_line() + mytheme
-pdt
-pdx <-rbind(pdt)
-setkey(pdx,Yr,Alternative)
-ggplot(pt,aes(x=Yr,y=Catch,color=config,shape=config)) + geom_line() + geom_point() + mytheme + geom_ribbon(aes(ymin=lb,ymax=ub,fill=config),alpha=0.25) + labs(x="Year")+ scale_x_continuous(breaks=seq(2015,2032,2))  + ylim(c(0,130))
-library(spmR)
-print_Tier3_tables(df)
-df
-library(spmR)
-df
-print_Tier3_tables(df)
-source("~/_mymods/afsc-assessments/spmR/R/readData.R")
-print_Tier3_tables(df)
-source("~/_mymods/afsc-assessments/spmR/R/readData.R")
-print_Tier3_tables(df)
-print_Tier3_tables(df)
-print_Tier3_tables(df) |> gt::gt()
-dim(df)
-df
-bf<-df
-# ,header=TRUE,as.is=TRUE))
-# Stock Alt Sim Yr  SSB Rec Tot_biom SPR_Implied F Ntot Catch ABC OFL AvgAge AvgAgeTot SexRatio FABC FOFL
-bfsum <- bf %>% select(Alternative,Yr,SSB,F,ABC ,Catch) %>% group_by(Alternative,Yr) %>% summarise(Catch=mean(Catch),SSB=mean(SSB),F=mean(F),ABC=mean(ABC))
-tC <- bfsum %>% select(Alternative,Yr,Catch) %>% spread(Alternative,Catch)
-names(tC) <- c("Catch","Scenario 1","Scenario 2","Scenario 3","Scenario 4","Scenario 5","Scenario 6","Scenario 7")
-tB <- bfsum %>% select(Alternative,Yr,SSB) %>% spread(Alternative,SSB)
-names(tB) <- c("SSB","Scenario 1","Scenario 2","Scenario 3","Scenario 4","Scenario 5","Scenario 6","Scenario 7")
-tF <- bfsum %>% select(Alternative,Yr,F) %>% spread(Alternative,F)
-names(tF) <- c("F","Scenario 1","Scenario 2","Scenario 3","Scenario 4","Scenario 5","Scenario 6","Scenario 7")
-tA <- bfsum %>% select(Alternative,Yr,ABC) %>% spread(Alternative,ABC)
-names(tA) <- c("ABC","Scenario 1","Scenario 2","Scenario 3","Scenario 4","Scenario 5","Scenario 6","Scenario 7")
-tab <- (data.frame(tC))
-rownames(tab)<-c()
-cap <- paste0("For the configuration named ",mod_names[mod_number],", ",tabcap[40])
-for (i in 2:length(tab[1,]) )
-mod_name="Atka base"
-cap <- paste0("For the configuration named ",mod_name)
-for (i in 2:length(tab[1,]) )
-tab[,i] <- formatC((tab[,i]), format="d", big.mark=",")
-tab <- xtable(tab, caption = cap, label=paste0("tab:",tablab[40]),digits=0, auto=TRUE, align=rep("r",(length(tab[1,])+1)) )
-tab <- xtable::xtable(tab, caption = cap, label=paste0("tab:",tablab[40]),digits=0, auto=TRUE, align=rep("r",(length(tab[1,])+1)) )
-tablab="Atka_base"
-tab <- xtable::xtable(tab, caption = cap, label=paste0("tab:",tablab),digits=0, auto=TRUE, align=rep("r",(length(tab[1,])+1)) )
-print(tab, caption.placement = "top",include.rownames = FALSE, sanitize.text.function = function(x){x}, scalebox=.85)
-gt::gt(print(tab, caption.placement = "top",include.rownames = FALSE, sanitize.text.function = function(x){x}, scalebox=.85))
-print(tab, caption.placement = "top",include.rownames = FALSE, sanitize.text.function = function(x){x}, scalebox=.85)
-tab <- (data.frame(tA))
-cap <- paste0("For the configuration named ",mod_name)
-for (i in 2:length(tab[1,]) )
-tab[,i] <- formatC(as.numeric(tab[,i]), format="d", big.mark=",")
-tab <- xtable::xtable(tab, caption = cap, label=paste0("tab:",tablab),digits=0, auto=TRUE, align=rep("r",(length(tab[1,])+1)) )
-print(tab, caption.placement = "top",include.rownames = FALSE, sanitize.text.function = function(x){x}, scalebox=.85)
-tab <- (data.frame(tF))
-cap <- paste0("For the configuration named ",mod_name)
 for (i in 2:length(tab[1,]) )
 tab[,i] <- formatC(as.numeric(tab[,i]), format="f",digits=3)
 tab <- xtable::xtable(tab, caption = cap, label=paste0("tab:",tablab),digits=0, auto=TRUE, align=rep("r",(length(tab[1,])+1)) )
@@ -510,3 +365,148 @@ install.packages(c("magick", "openssl", "pdftools", "drake"))
 install.packages(c("magick", "openssl", "pdftools", "drake"))
 install.packages('curl', repos = 'https://jeroen.r-universe.dev')
 Or enable a universe globally:
+library(spmR)
+?run_model
+?runSPM
+runSPM("examples/atka")
+df <- runSPM("examples/atka")
+print_Tier3_tables(df)
+library(tidyverse)
+print_Tier3_tables(df)
+print_Tier3_tables(df) |> gt::gt
+print_Tier3_tables(df) |> gt::gt()
+print_Tier3_tables(df)
+plotSPM()
+plotSPM()
+plotSPM(df)
+library(patchwork)
+plotSPM(df)
+plotSPM(df)
+library(spmR)
+plotSPM(df)
+df <- runSPM("examples/atka")
+plotSPM(df)
+p1 <- plotSPM(df)
+p1$data
+cat(sprintf(
+'---
+title: "Some title"
+date: 09/01/2014
+doi: %s
+---
+## Important links
+- [Article](https://doi.org/{{< meta doi >}})
+## DAG
+```{r}
+dag <- dagitty::dagitty(%s)
+tidy_dag <- ggdag::tidy_dagitty(dag)
+ggdag::ggdag_status(tidy_dag) +
+ggdag::theme_dag()
+```
+',
+doi_from_file,
+dag_from_file
+), file = 'index.qmd')
+source("~/_mymods/afsc-assessments/spmR/R/Make_doc.R", echo=TRUE)
+source("~/_mymods/afsc-assessments/spmR/R/Make_doc.R", echo=TRUE)
+makeqmd()
+cat(
+sprintf(
+'---
+title: "Some title"
+date: 09/01/2014
+doi: %s
+---
+## Important links
+- [Article](https://doi.org/{{< meta doi >}})
+## DAG
+```{r}
+dag <- dagitty::dagitty(%s)
+tidy_dag <- ggdag::tidy_dagitty(dag)
+ggdag::ggdag_status(tidy_dag) +
+ggdag::theme_dag()
+```
+',
+doi_from_file,
+dag_from_file
+), file = 'index.qmd')
+pak::pkg_install("dagitty")
+pak::pkg_install("ggdag")
+pak::pak_update()
+install.packages("broom")
+pak::pak_update()
+?pak
+makeqmd()
+source("~/_mymods/afsc-assessments/spmR/R/Make_doc.R", echo=TRUE)
+makeqmd()
+source("~/_mymods/afsc-assessments/spmR/R/Make_doc.R", echo=TRUE)
+makeqmd()
+install.packages("officer")
+makeqmd("10.1139/cjfas-2018-0128")
+source("~/_mymods/afsc-assessments/spmR/R/Make_doc.R", echo=TRUE)
+makeqmd("10.1139/cjfas-2018-0128")
+source("~/_mymods/afsc-assessments/spmR/R/Make_doc.R", echo=TRUE)
+makeqmd("10.1139/cjfas-2018-0128")
+source("~/_mymods/afsc-assessments/spmR/R/Make_doc.R", echo=TRUE)
+makeqmd("10.1139/cjfas-2018-0128")
+source("~/_mymods/afsc-assessments/spmR/R/Make_doc.R", echo=TRUE)
+cat(
+sprintf(
+'---
+title: "Some title"
+date: 09/01/2014
+doi: %s
+---
+## Important links
+- [Article](https://doi.org/{{< meta doi >}})
+## DAG
+```{r}
+#dag <- dagitty::dagitty(%s)
+#tidy_dag <- ggdag::tidy_dagitty(dag)
+#ggdag::ggdag_status(tidy_dag) +
+#ggdag::theme_dag()
+plot(1:10)
+```
+',
+#doi_from_file,
+#dag_from_file
+), file = 'index.qmd')
+cat(
+sprintf( '---
+title: "Some title"
+date: 09/01/2014
+doi: %s
+---
+## Important links
+- [Article](https://doi.org/{{< meta doi >}})
+## DAG
+```{r}
+dag <- dagitty::dagitty(%s)
+tidy_dag <- ggdag::tidy_dagitty(dag)
+ggdag::ggdag_status(tidy_dag) +
+ggdag::theme_dag()
+```
+',
+doi_from_file,
+dag_from_file
+), file = 'index.qmd')
+cat(
+sprintf( '---
+title: "Some title"
+date: 09/01/2014
+doi: %s
+---
+## Important links
+- [Article](https://doi.org/{{< meta doi >}})
+## DAG
+```{r}
+dag <- dagitty::dagitty(%s)
+tidy_dag <- ggdag::tidy_dagitty(dag)
+ggdag::ggdag_status(tidy_dag) +
+ggdag::theme_dag()
+```
+',
+"doi_from_file",
+"dag_from_file"
+), file = 'index.qmd')
+quarto::quarto_render("index.qmd")

DESCRIPTION

@@ -12,6 +12,7 @@ LazyData: true
 Suggests: 
     knitr, ggplot2,
     rmarkdown
-VignetteBuilder: knitr
+VignetteBuilder: 
+    quarto
 RoxygenNote: 7.3.1
 URL: http://afsc-assessments.github.io/spmR/

vignettes/00-spm-example.Rmd

@@ -18,6 +18,8 @@ knitr::opts_chunk$set(
 
 ```{r setupex}
 library(spmR)
+library(tidyverse)
+library(patchwork)
 here::here()
 
 ```
@@ -34,11 +36,13 @@ This vignette demonstrates how to use these functions to run the SPM model and a
 The following case studies have been applied.
 
 ## Atka mackerel
-```{r atka,eval=FALSE}
+```{r atka,eval=TRUE}
 df <- runSPM(here::here("examples","atka"),run=FALSE)
-setwd("spmR")
+#setwd("spmR")
 plotSPM(df)
 ```
+
+
 ## BSAI northern rock sole
 ```{r bsaiNRS,eval=FALSE}
 df <- runSPM(here::here("examples","BSAI NRS"),run=FALSE)