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updates for github
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kholsman committed Oct 4, 2024
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153 changes: 99 additions & 54 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -13,10 +13,12 @@ Repo maintained by: Kirstin Holsman
Alaska Fisheries Science Center
NOAA Fisheries, Seattle WA
**<kirstin.holsman@noaa.gov>**
<!-- *Last updated: Nov 29, 2023* -->
<!-- *Last updated: Oct 04, 2024* -->

------------------------------------------------------------------------

<img src="../Figs/futR_icon.png" style="width:25.0%" />

<!-- # Overview {.tabset .tabset-dropdown} -->

# Overview
Expand Down Expand Up @@ -95,15 +97,15 @@ recruitment, and *θ*<sup>*β*</sup> is a binary vector of length

$$\mathbf{X} = \left\[\begin{array}
{rrr}
x\_{1,1} & \dots & b\_{1,n_y} \\\\
\vdots & \ddots & \vdots \\\\
x\_{1,1} & \dots & b\_{1,n_y} \\
\vdots & \ddots & \vdots \\
x\_{n_k,1} & \dots & x\_{n_k,n_y}
\end{array}\right\]
,\\; \mathbf{\beta} = \left\[\begin{array}
,\\ \mathbf{\beta} = \left\[\begin{array}
{rrr}
\beta_1 \\\\
\vdots \\\\
\beta\_{n_k} \\\\
\beta_1 \\
\vdots \\
\beta\_{n_k} \\
\end{array}\right\]
$$

Expand All @@ -129,21 +131,21 @@ recommended $\hat{R_i}\sim0$ as $\hat{S_i}\to0$)

$$\mathbf{X} = \left\[\begin{array}
{rrr}
x\_{1,1} & \dots & b\_{1,n_y} \\\\
\vdots & \ddots & \vdots \\\\
x\_{1,1} & \dots & b\_{1,n_y} \\
\vdots & \ddots & \vdots \\
x\_{n_k,1} & \dots & x\_{n_k,n_y}
\end{array}\right\],\\;
\end{array}\right\],\\
\mathbf{\beta} = \left\[\begin{array}
{rrr}
\beta_1 \\\\
\vdots \\\\
\beta\_{n_k} \\\\
\end{array}\right\],\\;
\beta_1 \\
\vdots \\
\beta\_{n_k} \\
\end{array}\right\],\\
\mathbf{\lambda} = \left\[\begin{array}
{rrr}
\lambda_1 \\\\
\vdots \\\\
\lambda\_{n_k}\\\\
\lambda_1 \\
\vdots \\
\lambda\_{n_k}\\
\end{array}\right\]
$$

Expand Down Expand Up @@ -182,21 +184,21 @@ binary vectors of length *n*<sub>*k*</sub> of covariate inclusion (i.e.,

$$\mathbf{X} = \left\[\begin{array}
{rrr}
x\_{1,1} & \dots & b\_{1,n_y} \\\\
\vdots & \ddots & \vdots \\\\
x\_{1,1} & \dots & b\_{1,n_y} \\
\vdots & \ddots & \vdots \\
x\_{n_k,1} & \dots & x\_{n_k,n_y}
\end{array}\right\],\\;
\end{array}\right\],\\
\mathbf{\beta} = \left\[\begin{array}
{rrr}
\beta_1 \\\\
\vdots \\\\
\beta\_{n_k} \\\\
\end{array}\right\],\\;
\beta_1 \\
\vdots \\
\beta\_{n_k} \\
\end{array}\right\],\\
\mathbf{\lambda} = \left\[\begin{array}
{rrr}
\lambda_1 \\\\
\vdots \\\\
\lambda\_{n_k}\\\\
\lambda_1 \\
\vdots \\
\lambda\_{n_k}\\
\end{array}\right\]
$$

Expand Down Expand Up @@ -238,21 +240,21 @@ covariate effects on pre- and post-spawning success, respectively,and

$$\mathbf{X} = \left\[\begin{array}
{rrr}
x\_{1,1} & \dots & b\_{1,n_y} \\\\
\vdots & \ddots & \vdots \\\\
x\_{1,1} & \dots & b\_{1,n_y} \\
\vdots & \ddots & \vdots \\
x\_{n_k,1} & \dots & x\_{n_k,n_y}
\end{array}\right\],\\;
\end{array}\right\],\\
\mathbf{\beta} = \left\[\begin{array}
{rrr}
\beta_1 \\\\
\vdots \\\\
\beta\_{n_k} \\\\
\end{array}\right\],\\;
\beta_1 \\
\vdots \\
\beta\_{n_k} \\
\end{array}\right\],\\
\mathbf{\lambda} = \left\[\begin{array}
{rrr}
\lambda_1 \\\\
\vdots \\\\
\lambda\_{n_k}\\\\
\lambda_1 \\
\vdots \\
\lambda\_{n_k}\\
\end{array}\right\]
$$

Expand Down Expand Up @@ -373,14 +375,14 @@ The base function for fitting recruitment requires a data.frame of
recruitment and spawning biomass:

``` r
# rm(list=ls()); setwd("/Users/kholsman/Documents/GitHub/futR")
# rm(list=ls()); setwd("/Volumes/LaCie/GitHub_cloud/futR")
#___________________________________________
# 1. Set things up
#___________________________________________
# rm(list=ls()) ; dir()

# load data, packages, setup, etc.
source("R/01_make.R")
source(file.path("R","01_make.R"))

#___________________________________________
# 2. Compile futR (first time through - can skip this step after )
Expand All @@ -402,8 +404,8 @@ instructions [here](https://cran.r-project.org/bin/windows/Rtools/).*

``` r
# read in the data and create a datlist
datlist <- makefutR_data("data/in/futR_Inputs.xlsx" )
datlist <- makefutR_data(file.path("data-raw","in","futR_Inputs.xlsx" ))

# recruitment data:
datlist$rs_dat$R_obs
datlist$rs_dat$S_obs
Expand All @@ -416,19 +418,18 @@ instructions [here](https://cran.r-project.org/bin/windows/Rtools/).*
# which parameters to estimate with futR?
datlist$estparams

# starting values?
# starting values
datlist$parameters

# parameter map:
# parameter map
datlist$maplist

# which phases to estimate in (not yet coded up)
# which phases to estimate in
datlist$phases


# set some global values for the demo below:
estparams <- datlist$estparams[1:6]
rec <- data.frame(readxl::read_xlsx("data/in/futR_Inputs.xlsx" , sheet = "rec_data" ))
```

## Explore recruitment models
Expand Down Expand Up @@ -593,12 +594,14 @@ Ricker relationship.
$$\mathrm{ln}\hat{R_i}= \left(a+ \sum\_{k=1}^{n_k}{\theta_i^{\beta}\beta_k X\_{k,i}} \right)-\left(b+ \sum\_{k=1}^{n_k}{\theta_i^{\lambda}\lambda_k X\_{k,i}}\right)\hat{S_i}+\mathrm{ln}\hat{S_i}+\varepsilon_i $$

``` r
estparams_0 <- estparams
estparams_0$beta <- estparams_0$lambda <- FALSE
# makeDat will make the input values, data, and phases for the model:
datlist <- makeDat(
rectype = 4,
tauIN = 0,
sigMethod = 1, # (default, no random effects)
estparams = estparams,
estparams = estparams_0,
estMode = 1,
rec_years = rec$rec_year,
Rec = rec$Robs,
Expand All @@ -620,7 +623,7 @@ $$\mathrm{ln}\hat{R_i}= \left(a+ \sum\_{k=1}^{n_k}{\theta_i^{\beta}\beta_k X\_{k
dfR4 <- data.frame(model = "Rec 4",
estimate = as.vector(mm$sim),
parameter = names( mm$mle)[row(mm$sim)])
df <- rbind(df,dfR3)
df <- rbind(dfR4)
r4_fit <- getFit(mm, nm = "recType = 4")
rec_fit <- rbind(rec_fit,r4_fit)
rm(mm)
Expand All @@ -644,9 +647,13 @@ $$\mathrm{ln}\hat{R_i}= \left(a+ \sum\_{k=1}^{n_k}{\theta_i^{\beta}\beta_k X\_{k

``` r
# read in the data and create a datlist (rather than hand code it)
datlist <- makefutR_data("data/in/futR_Inputs.xlsx" )


#datlist <- makefutR_data("data/in/futR_Inputs.xlsx" )
datlist <- makefutR_data(file.path("data-raw","in","futR_Inputs.xlsx" ))

datlist_post <- datlist
datlist_pre <- datlist
datlist_post$estparams["beta"] <- FALSE
datlist_pre$estparams["lambda"] <- FALSE
# run the basic model
Rec4_covar <- mm <-runRecMod(dlistIN = datlist,
version = 'futR',
Expand All @@ -659,10 +666,48 @@ $$\mathrm{ln}\hat{R_i}= \left(a+ \sum\_{k=1}^{n_k}{\theta_i^{\beta}\beta_k X\_{k
dfR4_c <- data.frame(model = "Rec 4 with covar",
estimate = as.vector(mm$sim),
parameter = names( mm$mle)[row(mm$sim)])
df <- rbind(dfR4,dfR4_c)
r4_fit_c <- getFit(mm, nm = "recType = 4 with covar")
rec_fit <- rbind(r4_fit,r4_fit_c)
rm(mm)
df <- rbind(dfR4,dfR4_c)
r4_fit_c <- getFit(mm, nm = "recType = 4 with pre- and post- covar")
rec_fit <- rbind(r4_fit,r4_fit_c)
rm(mm)


# run the basic model
mm <-runRecMod(dlistIN = datlist_pre,
version = 'futR',
src_fldr = "src/TMB",
recompile = FALSE,
simulate = TRUE,
sim_nitr = 1000)

# summarize results
dfR4_c_pre <- data.frame(model = "Rec 4 with covar on pre",
estimate = as.vector(mm$sim),
parameter = names( mm$mle)[row(mm$sim)])
df <- rbind(df,dfR4_c_pre)
r4_fit_c_pre <- getFit(mm, nm = "recType = 4 with pre-covar")
rec_fit <- rbind(rec_fit,r4_fit_c_pre)

rm(mm)
# run the basic model
mm <-runRecMod(dlistIN = datlist_post,
version = 'futR',
src_fldr = "src/TMB",
recompile = FALSE,
simulate = TRUE,
sim_nitr = 1000)

# summarize results
dfR4_c_post <- data.frame(model = "Rec 4 with covar on post",
estimate = as.vector(mm$sim),
parameter = names( mm$mle)[row(mm$sim)])
df <- rbind(df,dfR4_c_post)
r4_fit_c_post <- getFit(mm, nm = "recType = 4 with post-covar")
rec_fit <- rbind(rec_fit,r4_fit_c_post)

rm(mm)


if(updatePlots){
jpeg("Figs/recplot5.jpg", width = W, height= H1, res = 250, units = "in")
print(plot_rs(rec_fit))
Expand Down
1 change: 1 addition & 0 deletions _config.yml
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@@ -0,0 +1 @@
theme: jekyll-theme-cayman
3,846 changes: 3,846 additions & 0 deletions index.html
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37 changes: 21 additions & 16 deletions vingettes/futR_demo.Rmd
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Expand Up @@ -2,14 +2,14 @@
title: "futR()"
author: "Kirstin Holsman"
output:
html_document:
df_print: paged
toc: true
toc_depth: 4
number_sections: true
toc_float:
collapsed: false
smooth_scroll: true
pdf_document:
toc: TRUE
fig_caption: yes
fig_height: 4
fig_width: 5
highlight: tango
keep_tex: yes
latex_engine: xelatex
header-includes:
- \usepackage{knputenc}
- \usepackage{unicode-math}
Expand All @@ -20,14 +20,14 @@ output:
fig_caption: yes
fig_width: 4
keep_md: yes
pdf_document:
toc: TRUE
fig_caption: yes
fig_height: 4
fig_width: 5
highlight: tango
keep_tex: yes
latex_engine: xelatex
html_document:
df_print: paged
toc: true
toc_depth: 4
number_sections: true
toc_float:
collapsed: false
smooth_scroll: true
---


Expand Down Expand Up @@ -70,6 +70,11 @@ NOAA Fisheries, Seattle WA

---


![](../Figs/futR_icon.png){width=25%}



<!-- # Overview {.tabset .tabset-dropdown} -->
# Overview

Expand Down
90 changes: 67 additions & 23 deletions vingettes/futR_demo.html
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