R_Scripts/OLD/iPLS, NN Model, All Comments.R
In John-R-Wallace-NOAA/FishNIRS: NIRS on fish structures.
####################################################################
# --- Initial setup (The curly brakets with a '###' comment and without indented lines directly below them, are there to enable the hiding of code sections using Notepad++.) ---
# (For those who dislike Rstudio, Notepad++ is here: https://notepad-plus-plus.org/ and NppToR that passes R code from Notepad++ to R is here: https://sourceforge.net/projects/npptor/)
# You will need a 'GITHUB_PAT' from GitHub set somewhere in R (If you need help, search the Web how to get one from GitHub.)
# Sys.setenv(GITHUB_PAT = "**************") # If you set GITHUB_PAT here, uncomment this line. Note, do not share your GITHUB_PAT, nor load it onto GitHib.
Sys.getenv("GITHUB_PAT")
####################################################################
# --- Initial settings setup ---
{ ###
if(interactive())
setwd(ifelse(.Platform$OS.type == 'windows', "C:/ALL_USR/JRW/SIDT/Train_NN_Model", "/more_home/h_jwallace/SIDT/Train_NN_Models")) # Change path to the Spectra Set's .GlobalEnv as needed
if(!interactive()) options(width = 120)
Spectra_Set <- c("Hake_2019", "Sable_2017_2019", "Sable_Combo_2022")[3] # Defaults for reading in the spectra sets are in the Read_OPUS_Spectra() function.
Spectra_Path <- "Model_Scans" # Put new spectra scans in a separate folder and enter the name of the folder below
dir.create('Figures', showWarnings = FALSE)
verbose <- c(TRUE, FALSE)[1]
plot <- c(TRUE, FALSE)[1]
# Default number of new spectra to be plotted in spectra figures. (The plot within Read_OPUS_Spectra() is given a different default below).
# All spectra in the Spectra_Path folder will be assigned an age regardless of the number plotted in the figure.
Max_N_Spectra <- list(50, 200, 'All')[[3]]
print(getwd())
print(Spectra_Set)
}
# --- Load functions and packages ---
{ ###
sourceFunctionURL <- function (URL, type = c("function", "script")[1]) {
" # For more functionality, see gitAFile() in the rgit package ( https://github.com/John-R-Wallace-NOAA/rgit ) which includes gitPush() and git() "
if (!any(installed.packages()[, 1] %in% "httr")) install.packages("httr")
File.ASCII <- tempfile()
if(type == "function")
on.exit(file.remove(File.ASCII))
getTMP <- httr::GET(gsub(' ', '%20', URL))
if(type == "function") {
write(paste(readLines(textConnection(httr::content(getTMP))), collapse = "\n"), File.ASCII)
source(File.ASCII)
}
if(type == "script") {
fileName <- strsplit(URL, "/")[[1]]
fileName <- rev(fileName)[1]
write(paste(readLines(textConnection(httr::content(getTMP))), collapse = "\n"), fileName)
}
}
# Toolbox functions
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/Ls.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/openwd.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/lib.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/get.subs.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/sort.f.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/predicted_observed_plot.R")
# sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/residuals_plot.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/as.num.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/match.f.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/Table.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/renum.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/agg.table.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/r.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/gof.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/Date.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/timeStamp.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/dec.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/loess.line.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/plot.loess.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/browsePlot.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/gPlot.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/recode.simple.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/headTail.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/factor.f.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/Correlation_R_squared_RMSE_MAE_SAD.R")
# FishNIRS funtion
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/FishNIRS/master/R/plotly.Spec.R")
# sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/FishNIRS/master/R/Mode.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/FishNIRS/master/R/agreementFigure.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/FishNIRS/master/R/FCNN_Model.R"); FCNN_model_ver_1 <- FCNN_model
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/FishNIRS/master/R/CNN_model_ver_5.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/FishNIRS/master/R/Read_OPUS_Spectra.R")
# sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/FishNIRS/master/R/CNN_model_2D.R") # Not working yet
lib(lattice)
lib(dplyr)
# remotes::install_github("r-lib/ragg@bc501c9951c5934afa55da6d36cdf03c2705d99f")
# lib(tidyverse)
lib(recipes)
lib(rsample)
lib(GGally)
lib(skimr)
lib(e1071)
lib(mdatools)
lib(plotly)
lib(reticulate)
lib(tensorflow)
lib(keras)
lib(prospectr)
lib(openxlsx)
# install.packages('RcppArmadillo') # Need to use 4.0 version
lib(RcppArmadillo)
# Configuration failed to find one of freetype2 libpng libtiff-4. Try installing:
# * deb: libfreetype6-dev, libpng-dev libtiff5-dev libjpeg-dev (Debian, Ubuntu, etc)
# * rpm: freetype-devel libpng-devel libtiff-devel libjpeg-turbo-devel (Fedora, CentOS, RHEL)
# * csw: libfreetype_dev libpng16_dev libtiff_dev libjpeg_dev (Solaris)
# If freetype2 libpng libtiff-4 is already installed, check that 'pkg-config' is in your
# PATH and PKG_CONFIG_PATH contains a freetype2 libpng libtiff-4.pc file. If pkg-config
# is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
# R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
# -------------------------- [ERROR MESSAGE] ---------------------------
# <stdin>:1:22: fatal error: ft2build.h: No such file or directory
# compilation terminated.
#
# --- Setup for TensorFlow and Keras ---
# --- Conda TensorFlow environment ---
Conda_TF_Eniv <- ifelse(.Platform$OS.type == 'windows', "C:/m3/envs/tf", "/more_home/h_jwallace/Python/tf_cpu_only/bin") # Change these paths as needed
Sys.setenv(RETICULATE_PYTHON = Conda_TF_Eniv)
Sys.getenv("RETICULATE_PYTHON")
if(.Platform$OS.type != 'windows') {
# https://github.com/rstudio/tensorflow/issues/412
config <- tf$compat$v1$ConfigProto(intra_op_parallelism_threads = 2L, inter_op_parallelism_threads = 2L)
session = tf$compat$v1$Session(config=config)
tf$compat$v1$keras$backend$set_session(session)
}
# Set pseudo random number seeds
Seed_Fold <- c(777, 747, 727, 787, 797)[3]
set.seed(Seed_Fold)
Seed_Model <- c(777, 747, 727, 787, 797)[3]
# Pick the NN model to use (CNN_model_2D currently not working.)
model_Name <- c('FCNN_model_ver_1', 'CNN_model_ver_5', 'CNN_model_2D')[1]
Disable_GPU <- model_Name == 'FCNN_model_ver_1' # Only using the CPU is faster for the FCNN model but slower for CNN_model_ver_5, at least on Sablefish with data from 2017 and 2019.
# Disable_GPU <- FALSE
cat("\nDisable_GPU =", Disable_GPU, "\n\n")
# !!! Disabling the GPU has to come first for it to work. !!! (Grrrr, finally found this on the Web applied to Python and it is true here also!)
# Use < nvidia-smi -l 5 > within e.g. < conda activate C:/m3/envs/tf > inside of Powershell or Command Prompt to see a more correct percent of GPU utilization then with Task Manager.
tensorflow::set_random_seed(Seed_Model, disable_gpu = Disable_GPU)
# Test to see if TensorFlow is working in R
cat("\n\n"); print(tf_config()); cat("\n")
a <- tf$Variable(5.56)
b <- tf$Variable(2.7)
print(a + b); cat("\n\n")
k_clear_session()
} ###
# --- If Model_Spectra.sg.iPLS and TMA_Vector are missing for the current spectra set, create them now ---
{ ###
if(!file.exists(paste0(Spectra_Set, '_Model_Spectra.sg.iPLS.RData'))) {
Model_Spectra_Meta <- Read_OPUS_Spectra(Spectra_Set, Spectra_Path = Spectra_Path, Max_N_Spectra = 300, Meta_Path = paste0(Spectra_Set, "_NIRS_Scanning_Session_Report.xlsx"),
verbose = verbose, plot = plot, htmlPlotFolder = paste0('Figures/', Spectra_Set, '_Spectra_Sample_of_300'))
# filenames X8000 X7992 X3952 project sample_year pacfin_code_id sequence_number age_structure_id specimen_id TMA sex structure_weight_g NWFSC_NIR_Project
# 1 SABL_COMBO2022_NIR0022A_PRD_1_102157421_O1 0.2202285 0.2201835 0.5198408 COMBO 2022 SABL 1 102157421-SABL-O 102157421 14 2 0.0228 PRD
# 2 SABL_COMBO2022_NIR0022A_PRD_10_102157430_O1 0.2037776 0.2037497 0.5039832 COMBO 2022 SABL 10 102157430-SABL-O 102157430 6 2 0.0173 PRD
# 3 SABL_COMBO2022_NIR0022A_PRD_100_102157520_O1 0.1761716 0.1760852 0.4924470 COMBO 2022 SABL 100 102157520-SABL-O 102157520 6 2 0.0196 PRD
# 4 SABL_COMBO2022_NIR0022A_PRD_11_102157431_O1 0.1911490 0.1911127 0.5683330 COMBO 2022 SABL 11 102157431-SABL-O 102157431 16 1 0.0265 PRD
# 5 SABL_COMBO2022_NIR0022A_PRD_12_102157432_O1 0.1880359 0.1880160 0.5052297 COMBO 2022 SABL 12 102157432-SABL-O 102157432 6 1 0.0200 PRD
# NWFSC_NIR_Scan_Session age_structure_side_scan crystallized_scan percent_crystallized_scan broken_scan tip_only_scan anterior_tip_missing posterior_tip_missing percent_missing_scan tissue_present_scan
# 1 NIR0022A L <NA> 0 <NA> <NA> <NA> <NA> 0 <NA>
# 2 NIR0022A L <NA> 0 <NA> <NA> <NA> <NA> 0 <NA>
# 3 NIR0022A L <NA> 0 <NA> <NA> <NA> <NA> 0 <NA>
# 4 NIR0022A R <NA> 0 <NA> <NA> <NA> <NA> 0 <NA>
# 5 NIR0022A L <NA> 0 <NA> <NA> <NA> <NA> 0 <NA>
# tissue_level_scan oil_clay_contamination_scan stained_scan contamination_other_scan notes_scan unscannable_BB unscannable_Broken_MissingPieces unscannable_Crystalized unscannable_sample_mixed unscannable_no_otolith
# 1 <NA> <NA> NA NA <NA> <NA> <NA> <NA> <NA> <NA>
# 2 <NA> <NA> NA NA <NA> <NA> <NA> <NA> <NA> <NA>
# 3 <NA> <NA> NA NA <NA> <NA> <NA> <NA> <NA> <NA>
# 4 <NA> <NA> NA NA <NA> <NA> <NA> <NA> <NA> <NA>
# 5 <NA> <NA> NA NA <NA> <NA> <NA> <NA> <NA> <NA>
# Length_cm Weight_kg Month_Scaled length_prop_max structure_weight_dg shortName
# 1 51.5 1.40 0.4166667 0.5885714 0.228 SABL_1_Combo
# 2 48.5 1.04 0.4166667 0.5542857 0.173 SABL_10_Combo
# 3 56.0 1.96 0.4166667 0.6400000 0.196 SABL_100_Combo
# 4 55.0 1.66 0.4166667 0.6285714 0.265 SABL_11_Combo
# 5 50.5 1.20 0.4166667 0.5771429 0.200 SABL_12_Combo
#
# Total number of oties read in: 1557. Number rejected based on metadata (including missing TMA, when asked for): 8. Number kept: 1549.
#
#
#
# (L) only one otolith in the cell (L) Only one otolith in the cell . (L) only one otolith in the cell.
# 1 1 3
# (L) Only one otolith in the cell. (L) only one otolith in the cell. (L) Only one otolith in the cell.
# 4 5 2
# 10% missing from the posterior end. 5% missing from the posterior end. Anterior portion missing from the otolith
# 1 1 1
# anterior portion missing from the otolith. Anterior portion missing of the otolith Anterior tip missing
# 1 1 1
# Both otoliths missing >30%, so did not weigh. Did scan, otolith missing anterior portion. L: Only one otolith in the cell. Left ololith missing anterior portion. Right otolith BB for TMA
# 1 2 1
# Left otolith was scanned, might had some clay residue on it. Otolith broken in two pieces. Otolith missing posterior end.
# 2 1 1
# tiny <NA>
# 2 1525
# # These are not matched to the scans, since they are unscannable
# Model_Spectra_Meta$unscannable_BB <- Model_Spectra_Meta$unscannable_Broken_MissingPieces <- Model_Spectra_Meta$unscannable_Crystalized <- Model_Spectra_Meta$unscannable_sample_mixed <- Model_Spectra_Meta$unscannable_no_otolith <- NULL
#
# Model_Spectra_Meta$sex <- recode.simple(Model_Spectra_Meta$sex, cbind(c(1, 2, 3), c('M', 'F', 'U'))) # Wow, sex still in numbers!!
# # xyplot(length_cm ~ age_best, group = sex, data = Model_Spectra_Meta, auto = TRUE)
#
# Model_Spectra_Meta$crystallized_scan <- !is.na(Model_Spectra_Meta$crystallized_scan)
# Table(Model_Spectra_Meta$crystallized_scan)
#
# Table(Model_Spectra_Meta$percent_crystallized_scan, Model_Spectra_Meta$crystallized_scan) # All NA percent_crystallized_scan's are zeros
# Model_Spectra_Meta$percent_crystallized_scan[is.na(Model_Spectra_Meta$percent_crystallized_scan)] <- 0 # Change NA to zero so that a numerical test can be done (see below).
# Table(Model_Spectra_Meta$percent_crystallized_scan, Model_Spectra_Meta$crystallized_scan)
#
# Table(Model_Spectra_Meta$broken_scan) # Do all of these broken pieces fit together well? What about entering the number of pieces the otie is broken into - zero for an unbroken ototlith.
# # Are the oties ever broken during scanning or the handling of the otie for scanning?
#
# Table(Model_Spectra_Meta$tip_only_scan) # is there a difference between 'no' and an NA for this one?
#
# Table(Model_Spectra_Meta$anterior_tip_missing)
#
# Table(Model_Spectra_Meta$posterior_tip_missing)
#
# Table(Model_Spectra_Meta$percent_missing_scan)
# Model_Spectra_Meta$percent_missing_scan[is.na(Model_Spectra_Meta$percent_missing_scan)] <- 0 # Now a numerical test can be done (see below).
# Table(Model_Spectra_Meta$percent_missing_scan)
#
# Table(Model_Spectra_Meta$tissue_present_scan)
#
# Table(Model_Spectra_Meta$tissue_level_scan) # Change this to 'percent_tissue_level_scan'?
# Model_Spectra_Meta$tissue_level_scan[is.na(Model_Spectra_Meta$tissue_level_scan)] <- 0 # Now a numerical test can be done (see below).
# Table(Model_Spectra_Meta$tissue_level_scan)
#
# Table(Model_Spectra_Meta$oil_clay_contamination_scan) # No percentage for this one
#
# Table(Model_Spectra_Meta$stained_scan) # All NA's. Is this 'yes'/'no' or percentage?
#
# Table(Model_Spectra_Meta$contamination_other_scan) # All NA's. Is this 'yes'/'no' or percentage?
#
#
# names(Model_Spectra_Meta)[names(Model_Spectra_Meta) %in% 'age_best'] <- "TMA"
# Table(is.finite(Model_Spectra_Meta$TMA))
#
# rev(sort(Model_Spectra_Meta$TMA))[1:20]
#
# dim(Model_Spectra_Meta) # Sable Combo 2022: 1557 rows 535 cols
#
# TF <- !is.na(Model_Spectra_Meta$TMA) & Model_Spectra_Meta$percent_crystallized_scan <= 15 & Model_Spectra_Meta$percent_crystallized_scan <= 10 &
# Model_Spectra_Meta$tissue_level_scan <= 10 & !is.na(Model_Spectra_Meta$length_cm) & !is.na(Model_Spectra_Meta$structure_weight_g)
# c(sum(TF), sum(!TF), sum(TF) + sum(!TF))
#
# sort(fileNamesRemove <- Model_Spectra_Meta$filenames[!TF])
#
# file.remove(paste0(Spectra_Path, "/", fileNamesRemove, ".0"), recursive = TRUE) # Bad raw scans removed here
#
# Model_Spectra_Meta <- Model_Spectra_Meta[TF, ] # --- Doing an overwrite here!! --- Gettin rid of bad scans or ones with no metadata that is wanted
# dim(Model_Spectra_Meta) # Sable Combo 2022: 1528 rows
#
# Model_Spectra_Meta$shortName <- apply(Model_Spectra_Meta[, 'filenames', drop = FALSE], 1, function(x) paste(get.subs(x, sep = "_")[c(1, 5)], collapse = "_"))
#
#
# # Look at the data with plotly and remove rogue oties if needed#
# plotly.Spec(Model_Spectra_Meta, 'all', htmlPlotFolder = paste0(Figures, '/Spectra Figure by TMA'))
# # Model_Spectra_Meta <- Model_Spectra_Meta[!Model_Spectra_Meta$shortName %in% 'HAKE_48', ] # Example of removing a rogue otie for Hake 2019
# # plotly.Spec(Model_Spectra_Meta, 'all') # Decide to save figure with rogue otie or the figure without the rogue otie, or both.
#
save(Model_Spectra_Meta, file = paste0(Spectra_Set, '_Model_Spectra_Meta_ALL_GOOD_DATA.RData')) # 1528
# load(file = paste0(Spectra_Set, '_Model_Spectra_Meta_ALL_GOOD_DATA.RData'))
# TMA only
TMA_Vector <- Model_Spectra_Meta$TMA
length(TMA_Vector) # 1528 After bad scans or missing dat - before saving out oties for final model check
# Save out 15 oties for final model check.
set.seed(Seed_Fold)
TMA_Tab <- Table(TMA_Vector)
(Low_strata <- sum(TMA_Tab[1:3]))
(Mid_strata <- sum(TMA_Tab[4:20]))
(High_strata <- sum(TMA_Tab[21:length(TMA_Tab)]))
(SaveOutOties <- c(sample(order(TMA_Vector)[1:Low_strata], 5), sample(order(TMA_Vector)[Low_strata + 1:Mid_strata], 5), sample(order(TMA_Vector)[Low_strata + Mid_strata + 1:High_strata], 5)) )
sort(TMA_Vector[SaveOutOties]) # Check the results
save(SaveOutOties, file = paste0(Spectra_Set, '_SaveOutOties_Seed_', Seed_Fold, '.RData'))
# TMA_Vector_SaveOutOties <- TMA_Vector[SaveOutOties]
# save(TMA_Vector_SaveOutOties, file = paste0(Spectra_Set, '_TMA_Vector_SaveOutOties.RData'))
#
# Model_Spectra_Meta_SaveOutOties <- Model_Spectra_Meta[SaveOutOties, ]
# save(Model_Spectra_Meta_SaveOutOties, file = paste0(Spectra_Set, '_Model_Spectra_Meta_SaveOutOties.RData'))
dim(Model_Spectra_Meta) # 1528 536
Model_Spectra_Meta <- Model_Spectra_Meta[-SaveOutOties, ] # --- Doing an overwrite here!! ---
dim(Model_Spectra_Meta) # 1513 536
# Now recreate the spectra only file Model_Spectra so that bad rows and saved out oties are removed
Model_Spectra <- cbind(Model_Spectra_Meta[, 2:((1:ncol(Model_Spectra_Meta))[names(Model_Spectra_Meta) %in% 'project'] - 1)]) # --- Overwrite of the spectra only file: Model_Spectra ---
dim(Model_Spectra_Meta) # 1513 536
dim(Model_Spectra) # 1513 507
Model_Spectra[1:3, c(1:2, 505:507)]
# TMA only vector that matches the recreated Model_Spectra above
TMA_Vector <- Model_Spectra_Meta$TMA # --- Doing another overwrite here!! ---
length(TMA_Vector) # 1513
# Use full file names - with '.0' at the end
fileNames.0 <- dir(path = Spectra_Path) # Need new list of filenames after removals above
length(fileNames.0)
fileNames.0[1:5]
# These are the oties that are not used in the NN model and are saved out for testing
sort(fileNames.0[SaveOutOties])
dir.create(paste0(Spectra_Set, '_Saved_Out'), showWarnings = FALSE)
file.copy(paste0(Spectra_Path, "/", fileNames.0[SaveOutOties]), paste0(Spectra_Set, '_Saved_Out'), recursive = TRUE, copy.date = TRUE)
file.remove(paste0(Spectra_Path, "/", fileNames.0[SaveOutOties]), recursive = TRUE) # Leave out raw scans removed here - number of scans left should match Model_Spectra_Meta, Model_Spectra, and TMA_Vector
}
# Savitzky-Golay smoothing
{ ###
###################################################################################################################
### Perform Savitzky-Golay 1st derivative with 17 point window smoothing 2rd order polynomial fit and visualize ###
### Intro: http://127.0.0.1:30354/library/prospectr/doc/prospectr.html
###################################################################################################################
### NOTE ### If there are multiple years of data, all subsequent transformations should be applied to the whole data set, then re-subset
Model_Spectra.sg <- data.frame(prospectr::savitzkyGolay(Model_Spectra, m = 1, p = 2, w = 15))
####################################################
### iPLS algorithm in mdatools ###
####################################################
# Maximum number of components to calculate.
nComp <- c(10, 15)[2]
Model_Spectra.iPLS.F <- mdatools::ipls(Model_Spectra.sg, TMA_Vector, glob.ncomp = nComp, center = TRUE, scale = TRUE, cv = 100,
int.ncomp = nComp, int.num = nComp, ncomp.selcrit = "min", method = "forward", silent = FALSE)
summary(Model_Spectra.iPLS.F)
# iPLS variable selection results
# Method: forward
# Validation: random with 100 segments
# Number of intervals: 15
# Number of selected intervals: 9
# RMSECV for global model: 2.964359 (15 LVs)
# RMSECV for optimized model: 2.880144 (14 LVs)
#
# Summary for selection procedure:
# n start end selected nComp RMSE R2
# 1 0 1 493 FALSE 15 2.964359 0.920
# 2 15 462 493 TRUE 12 3.437861 0.893
# 3 8 232 264 TRUE 15 3.066425 0.915
# 4 6 166 198 TRUE 14 3.037084 0.916
# 5 5 133 165 TRUE 12 3.017657 0.917
# 6 3 67 99 TRUE 14 2.941591 0.921
# 7 13 397 429 TRUE 15 2.927269 0.922
# 8 12 364 396 TRUE 14 2.907818 0.923
# 9 4 100 132 TRUE 15 2.897542 0.924
# 10 11 331 363 TRUE 14 2.883531 0.925
# plot the newly selected spectra regions
browsePlot('plot(Model_Spectra.iPLS.F)')
Model_Spectra.iPLS.F$int.selected
sort(Model_Spectra.iPLS.F$var.selected)
# dev.new() - With a main title
# plot(Model_Spectra.iPLS.F, main = NULL)
# plot predictions before and after selection
browsePlot('
par(mfrow = c(2, 1))
mdatools::plotPredictions(Model_Spectra.iPLS.F$gm) # gm = global PLS model with all variables included
mdatools::plotPredictions(Model_Spectra.iPLS.F$om) # om = optimized PLS model with selected variables
')
browsePlot('mdatools::plotRMSE(Model_Spectra.iPLS.F)')
# RMSE before and after selection
# Visually find the ylim to apply to both figures and over all areas and WB
browsePlot('
par(mfrow = c(2, 1))
mdatools::plotRMSE(Model_Spectra.iPLS.F$gm)
mdatools::plotRMSE(Model_Spectra.iPLS.F$om)
')
# Use the ylim for both plots
browsePlot('
par(mfrow = c(2, 1))
mdatools::plotRMSE(Model_Spectra.iPLS.F$gm, ylim = c(2.4, 6.5))
mdatools::plotRMSE(Model_Spectra.iPLS.F$om, ylim = c(2.4, 6.5))
')
# Select iPLS vars and add metadata wanted
# (p <- length(Model_Spectra.iPLS.F$var.selected)) # 380 freq selected out of a total of 1140
# Model_Spectra.sg.iPLS <- data.frame(Model_Spectra.sg[, sort(Model_Spectra.iPLS.F$var.selected)], length_prop_max = Model_Spectra_Meta$length_cm/max(Model_Spectra_Meta$length_cm),
# structure_weight_dg = 10 * Model_Spectra_Meta$structure_weight_g) # dg = decigram
Model_Spectra.sg.iPLS <- data.frame(Model_Spectra.sg[, sort(Model_Spectra.iPLS.F$var.selected)], Model_Spectra_Meta[, c('length_prop_max', 'structure_weight_dg', 'Month_Scaled')]) # dg = decigram
save(Model_Spectra.sg.iPLS, file = paste0(Spectra_Set, '_Model_Spectra.sg.iPLS.RData'))
save(TMA_Vector, file = paste0(Spectra_Set, '_TMA_Vector.RData'))
if(FALSE) {
Model_Spectra.Age.sg.iPLS <- data.frame(Age = TMA_Vector, Model_Spectra.sg.iPLS)
dim(Model_Spectra.Age.sg.iPLS)
# 2D plot
# Model_Spectra.sg.iPLS.PLOT <- cbind(Model_Spectra_Meta[, 1, drop = FALSE], Model_Spectra.sg.iPLS, Model_Spectra_Meta[, ncol(Model_Spectra):ncol(Model_Spectra_Meta)])
# plotly.Spec(Model_Spectra.sg.iPLS.PLOT, 'all')
# Plot the transformed spectra by age using only variables selected using iPLS
(Model_Spectra.Age.sg.iPLS.Long <- reshape2::melt(Model_Spectra.Age.sg.iPLS, id = 'Age', variable.name = 'Freq', value.name = 'Absorbance'))[1:4, ]
Model_Spectra.Age.sg.iPLS.Long$Freq <- as.numeric(substring(Model_Spectra.Age.sg.iPLS.Long$Freq, 2))
Model_Spectra.Age.sg.iPLS.Long <- sort.f(Model_Spectra.Age.sg.iPLS.Long, 'Freq')
Model_Spectra.Age.sg.iPLS.Agg <- aggregate(list(Absorbance = Model_Spectra.Age.sg.iPLS.Long$Absorbance),
list(Freq = Model_Spectra.Age.sg.iPLS.Long$Freq, Age = Model_Spectra.Age.sg.iPLS.Long$Age), mean, na.rm = TRUE)
Model_Spectra.Age.sg.iPLS.Agg$Age <- ordered(Model_Spectra.Age.sg.iPLS.Agg$Age, sort(unique(Model_Spectra.Age.sg.iPLS.Agg$Age)))
plotly::ggplotly(ggplot2::ggplot(data = Model_Spectra.Age.sg.iPLS.Agg, aes(x = Freq, y = Absorbance, z = Age)) + geom_line(aes(colour = Age), size = 0.2) +
scale_color_manual(values=rainbow(length(unique(Model_Spectra.Age.sg.iPLS.Agg$Age)), alpha = 1)))
# --------------- Try ipls() with smoothed spectra data and metadata - NO METADATA WAS SELECTED HERE ------------------------
# Remove NA's with predictors and response together - then re-split
Model_Spectra.sg.META <- na.omit(cbind(Model_Spectra.sg, Model_Spectra_Meta[, c("latitude", "longitude", "length", "weight", "sex")], TMA = TMA_Vector))
Ncol <- ncol(Model_Spectra.sg.META)
Model_Spectra.sg.META[1:3, c(1:2, (Ncol - 4):Ncol)]
TMA.META <- Model_Spectra.sg.META[, Ncol]
Model_Spectra.sg.META <- Model_Spectra.sg.META[, -Ncol]
Model_Spectra.iPLS.META.F <- mdatools::ipls(Model_Spectra.sg.META, TMA.META, glob.ncomp = nComp, center = TRUE, scale = TRUE, cv = 100,
int.ncomp = nComp, int.num = nComp, ncomp.selcrit = "min", method = "forward", silent = FALSE)
summary(Model_Spectra.iPLS.META.F)
# Plot the newly selected spectra regions
dev.new()
plot(Model_Spectra.iPLS.META.F)
Model_Spectra.iPLS.META.F$int.selected
sort(Model_Spectra.iPLS.META.F$var.selected)
Model_Spectra.sg.META[, Model_Spectra.iPLS.F$var.selected][1:3, c(1:3, 373:380)]
names(Model_Spectra.sg.META[, Model_Spectra.iPLS.F$var.selected])
}
}
} ###
# --- NN Model ---
{ ###
# Load the data if needed
base::load(paste0(Spectra_Set, '_Model_Spectra.sg.iPLS.RData')); print(dim(Model_Spectra.sg.iPLS))
# base::load(paste0(Spectra_Set, '_TMA_Vector.RData')); print(length(TMA_Vector))
base::load(paste0(Spectra_Set, '_Model_Spectra_Meta_ALL_GOOD_DATA.RData')) # Model_Spectra_Meta with SaveOutOties removed is only needed for TMA_Vector and the 'filenames' below
base::load(paste0(Spectra_Set, '_SaveOutOties_Seed_727.RData')); print(length(SaveOutOties))
Model_Spectra_Meta <- Model_Spectra_Meta[-SaveOutOties, ]; print(dim(Model_Spectra_Meta))
print(Model_Spectra_Meta[1:3, c(1, (grep('project', names(Model_Spectra_Meta))):ncol(Model_Spectra_Meta))])
TMA_Vector <- Model_Spectra_Meta$TMA
print(length(TMA_Vector))
fileNames = Model_Spectra_Meta$filenames
print(length(fileNames))
# ----- Remove both metadata columns for testing -----
# Model_Spectra.sg.iPLS$length_prop_max <- Model_Spectra.sg.iPLS$structure_weight_dg <- NULL
# ----- Leave only the fish length for testing -----
# Model_Spectra.sg.iPLS$structure_weight_dg <- NULL
# ----- Leave only the otie weight for testing -----
# Model_Spectra.sg.iPLS$length_prop_max <- NULL
print(dim(Model_Spectra.sg.iPLS))
# print(Model_Spectra.sg.iPLS$length_prop_max[1:4])
# print(Model_Spectra.sg.iPLS$structure_weight_dg[1:4])
print(headTail(Model_Spectra.sg.iPLS, 3, 0, 3, 5))
# --------- Special code to test 'Month_Scaled', 'Depth_m', 'Sex', 'Weight_kg', 'Days_into_Year', and reduced model size in the NN Model with the same scans in Model_Spectra.sg.iPLS ------------------------------
base::load("C:\\ALL_USR\\JRW\\SIDT\\Get Otie Info from Data Warehouse\\selectSpAgesFramFeb2024.RData") # From NWFSC Data Warehouse
# ===> Fish length and Otie Wgt: # SAD: 2050; RMSE: 2.7280
# Model_Spectra.sg.iPLS <- match.f(data.frame(Model_Spectra.sg.iPLS, specimen_id = as.character(Model_Spectra_Meta$specimen_id)), selectSpAgesFramFeb2024, "specimen_id", "AgeStr_id", c('Month_Scaled', 'Depth_m', 'Sex', 'Weight_kg')) # Very poor results
# Model_Spectra.sg.iPLS <- match.f(data.frame(Model_Spectra.sg.iPLS, specimen_id = as.character(Model_Spectra_Meta$specimen_id)), selectSpAgesFramFeb2024, "specimen_id", "AgeStr_id", c('Month_Scaled', 'Weight_kg', 'Depth_m')) # SAD: 2029; RMSE: 2.7678
Model_Spectra.sg.iPLS <- match.f(data.frame(Model_Spectra.sg.iPLS, specimen_id = as.character(Model_Spectra_Meta$specimen_id)), selectSpAgesFramFeb2024, "specimen_id", "AgeStr_id", c('Weight_kg', 'Depth_m')) # SAD: 2002; RMSE: 2.6742
# Model_Spectra.sg.iPLS <- match.f(data.frame(Model_Spectra.sg.iPLS, filenames = Model_Spectra_Meta$filenames, specimen_id = as.character(Model_Spectra_Meta$specimen_id)), selectSpAgesFramFeb2024, "specimen_id", "AgeStr_id", c('Weight_kg', 'Depth_m', 'Length_cm', 'Age')) # Stratified Random
# Model_Spectra.sg.iPLS <- match.f(data.frame(Model_Spectra.sg.iPLS, specimen_id = as.character(Model_Spectra_Meta$specimen_id)), selectSpAgesFramFeb2024, "specimen_id", "AgeStr_id", 'Weight_kg') # SAD: 2088; RMSE: 2.7389
# Model_Spectra.sg.iPLS <- match.f(data.frame(Model_Spectra.sg.iPLS, specimen_id = as.character(Model_Spectra_Meta$specimen_id)), selectSpAgesFramFeb2024, "specimen_id", "AgeStr_id", 'Depth_m') # SAD: 2042; RMSE: 2.7404
# Model_Spectra.sg.iPLS <- match.f(data.frame(Model_Spectra.sg.iPLS, specimen_id = as.character(Model_Spectra_Meta$specimen_id)), selectSpAgesFramFeb2024, "specimen_id", "AgeStr_id", 'Month_Scaled') # SAD: ????; RMSE: ????
# Model_Spectra.sg.iPLS <- match.f(data.frame(Model_Spectra.sg.iPLS, specimen_id = as.character(Model_Spectra_Meta$specimen_id)), selectSpAgesFramFeb2024, "specimen_id", "AgeStr_id", c('Weight_kg', 'Depth_m', 'Days_into_Year')) # SAD: 2090; RMSE: 2.8047
Model_Spectra.sg.iPLS$specimen_id <- NULL # specimen_id only needed for the matching above
# ---- Metadata only model run----
# Commented out the random selection code below so that the number oties is not reduced
Model_Spectra.sg.iPLS <- Model_Spectra.sg.iPLS[, (grep('length_prop_max', names(Model_Spectra.sg.iPLS))):ncol(Model_Spectra.sg.iPLS)]
headTail(Model_Spectra.sg.iPLS, 3, 2, 3, 5)
# Check for missing data
print(dim(Model_Spectra.sg.iPLS))
print(dim(na.omit(Model_Spectra.sg.iPLS)))
################ OLD ###############
# These 3 oties in the metadata were missing from the Data WareHouse: AgeStr_id %in% 102133144:102133146 ????????????????
# Model_Spectra.sg.iPLS$Month_Scaled[is.na(Model_Spectra.sg.iPLS$Month_Scaled)] <- 6:8/12
# Model_Spectra.sg.iPLS$Depth_m[is.na(Model_Spectra.sg.iPLS$Depth_m)] <- mean(Model_Spectra.sg.iPLS$Depth_m, na.rm = TRUE)
# Model_Spectra.sg.iPLS$Weight_kg[is.na(Model_Spectra.sg.iPLS$Weight_kg)] <- mean(Model_Spectra.sg.iPLS$Weight_kg, na.rm = TRUE)
# Model_Spectra.sg.iPLS$Sex[is.na(Model_Spectra.sg.iPLS$Sex)] <- c('M','F', 'M')
# print(dim(na.omit(Model_Spectra.sg.iPLS)))
# print(headTail(Model_Spectra.sg.iPLS, 3, 2, 3, 5))
################################
if(!is.null(Model_Spectra.sg.iPLS$Sex)) {
Model_Spectra.sg.iPLS$Sex_prop_max <- as.numeric(recode.simple(Model_Spectra.sg.iPLS$Sex, data.frame(c('F','M', 'U'), 0:2)))/2 # ** All variables have to be numeric **
Model_Spectra.sg.iPLS$Sex <- NULL
}
if(!is.null(Model_Spectra.sg.iPLS$Depth_m)) {
Model_Spectra.sg.iPLS$Depth_prop_max <- (Model_Spectra.sg.iPLS$Depth_m - min(Model_Spectra.sg.iPLS$Depth_m))/(max(Model_Spectra.sg.iPLS$Depth_m) - min(Model_Spectra.sg.iPLS$Depth_m))
Model_Spectra.sg.iPLS$Depth_m <- NULL
}
if(!is.null(Model_Spectra.sg.iPLS$Weight_kg)) {
Model_Spectra.sg.iPLS$Weight_prop_max <- (Model_Spectra.sg.iPLS$Weight_kg - min(Model_Spectra.sg.iPLS$Weight_kg))/(max(Model_Spectra.sg.iPLS$Weight_kg) - min(Model_Spectra.sg.iPLS$Weight_kg))
Model_Spectra.sg.iPLS$Weight_kg <- NULL
}
if(!is.null(Model_Spectra.sg.iPLS$Days_into_Year)) {
Model_Spectra.sg.iPLS$Days_into_Year_prop_max <- (Model_Spectra.sg.iPLS$Days_into_Year - min(Model_Spectra.sg.iPLS$Days_into_Year))/(max(Model_Spectra.sg.iPLS$Days_into_Year) - min(Model_Spectra.sg.iPLS$Days_into_Year))
Model_Spectra.sg.iPLS$Days_into_Year <- NULL
}
headTail(Model_Spectra.sg.iPLS, 3, 2, 3, 5)
# = = = = = = = = = = = = = = = = = Intial setup = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
# Special seed setting for model testing
Seed_Fold <- 787 # Seed_Fold = 787 for Run 3. Seed 747 used for Fish_Len_Otie_Wgt_Run_2 . Using a different seed starting here, to test main run of Sable_2022 with fish length and otie weight (and other metadata runs)
# Seed_Fold = 727 used in the code above and for previous runs (Fish_Len_Otie_Wgt Run 1) of Sable_2022 before 28 Dec 2023
# ------- Reduce model size to see the change in prediction ability ----------------------
set.seed(Seed_Fold)
# --- Random selection of a reduced number of oties ---
# Rdm_Oties <- sample(1:nrow(Model_Spectra.sg.iPLS), 750) # nrow(Model_Spectra.sg.iPLS) for Sablefish 2022 is 1,513
#
# Model_Spectra.sg.iPLS <- Model_Spectra.sg.iPLS[Rdm_Oties, ]
# print(dim(Model_Spectra.sg.iPLS))
# print(headTail(Model_Spectra.sg.iPLS, 3, 2, 3, 5))
#
# # Model_Spectra_Meta <- Model_Spectra_Meta[Rdm_Oties, ]
# # print(Model_Spectra_Meta[1:3, c(1, (grep('project', names(Model_Spectra_Meta))):ncol(Model_Spectra_Meta))])
#
# TMA_Vector <- TMA_Vector[Rdm_Oties]
# print(length(TMA_Vector))
#
# fileNames = Model_Spectra_Meta$filenames[Rdm_Oties]
# print(length(fileNames))
# --- Stratified random selection of a reduced number of oties---
# print(Bin_Num <- Table(factor.f(Model_Spectra.sg.iPLS$Length_cm, breaks = c(0, 25, 45, 65, Inf))))
# print(Mid_Split <- (500 - Bin_Num[1] - Bin_Num[4])/2)
#
# Model_Spectra.sg.iPLS <- rbind(Model_Spectra.sg.iPLS[Model_Spectra.sg.iPLS$Length_cm <= 25 | Model_Spectra.sg.iPLS$Length_cm > 65, ],
# Model_Spectra.sg.iPLS[Model_Spectra.sg.iPLS$Length_cm > 25 & Model_Spectra.sg.iPLS$Length_cm <= 45, ][sample(1:Bin_Num[2], floor(Mid_Split)), ],
# Model_Spectra.sg.iPLS[Model_Spectra.sg.iPLS$Length_cm > 45 & Model_Spectra.sg.iPLS$Length_cm <= 65, ][sample(1:Bin_Num[2], ceiling(Mid_Split)), ])
# print(dim(Model_Spectra.sg.iPLS))
#
# TMA_Vector <- Model_Spectra.sg.iPLS$Age
# fileNames <- Model_Spectra.sg.iPLS$filenames
#
# Model_Spectra.sg.iPLS$Length_cm <- NULL
# Model_Spectra.sg.iPLS$Age <- NULL
# Model_Spectra.sg.iPLS$filenames <- NULL
#
# print(headTail(Model_Spectra.sg.iPLS, 3, 2, 3, 5))
# --- Setup graphic windows ---
graphics.off()
dev.new(width = 14, height = 6) #2
dev.new() # 3
dev.new(width = 11, height = 8) # 4
dev.new(width = 11, height = 8) # 5
dev.new(width = 10, height = 10) # 6
dev.new(width = 10, height = 10) # 7
# = = = = = = Pick number of random reps (Rdm_reps), number of folds (num_folds), and iteration number (Iter_Num), then run the NN code to the next '= = =' line and expect long run times = = = = = = = = =
Rdm_reps <- 20 # j loop
num_folds <- 20 # i loop # Checking how many folds work best for metadata only model
Iter_Num <- 8 # Iter while() loop
# (Rdm_reps <- ifelse(model_Name == 'FCNN_model_ver_1', 20, 10))
Seed_Main <- Seed_Fold + 20 # Seed_Fold 747 used for Fish_Len_Otie_Wgt_Run_2. Seed_Main <- 707 used for previous runs of Sable_2022 before 28 Dec 2023 # Reducing the number of seeds will be considered later
set.seed(Seed_Main)
Seed_reps <- sample(1e7, Rdm_reps)
# Start fresh or continue by loading a file with model iterations already finished (see the commented line with an example model file).
Rdm_models <- list()
Rdm_folds_index <- list()
# base::load("Sable_Combo_2022_FCNN_model_ver_1_1_Rdm_model_11_Mar_2024_12_38_45.RData")
file.create('Run_NN_Model_Flag', showWarnings = TRUE) # Stopping the model with this flag is broken by the nested loops, but left for now in a hope that it can prehaps be fixed.
# Note that errors from plot.loess() are trapped by try() and are normal early in the iteration loop since there is not enough data to smooth.
for(j in (length(Rdm_folds_index) + 1):Rdm_reps) {
cat(paste0("\n\nStart of Random Rep = ", j , "\n\n"))
Seed_Data <- Seed_reps[j]
# Split the data into folds, spitting the remainder of an un-even division into the first folds, one otie per fold until finished.
# The split is based on the current seed which is dictated by Seed_Main (see above).
set.seed(Seed_Data)
index_org <- 1:nrow(Model_Spectra.sg.iPLS)
(fold_size_min <- floor(length(index_org)/num_folds))
(num_extra <- num_folds * dec(length(index_org)/num_folds))
index <- index_org
folds_index <- list()
for(i in 1:(num_folds - 1)) {
print(c(fold_size_min, i, num_extra, i <= num_extra, fold_size_min + ifelse(i <= num_extra, 1, 0), i - num_extra))
folds_index[[i]] <- sample(index, fold_size_min + ifelse(i < (num_extra + 0.1), 1, 0)) # Finite math - grr!
index <- index[!index %in% folds_index[[i]]]
}
folds_index[[num_folds]] <- index # Remainder from the above for() loop goes into the last fold index
print(lapply(folds_index, length)) # Check the binning result
print(c(sum(unlist(lapply(folds_index, length))), length(index_org)))
Fold_models <- list()
for (i in 1:num_folds) {
Model_Spectra.sg.iPLS.F <- Model_Spectra.sg.iPLS[-folds_index[[i]], ]
TMA_Vector.F <- TMA_Vector[-folds_index[[i]]]
# Split the data into training set (2/3) and test set (1/3)
set.seed(Seed_Data)
index <- 1:nrow(Model_Spectra.sg.iPLS.F)
testindex <- sample(index, trunc(length(index)/3))
x.test <- 1000 * Model_Spectra.sg.iPLS.F[testindex, ]
x.train <- 1000 * Model_Spectra.sg.iPLS.F[-testindex, ]
y.test <- TMA_Vector.F[testindex]
y.train <- TMA_Vector.F[-testindex]
cat(paste0("\n\nDimension of x.train = ", paste(dim(x.train), collapse = ' '), '\n\n')) # 906 380; 905 380 with crystallized otie removed
# Same learning rate for all models
learningRate <- c(0.00088, 0.0009)[2]
layer_dropout_rate <- NULL
# layer_dropout_rate <- 0.2
if(model_Name == 'FCNN_model_ver_1') model <- FCNN_model_ver_1(layer_dropout_rate = layer_dropout_rate)
if(model_Name == 'CNN_model_ver_5') model <- CNN_model_ver_5()
if(model_Name == 'CNN_model_2D') model <- CNN_model_2D()
# -- Don't reset Iter, Cor, CA_diag, SAD, or .Random.seed when re-starting the same run ---
tensorflow::set_random_seed(Seed_Model, disable_gpu = Disable_GPU); Seed_Model # Trying to this here and above (see the help for: tensorflow::set_random_seed)
set.seed(Seed_Data); Seed_Data # Re-setting the 'data' seed here to know where the model starts, also the Keras backend needs to cleared and the model reloaded - see above.
Iter <- 0
Cor <- RMSE <- CA_diag <- SAD <- saveModels <- NULL
saveModels_List <- list()
while(file.exists('Run_NN_Model_Flag')) { # The multiple full fold version breaks the stop by removing the file flag, but it remains for now
# R memory garbage collection
gc()
# Clear TensorFlow's session
k_clear_session()
(Iter <- Iter + 1)
cat(paste0("\n\nRandom Replicates = ", j, ": Fold number = ", i, ": Iter = ", Iter,"\n"))
if(Iter > 1) {
Iter_Loop_Time_Min <- as.numeric(difftime(Sys.time(), Loop_Start_Time, units = "mins"))
cat("\nThe last 500 epochs took", format(Iter_Loop_Time_Min, digits = 4), "minutes. ") # 500 epochs is hardwired - see below
Time_Left_Min <- ((Rdm_reps - j + 1) * num_folds * Iter_Num + (num_folds - i + 1) * Iter_Num + (Iter_Num - Iter + 1)) * Iter_Loop_Time_Min
if(Time_Left_Min < 60) cat("Around", format(Time_Left_Min, digits = 4), "minutes left.\n\n")
if(Time_Left_Min >= 60 & Time_Left_Min < 60 * 24) cat("Around", format(Time_Left_Min/60, digits = 4), "hours left.\n\n")
if(Time_Left_Min >= 60 * 24) cat("Around", format(Time_Left_Min/60/24, digits = 4), "days left.\n\n")
}
Loop_Start_Time <- Sys.time()
# config <- tf$compat.v1.ConfigProto(intra_op_parallelism_threads = 2L, inter_op_parallelism_threads = 2L)
# session <- tf$Session(config = config)
# k_set_session(session)
# blas_set_num_threads(4)
# blas_get_num_procs()
# FCNN model
if(model_Name == 'FCNN_model_ver_1') {
x.train.array <- as.matrix(x.train)
# callback_tensorboard() writes a log for TensorBoard, which allows you to visualize dynamic graphs of your training and test metrics.
history <- fit(model, x.train.array, y.train, epochs = 1, batch_size = 32, validation_split = 0.2, verbose = 2,
callbacks = if(file.exists('NN_Verbose_Flag.txt')) list(callback_tensorboard(histogram_freq = 1, profile_batch = 2)) else NULL, view_metrics = FALSE)
history <- fit(model, x.train.array, y.train, epochs = 198, batch_size = 32, validation_split = 0.2, verbose = ifelse(file.exists('NN_Verbose_Flag.txt'), 2, 0), view_metrics = ifelse(file.exists('NN_Verbose_Flag.txt'), TRUE, FALSE))
history <- fit(model, x.train.array, y.train, epochs = 1, batch_size = 32, validation_split = 0.2, verbose = 2, view_metrics = FALSE)
history <- fit(model, x.train.array, y.train, epochs = 99, batch_size = 32, validation_split = 0.2, verbose = 0, view_metrics = FALSE)
history <- fit(model, x.train.array, y.train, epochs = 1, batch_size = 32, validation_split = 0.2, verbose = 2, view_metrics = FALSE)
history <- fit(model, x.train.array, y.train, epochs = 200, batch_size = 32, validation_split = 0.2, verbose = 0, view_metrics = FALSE)
x.test.array <- as.matrix(x.test)
}
viewMetrics <- c(TRUE, FALSE)[2]
# CNN_model ver 1,3,4,5
if(model_Name == 'CNN_model_ver_5') {
x.train.array <- array(as.matrix(x.train), c(nrow(x.train), ncol(x.train), 1))
history <- fit(model, x.train.array, y.train, epochs = 50, batch_size = 32, validation_split = 0.2, verbose = 2,
view_metrics = viewMetrics)
# view_metrics = viewMetrics, callbacks = list(callback_tensorboard(histogram_freq = 1, profile_batch = 2))) # profile_batch = c(1, 5)
x.test.array <- array(as.matrix(x.test), c(nrow(x.test), ncol(x.test), 1))
}
# CNN_model ver 2
# x.train.array <- array(as.matrix(x.train), c(nrow(x.train), ncol(x.train), 1))
# history <- fit(model, x.train.array, y.train, epochs = 1, batch_size = 32, validation_split = 0.2, verbose = 2, view_metrics = viewMetrics)
# history <- fit(model, x.train.array, y.train, epochs = 99, batch_size = 32, validation_split = 0.2, verbose = 0, view_metrics = viewMetrics)
# history <- fit(model, x.train.array, y.train, epochs = 1, batch_size = 32, validation_split = 0.2, verbose = 2, view_metrics = viewMetrics)
# history <- fit(model, x.train.array, y.train, epochs = 199, batch_size = 32, validation_split = 0.2, verbose = 0, view_metrics = viewMetrics)
# x.test.array <- array(as.matrix(x.test), c(nrow(x.test), ncol(x.test), 1))
if(model_Name == 'CNN_model_2D') {
x.train.array <- array(as.matrix(x.train), c(nrow(x.train), ncol(x.train), 1))
history <- fit(model, x.train.array, y.train * diag(length(y.train)), epochs = 50, batch_size = 32, validation_split = 0.2, verbose = 2, view_metrics = viewMetrics)
x.test.array <- array(as.matrix(x.test), c(nrow(x.test), ncol(x.test), 1))
}
evaluate(model, x.test.array, y.test, verbose = 0)
cat("\n")
print(summary(history))
dev.set(3)
print(plot(history))
if(file.exists('NN_Verbose_Flag.txt'))
browsePlot('print(plot(history))', file = paste0("NN_History_Iter_", Iter, ".png")) # Save NN History figures
# Predict using the test set; plot, create statistics, and create an agreement table
y.test.pred <- predict(model, x.test.array)
if(model_Name == 'FCNN_model_ver_1' & is.null(layer_dropout_rate)) Delta <- -0.05 # Delta is a previous estimate or guess for now, which varies by species.
if(model_Name == 'FCNN_model_ver_1' & !is.null(layer_dropout_rate)) Delta <- -0.3
if(model_Name == 'CNN_model_ver_5') Delta <- -0.2
if(model_Name == 'CNN_model_2D') Delta <- 0
y.test.pred.rd <- round(y.test.pred + Delta) # Rounding with a added delta (which is a negative number)
dev.set(4)
# plot(y.test, y.test.pred)
# abline(0, 1, col = 'green', lty = 2)
print(predicted_observed_plot(y.test, y.test.pred, xlab = 'y.test', ylab = 'y.test.pred'))
# SAD vector the Sum of absolute differences plot
# SAD <- c(SAD, sqrt(sum((y.test - y.test.pred.rd)^2)/(length(y.test) - 1))) # RMSE
SAD <- c(SAD, sum(abs(y.test - y.test.pred.rd)))
# Correlation vector for the iterations plot
Cor <- c(Cor, cor(y.test, y.test.pred))
# RMSE vector for the iterations plot
RMSE <- c(RMSE, sqrt(mean((y.test - y.test.pred)^2, na.rm = TRUE)))
# e1071::classAgreement diagonal
CA_diag <- c(CA_diag, e1071::classAgreement(Table(y.test.pred.rd, y.test), match.names = FALSE)$diag)
cat("\nclassAgreement Diagonal =", rev(CA_diag)[1], "\n")
cat("\n\n")
# print(e1071::classAgreement(Table(y.test.pred.rd, y.test), match.names = TRUE)$diag) # match.names = TRUE option
# Correlation Between Sum of Absolute Differences and the classAgreement diagonal
if(length(SAD) >= 10)
# cat("\nCorrelation between sum of Absolute Differences and the classAgreement Diagonal =", signif(cor(SAD[5:length(SA)], CA_diag[5:length(CA_diag)]), 6), "\n")
cat("\nCorrelation between sum of Absolute Differences and the classAgreement Diagonal =", signif(cor(SAD, tail(CA_diag, length(SAD))), 6), "\n")
# dev.new(width = 14, height = 10)
# agreementFigure(y.test, y.test.pred, Delta, full = TRUE)
dev.set(5) # agreementFigure() also prints out the Correlation, R_squared, RMSE, MAE, SAD (Sum of Absolute Differences)
agreementFigure(y.test, y.test.pred, Delta, main = paste0("Random Reps = ", j, ": Fold Num = ", i, ": Iter = ", Iter))
dev.set(2)
par(mfrow = c(3, 1))
plot(1:length(RMSE), RMSE, col = 'green', type = 'b', ylab = "RMSE (green)", xlab = "Iteration Number")
abline(h = 4, lty = 2, col ='grey39', lwd = 1.25)
if(Iter < 5)
try(plot(1:length(CA_diag), CA_diag, col = 'red', type = 'b', ylab = "Diagonal of Class Agreement (red)", xlab = "Iteration Number"))
else
try(plot.loess(1:length(CA_diag), CA_diag, col = 'red', line.col = 'deeppink', type = 'b', ylab = "Diagonal of Class Agreement (red)", xlab = "Iteration Number"))
abline(h = 0.2, lty = 2, col ='grey39', lwd = 1.25)
# Avoiding high SAD values at the beginning, and rarely, during a run.
SAD_plot <- SAD
SAD_plot[SAD_plot > 1400] <- NA # Extreme model runs can, on a very rare occasion, put the value of SAD above 1,400 beyond the initial runs
if(Iter < 5)
try(plot(1:length(SAD_plot), SAD_plot, col = 'blue', type = 'b', ylab = "Sum of Absolute Differences (blue)", xlab = "Iteration Number"))
else
try(plot.loess(1:length(SAD_plot), SAD_plot, col = 'blue', line.col = 'dodgerblue', type = 'b', ylab = "Sum of Absolute Differences (blue)", xlab = "Iteration Number"))
abline(h = 950, lty = 2, col ='grey39', lwd = 1.25)
# Save all the iteration models until the best one is found
print(saveName <- paste0(Spectra_Set, '_', paste(get.subs(model_Name, "_")[-2], collapse = "_"), '_SM_', Seed_Model, '_RI_', j, '_LR_',
format(learningRate, sci = FALSE), '_LD_', ifelse(is.null(layer_dropout_rate), 0, layer_dropout_rate), '_It_', length(SAD),
'_SAD_', rev(SAD)[1], '_', timeStamp()))
assign(saveName, keras::serialize_model(model, include_optimizer = TRUE))
# save(Iter, Cor, CA_diag, SAD, learningRate, layer_dropout_rate, .Random.seed, list = saveName, file = paste0(saveName, '.RData')) # For debugging
saveModels <- c(saveModels, saveName)
saveModels_List[[saveName]] <- keras::serialize_model(model, include_optimizer = TRUE)
if(Iter == Iter_Num)
break
} # Iter while() loop
if(!file.exists('Run_NN_Model_Flag'))
break
Iter_Best_Model <- sort.f(data.frame(SAD, RMSE, CA_diag, Iter = 1:Iter_Num), c(1, 2))[1, 4] # Best model is when SAD is lowest, with ties broken by RMSE
print(sort.f(data.frame(SAD, RMSE, CA_diag, Iter = 1:Iter_Num), c(1, 3)))
cat(paste0('\n\nBest_Model Number = ', Iter_Best_Model, '\n\n'))
Fold_models[[i]] <- saveModels_List[[Iter_Best_Model]]
cat(paste0('\nBest Model Name = ', saveModels[Iter_Best_Model], "\n\n"))
rm(list = saveModels)
x.fold.test <- as.matrix(1000 * Model_Spectra.sg.iPLS[folds_index[[i]], ])
y.fold.test <- TMA_Vector[folds_index[[i]]]
y.fold.test.pred <- predict(keras::unserialize_model(Fold_models[[i]], custom_objects = NULL, compile = TRUE), x.fold.test)
dev.set(6)
agreementFigure(y.fold.test, y.fold.test.pred, Delta = Delta, full = TRUE, main = paste0("Random Rep = ", j, ": Fold Num = ", i))
dev.set(7)
agreementFigure(y.fold.test, y.fold.test.pred, Delta = Delta, full = FALSE, main = paste0("Random Rep = ", j, ": Fold Num = ", i))
} # j Fold loop
if(!file.exists('Run_NN_Model_Flag'))
break
Rdm_models[[j]] <- Fold_models # List of lists being assigned to an element of a list - the best model for each fold (10 or other used) within the jth random rep
Rdm_folds_index[[j]] <- folds_index # List of vectors being assigned to an element of a list - the index for each fold (10 or other used) within the jth random rep
x.fold.test.ALL <- NULL
y.fold.test.ALL <- NULL
y.fold.test.pred.ALL <- NULL
for (k in 1:length(Fold_models)) {
x.fold.test <- as.matrix(1000 * Model_Spectra.sg.iPLS[folds_index[[k]], ])
x.fold.test.ALL <- rbind(x.fold.test.ALL, x.fold.test)
y.fold.test.ALL <- c(y.fold.test.ALL, TMA_Vector[folds_index[[k]]])
print(length(predict(keras::unserialize_model(Fold_models[[k]], custom_objects = NULL, compile = TRUE), x.fold.test)))
y.fold.test.pred.ALL <- c(y.fold.test.pred.ALL, predict(keras::unserialize_model(Fold_models[[k]], custom_objects = NULL, compile = TRUE), x.fold.test))
}
browsePlot('agreementFigure(y.fold.test.ALL, y.fold.test.pred.ALL, Delta = Delta, full = TRUE, main = paste0("Random Rep = ", j))')
SG_Variables_Selected <- names(Model_Spectra.sg.iPLS)
roundingDelta <- Delta # This Delta is only the previous estimate or guess for now (see above). The best rounding Delta is again tested for in the predict script.
save(Iter, i, j, Cor, CA_diag, SAD, learningRate, layer_dropout_rate, Seed_Fold, Seed_Model, Seed_Main, Rdm_models,
Rdm_folds_index, SG_Variables_Selected, roundingDelta, file = paste0(Spectra_Set, '_', model_Name, '_', length(Rdm_folds_index), '_Rdm_model_', timeStamp(), '.RData'))
} # k Random Replicate loop
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
} ###
# --- Find Median over all Rdm_reps Models and create figures ---
{ ###
# Only 2 loads needed to redo this section with new data - the Model_Spectra.sg.iPLS has to, of course, match the Rdm_model and Rdm_folds_index and the Conda eniv needs to be loaded properly using the code above.
# base::load("C:\\ALL_USR\\JRW\\SIDT\\Sablefish 2022 Combo\\Sable_Combo_2022_NN_Fish_Len_Otie_Wgt_GPU_Machine\\Sable_Combo_2022_FCNN_model_ver_1_5_Rdm_model_21_Dec_2023_08_14_19.RData")
# base::load("C:\\ALL_USR\\JRW\\SIDT\\Sablefish 2022 Combo\\Sable_Combo_2022_NN_Fish_Len_Otie_Wgt\\Sable_Combo_2022_Model_Spectra.sg.iPLS.RData")
# A generic Model_Spectra.sg.iPLS may need metadata added to the scans - compare to the end of SG_Variables_Selected (found within e.g. ...FCNN_model_ver_1_20_Pred_Median_TMA.RData).
# If the model has a reduced number of otoliths, then the correct Run number's pseudo random number seed has to set.
# cor(Sable_Combo_2022_NN_Pred_Median_TMA$TMA, TMA_Vector) needs to be 1 (one).
# ----------------------- Put the fitted results for each random reps (Rdm_reps) full fold model into a data frame: y.fold.test.pred_RDM ------------------------
(Rdm_reps <- length(Rdm_folds_index))
y.fold.test.pred_RDM <- NULL
for (j in 1:Rdm_reps) {
folds_index <- Rdm_folds_index[[j]]
Fold_models <- Rdm_models[[j]]
y.fold.test.pred.ALL <- NULL
for (i in 1:length(Fold_models)) {
if(verbose)
cat(paste0("\nRdm_reps ", j, ": Fold_model ", i, "\n"))
x.fold.test <- as.matrix(1000 * Model_Spectra.sg.iPLS[folds_index[[i]], ])
y.fold.test.pred <- as.vector(predict(keras::unserialize_model(Fold_models[[i]], custom_objects = NULL, compile = TRUE), x.fold.test))
if(verbose)
print(c(length(folds_index[[i]]), length(y.fold.test.pred)))
y.fold.test.pred.ALL <- rbind(y.fold.test.pred.ALL, cbind(Index = folds_index[[i]], y.test.fold.pred = y.fold.test.pred))
}
cat(paste0("\nFold_model ", j, "\n"))
print(dim(y.fold.test.pred.ALL ))
y.test.pred <- sort.f(data.frame(y.fold.test.pred.ALL))[, 2] # Sort on the Index to match back to the order of the full TMA_Vector and Model_Spectra.sg.iPLS
y.fold.test.pred_RDM <- rbind(y.fold.test.pred_RDM, y.test.pred)
cat(paste0("\nRdm_reps ", j, "\n"))
print(dim(y.fold.test.pred_RDM))
# dev.new(width = 11, height = 8)
# agreementFigure(TMA_Vector, y.test.pred, Delta = -0.05, full = TRUE, main = paste0("Random Rep = ", j))
# if(verbose)
# browsePlot('agreementFigure(TMA_Vector, y.test.pred, Delta = -0.05, full = TRUE, main = paste0("Random Rep = ", j))') # Delta is a previous estimate or guess for now
# Full figure only needed for a long-lived species like Sablefish
# dev.new(width = 11, height = 8)
# agreementFigure(TMA_Vector, y.test.pred, Delta = -0.25, full = FALSE, main = paste0("Random Rep = ", j))
}
# ----------------------- Median over all Rdm_reps Models ------------------------
# Look to see if all random reps fit well and didn't have an issue with good fitting (only seen in the metadata only models). Also compare the agreement figures.
renum(t(apply(y.fold.test.pred_RDM, 1, function(x) unlist(Correlation_R_squared_RMSE_MAE_SAD(x, TMA_Vector)))))
y.fold.test.pred_RDM_median <- apply(y.fold.test.pred_RDM, 2, median)
# y.fold.test.pred_RDM_median <- apply(y.fold.test.pred_RDM[1, , drop = FALSE], 2, median) # Select only those random runs which show good fits # SAD = 3300. R2 = 0.8432
# Delta <- -0.05 # Previous estimate or guess
data.frame(Delta = Delta, Correlation_R_squared_RMSE_MAE_SAD(TMA_Vector, round(y.fold.test.pred_RDM_median + Delta)))
# What is the best Delta (by SAD, with ties broken by RMSE) on the median over all, Rdm_reps, full k-folds
Delta_Table <- NULL
for (Delta. in seq(0, -0.45, by = -0.05)) {
# cat("\n\n")
# print(c(Delta = Delta., Correlation_R_squared_RMSE_MAE_SAD(TMA_Vector, round(y.fold.test.pred_RDM_median + Delta.))))
Delta_Table <- rbind(Delta_Table, c(Delta = Delta., unlist(Correlation_R_squared_RMSE_MAE_SAD(TMA_Vector, round(y.fold.test.pred_RDM_median + Delta.)))))
}
print(Delta_Table <- data.frame(Delta_Table))
# Best Delta from table above
(Delta <- Delta_Table$Delta[order(Delta_Table$SAD, Delta_Table$RMSE)[1]])
SG_Variables_Selected <- names(Model_Spectra.sg.iPLS)
roundingDelta <- Delta
# Do a final save after the best rounding Delta is official found for this spectra set - the best rounding Delta is again tested for in the predict script.
save(Iter, i, j, Cor, CA_diag, SAD, learningRate, layer_dropout_rate, Seed_Fold, Seed_Model, Seed_Main, Rdm_models,
Rdm_folds_index, SG_Variables_Selected, roundingDelta, file = paste0(Spectra_Set, '_', model_Name, '_', length(Rdm_folds_index), '_Rdm_model_', timeStamp(), '.RData'))
# Agreement Figures (standard and zoomed) using the best delta from above
# dev.new(width = 11, height = 8) # R plot window version
# agreementFigure(TMA_Vector, y.fold.test.pred_RDM_median, Delta = Delta, full = TRUE, main = paste0("Median over ", Rdm_reps, ' Full k-Fold Models'), cex = 1.25) # R plot window version
# browsePlot('agreementFigure(TMA_Vector, y.fold.test.pred_RDM_median, Delta = Delta, full = TRUE, main = paste0("Median over ", Rdm_reps, " Full k-Fold Models"), cex = 1.25)', file = 'Figures/Sable_2022_Combo_20_Rdm_Final.pdf', pdf = TRUE) # PDF version
browsePlot('agreementFigure(TMA_Vector, y.fold.test.pred_RDM_median, Delta = Delta, full = TRUE, main = paste0("Median over ", Rdm_reps, " Full k-Fold Models"))', file = paste0('Figures/', Spectra_Set, '_', length(Rdm_folds_index), '_Rdm_Final.png'))
browsePlot('agreementFigure(TMA_Vector, y.fold.test.pred_RDM_median, Delta = Delta, full = FALSE, main = paste0("Median over ", Rdm_reps, " Full k-Fold Models"))', file = paste0('Figures/', Spectra_Set, '_', length(Rdm_folds_index), '_Rdm_Final_Zoomed.png'))
# Apply that best Delta (from above) to all Rdm_reps models individually
Stats_RDM_median_by_model <- NULL
for(numRdmModels in 1:Rdm_reps) {
y.fold.test.pred_RDM_median_one_rep <- apply(y.fold.test.pred_RDM[numRdmModels, ,drop = FALSE], 2, median)
Stats_RDM_median_by_model <- rbind(Stats_RDM_median_by_model, data.frame(t(unlist(Correlation_R_squared_RMSE_MAE_SAD(TMA_Vector, round(y.fold.test.pred_RDM_median_one_rep + Delta))))))
}
print(Stats_RDM_median_by_model)
# An additional full k-fold added to the total number of models at each step in turn
# dev.new(width = 11, height = 8)
{ # matplot of Various stats vs nunber of complete Folds
browsePlot("
par(mfrow = c(3,2))
# Delta <- -0.05 # Reset Delta if recreating this figure as an old Delta may linger.
Stats_RDM_median_by_model_added <- NULL
for(numRdmModels in 1:Rdm_reps) {
y.fold.test.pred_RDM_median <- apply(y.fold.test.pred_RDM[1:numRdmModels, ,drop = FALSE], 2, median)
Stats_RDM_median_by_model_added <- rbind(Stats_RDM_median_by_model_added, data.frame(t(unlist(Correlation_R_squared_RMSE_MAE_SAD(TMA_Vector, round(y.fold.test.pred_RDM_median + Delta))))))
}
print(Stats_RDM_median_by_model_added)
min.stats <- apply(Stats_RDM_median_by_model_added[, c(3,5)], 2, min)
minAdj <- sweep(data.matrix(Stats_RDM_median_by_model_added[, c(3,5)]), 2, min.stats)
max.of.Adj <- apply(minAdj, 2, max)
print(Stats_0_1_interval <- cbind(Stats_RDM_median_by_model_added[, 1:2], t(t(minAdj)/max.of.Adj)))
matplot(1:Rdm_reps, Stats_0_1_interval, type = 'o', col = c(1:3, 6), xlab = 'Number of Complete Folds', ylab = 'Various Stats', main = 'Original Order')
# Add 5 more Randomized order figures
set.seed(Seed_Main)
(Seed_reps <- round(runif(6, 0, 1e8)))
for (i in 1:5) {
set.seed(Seed_reps[i])
(Rdm_Vec <- sample(1:Rdm_reps))
Stats_RDM_median_by_model_added <- NULL
for(numRdmModels in 1:Rdm_reps) {
y.fold.test.pred_RDM_median <- apply(y.fold.test.pred_RDM[Rdm_Vec[1:numRdmModels], , drop = FALSE], 2, median)
Stats_RDM_median_by_model_added <- rbind(Stats_RDM_median_by_model_added, data.frame(t(unlist(Correlation_R_squared_RMSE_MAE_SAD(TMA_Vector, round(y.fold.test.pred_RDM_median + Delta))))))
}
min.stats <- apply(Stats_RDM_median_by_model_added[, c(3,5)], 2, min)
minAdj <- sweep(data.matrix(Stats_RDM_median_by_model_added[, c(3,5)]), 2, min.stats)
max.of.Adj <- apply(minAdj, 2, max)
(Stats_0_1_interval <- cbind(Stats_RDM_median_by_model_added[, 1:2], t(t(minAdj)/max.of.Adj)))
matplot(1:Rdm_reps, Stats_0_1_interval, type = 'o', col = c(1:3, 6), xlab = 'Number of Complete Folds', ylab = 'Various Stats', main = 'Randomized Order')
}
", width = 11, height = 8, file = paste0('Figures/Full_k-fold_models_added_sequentially.png'))
}
# --- NN prediction for each otie in the NN model ---
Pred_median <- r(data.frame(NN_Pred_Median = apply(y.fold.test.pred_RDM, 2, median),
Lower_Quantile_0.025 = apply(y.fold.test.pred_RDM, 2, quantile, probs = 0.025, na.rm = TRUE),
Upper_Quantile_0.975 = apply(y.fold.test.pred_RDM, 2, quantile, probs = 0.975, na.rm = TRUE)), 4)
cat(paste0("\n\n--- Note: The quantiles are a reflection of the NN models precision based on ", length(Rdm_models), " full 10-fold randomized models, not the accuracy to a TMA Age ---\n\n"))
assign(paste0(Spectra_Set, '_NN_Pred_Median_TMA'), data.frame(filenames = fileNames, Pred_median, TMA = TMA_Vector), pos = 1)
save(list = paste0(Spectra_Set, '_NN_Pred_Median_TMA'), file = paste0(Spectra_Set, '_', model_Name, '_', length(Rdm_folds_index), '_Pred_Median_TMA_', timeStamp(), '.RData'))
# This agreementFigure() already produced above
# (y.fold.test.pred_RDM_median <- apply(y.fold.test.pred_RDM, 2, median))[1:10]
# browsePlot('agreementFigure(TMA_Vector, y.fold.test.pred_RDM_median, Delta = Delta, full = TRUE, main = paste0("Median over ", Rdm_reps, " Full k-Fold Models"), cex = 1.25)')
# Copy the spectra set prediction to a generic name and add a rounded prediction by adding the best delta found above
Model_Ages <- get(paste0(Spectra_Set, '_NN_Pred_Median_TMA'))
Model_Ages$Pred_Age_Rounded <- round(Model_Ages$NN_Pred_Median + Delta)
Model_Ages[1:5,]
# -- Plot by sorted difference --
# g <- ggplot(Model_Ages_Sub, aes(jitter(TMA, 1.25), TMA - NN_Pred_Median)) +
# geom_point()
# browsePlot('print(g)', file = paste0('Figures/TMA_minus_NN_Pred_vs_TMA.png'))
# Jitter TMA; vertical line for each unique TMA - without standard grid - all the data used for the training (not a subset like below).
xlim <- c(min(Model_Ages$TMA) - 1.25, max(Model_Ages$TMA) + 1.25)
Model_Ages$TMA_Minus_Pred_Age_Rounded <- Model_Ages$TMA - Model_Ages$Pred_Age_Rounded
browsePlot('set.seed(707); gPlot(Model_Ages, "TMA", "TMA_Minus_Pred_Age_Rounded", ylab = "TMA - Pred_Age_Rounded", xFunc = jitter, ylim = c(-xlim[2], xlim[2]), xlim = xlim,
grid = FALSE, vertLineEachPoint = TRUE)', file = paste0('Figures/TMA_minus_round_NN_Pred_vs_TMA_Jitter.png'))
# ====== Using a SAMPLE of 100 ages so the figures are not too crowded =====
set.seed(Seed_Fold)
Model_Ages_Sub <- Model_Ages[sample(1:nrow(Model_Ages), 100), ]
Model_Ages_Sub$Index <- 1:nrow(Model_Ages_Sub)
# - Plot by order implied by the spectra file names - ggplotly() changes how scale_color_manual() works ?????????????????
cols <- c('green', 'red')
g <- ggplot(Model_Ages_Sub, aes(Index, NN_Pred_Median)) +
geom_point() +
geom_errorbar(aes(ymin = Lower_Quantile_0.025, ymax = Upper_Quantile_0.975)) +
geom_point(aes(Index, Pred_Age_Rounded, col = cols[1])) +
geom_point(aes(Index + 0.1, TMA, col = cols[2])) +
scale_color_manual(labels = c('Rounded Age', 'TMA'), values = cols, name = ' ')
browsePlot('print(g)', file = paste0('Figures/Predicted_Ages_Order_by_File_Names_Subset.png'))
# -- Plot by sorted NN predicted ages --
Model_Ages_Sub_Sorted <- sort.f(Model_Ages_Sub, 'NN_Pred_Median') # Sort Model_Ages_Sub by NN_Pred_Median, except for "Index" (see the next line below)
Model_Ages_Sub_Sorted$Index <- sort(Model_Ages_Sub_Sorted$Index) # Reset Index for graphing
if(verbose) head(Model_Ages_Sub_Sorted, 10)
cols <- c('green', 'red')
g <- ggplot(Model_Ages_Sub_Sorted, aes(Index, NN_Pred_Median)) +
# xlim(0, 65) + ylim(0, 20) +
geom_point() +
geom_errorbar(aes(ymin = Lower_Quantile_0.025, ymax = Upper_Quantile_0.975)) +
geom_point(aes(Index, Pred_Age_Rounded, col = cols[1])) +
geom_point(aes(Index + 0.1, TMA, col = cols[2])) +
scale_color_manual(labels = c('Rounded Age', 'TMA'), values = cols, name = ' ')
browsePlot('print(g)', file = paste0('Figures/Predicted_Ages_Sorted_Subset.png'))
# -- Plot by sorted TMA --
Model_Ages_Sub_Sorted <- sort.f(Model_Ages_Sub, 'TMA') # Sort Model_Ages_Sub by TMA, except for "Index" (see the next line below)
Model_Ages_Sub_Sorted$Index <- sort(Model_Ages_Sub_Sorted$Index) # Reset Index for graphing
if(verbose) head(Model_Ages_Sub_Sorted, 10)
cols <- c('green', 'red')
g <- ggplot(Model_Ages_Sub_Sorted, aes(Index, NN_Pred_Median)) +
# xlim(0, 65) + ylim(0, 20) +
geom_point() +
geom_errorbar(aes(ymin = Lower_Quantile_0.025, ymax = Upper_Quantile_0.975)) +
geom_point(aes(Index, TMA, col = cols[2])) +
geom_point(aes(Index + 0.1, Pred_Age_Rounded, col = cols[1])) +
scale_color_manual(labels = c('Rounded Age', 'TMA'), values = cols, name = ' ')
browsePlot('print(g)', file = paste0('Figures/TMA_Sorted_Subset.png'))
# How many TMA ages are 3 or under
print(Table(TMA_Vector <= 3)/length(TMA_Vector))
# How many TMA ages are 15 or under
print(Table(TMA_Vector <= 15)/length(TMA_Vector))
# How many TMA ages are 20 or under
print(Table(TMA_Vector <= 20)/length(TMA_Vector))
}
John-R-Wallace-NOAA/FishNIRS documentation built on April 12, 2025, 12:59 a.m.
R Package Documentation
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####################################################################
# --- Initial setup (The curly brakets with a '###' comment and without indented lines directly below them, are there to enable the hiding of code sections using Notepad++.) ---
# (For those who dislike Rstudio, Notepad++ is here: https://notepad-plus-plus.org/ and NppToR that passes R code from Notepad++ to R is here: https://sourceforge.net/projects/npptor/)
# You will need a 'GITHUB_PAT' from GitHub set somewhere in R (If you need help, search the Web how to get one from GitHub.)
# Sys.setenv(GITHUB_PAT = "**************") # If you set GITHUB_PAT here, uncomment this line. Note, do not share your GITHUB_PAT, nor load it onto GitHib.
Sys.getenv("GITHUB_PAT")
####################################################################
# --- Initial settings setup ---
{ ###
if(interactive())
setwd(ifelse(.Platform$OS.type == 'windows', "C:/ALL_USR/JRW/SIDT/Train_NN_Model", "/more_home/h_jwallace/SIDT/Train_NN_Models")) # Change path to the Spectra Set's .GlobalEnv as needed
if(!interactive()) options(width = 120)
Spectra_Set <- c("Hake_2019", "Sable_2017_2019", "Sable_Combo_2022")[3] # Defaults for reading in the spectra sets are in the Read_OPUS_Spectra() function.
Spectra_Path <- "Model_Scans" # Put new spectra scans in a separate folder and enter the name of the folder below
dir.create('Figures', showWarnings = FALSE)
verbose <- c(TRUE, FALSE)[1]
plot <- c(TRUE, FALSE)[1]
# Default number of new spectra to be plotted in spectra figures. (The plot within Read_OPUS_Spectra() is given a different default below).
# All spectra in the Spectra_Path folder will be assigned an age regardless of the number plotted in the figure.
Max_N_Spectra <- list(50, 200, 'All')[[3]]
print(getwd())
print(Spectra_Set)
}
# --- Load functions and packages ---
{ ###
sourceFunctionURL <- function (URL, type = c("function", "script")[1]) {
" # For more functionality, see gitAFile() in the rgit package ( https://github.com/John-R-Wallace-NOAA/rgit ) which includes gitPush() and git() "
if (!any(installed.packages()[, 1] %in% "httr")) install.packages("httr")
File.ASCII <- tempfile()
if(type == "function")
on.exit(file.remove(File.ASCII))
getTMP <- httr::GET(gsub(' ', '%20', URL))
if(type == "function") {
write(paste(readLines(textConnection(httr::content(getTMP))), collapse = "\n"), File.ASCII)
source(File.ASCII)
}
if(type == "script") {
fileName <- strsplit(URL, "/")[[1]]
fileName <- rev(fileName)[1]
write(paste(readLines(textConnection(httr::content(getTMP))), collapse = "\n"), fileName)
}
}
# Toolbox functions
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/Ls.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/openwd.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/lib.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/get.subs.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/sort.f.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/predicted_observed_plot.R")
# sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/residuals_plot.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/as.num.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/match.f.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/Table.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/renum.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/agg.table.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/r.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/gof.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/Date.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/timeStamp.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/dec.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/loess.line.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/plot.loess.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/browsePlot.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/gPlot.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/recode.simple.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/headTail.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/factor.f.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/JRWToolBox/master/R/Correlation_R_squared_RMSE_MAE_SAD.R")
# FishNIRS funtion
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/FishNIRS/master/R/plotly.Spec.R")
# sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/FishNIRS/master/R/Mode.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/FishNIRS/master/R/agreementFigure.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/FishNIRS/master/R/FCNN_Model.R"); FCNN_model_ver_1 <- FCNN_model
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/FishNIRS/master/R/CNN_model_ver_5.R")
sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/FishNIRS/master/R/Read_OPUS_Spectra.R")
# sourceFunctionURL("https://raw.githubusercontent.com/John-R-Wallace-NOAA/FishNIRS/master/R/CNN_model_2D.R") # Not working yet
lib(lattice)
lib(dplyr)
# remotes::install_github("r-lib/ragg@bc501c9951c5934afa55da6d36cdf03c2705d99f")
# lib(tidyverse)
lib(recipes)
lib(rsample)
lib(GGally)
lib(skimr)
lib(e1071)
lib(mdatools)
lib(plotly)
lib(reticulate)
lib(tensorflow)
lib(keras)
lib(prospectr)
lib(openxlsx)
# install.packages('RcppArmadillo') # Need to use 4.0 version
lib(RcppArmadillo)
# Configuration failed to find one of freetype2 libpng libtiff-4. Try installing:
# * deb: libfreetype6-dev, libpng-dev libtiff5-dev libjpeg-dev (Debian, Ubuntu, etc)
# * rpm: freetype-devel libpng-devel libtiff-devel libjpeg-turbo-devel (Fedora, CentOS, RHEL)
# * csw: libfreetype_dev libpng16_dev libtiff_dev libjpeg_dev (Solaris)
# If freetype2 libpng libtiff-4 is already installed, check that 'pkg-config' is in your
# PATH and PKG_CONFIG_PATH contains a freetype2 libpng libtiff-4.pc file. If pkg-config
# is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
# R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
# -------------------------- [ERROR MESSAGE] ---------------------------
# <stdin>:1:22: fatal error: ft2build.h: No such file or directory
# compilation terminated.
#
# --- Setup for TensorFlow and Keras ---
# --- Conda TensorFlow environment ---
Conda_TF_Eniv <- ifelse(.Platform$OS.type == 'windows', "C:/m3/envs/tf", "/more_home/h_jwallace/Python/tf_cpu_only/bin") # Change these paths as needed
Sys.setenv(RETICULATE_PYTHON = Conda_TF_Eniv)
Sys.getenv("RETICULATE_PYTHON")
if(.Platform$OS.type != 'windows') {
# https://github.com/rstudio/tensorflow/issues/412
config <- tf$compat$v1$ConfigProto(intra_op_parallelism_threads = 2L, inter_op_parallelism_threads = 2L)
session = tf$compat$v1$Session(config=config)
tf$compat$v1$keras$backend$set_session(session)
}
# Set pseudo random number seeds
Seed_Fold <- c(777, 747, 727, 787, 797)[3]
set.seed(Seed_Fold)
Seed_Model <- c(777, 747, 727, 787, 797)[3]
# Pick the NN model to use (CNN_model_2D currently not working.)
model_Name <- c('FCNN_model_ver_1', 'CNN_model_ver_5', 'CNN_model_2D')[1]
Disable_GPU <- model_Name == 'FCNN_model_ver_1' # Only using the CPU is faster for the FCNN model but slower for CNN_model_ver_5, at least on Sablefish with data from 2017 and 2019.
# Disable_GPU <- FALSE
cat("\nDisable_GPU =", Disable_GPU, "\n\n")
# !!! Disabling the GPU has to come first for it to work. !!! (Grrrr, finally found this on the Web applied to Python and it is true here also!)
# Use < nvidia-smi -l 5 > within e.g. < conda activate C:/m3/envs/tf > inside of Powershell or Command Prompt to see a more correct percent of GPU utilization then with Task Manager.
tensorflow::set_random_seed(Seed_Model, disable_gpu = Disable_GPU)
# Test to see if TensorFlow is working in R
cat("\n\n"); print(tf_config()); cat("\n")
a <- tf$Variable(5.56)
b <- tf$Variable(2.7)
print(a + b); cat("\n\n")
k_clear_session()
} ###
# --- If Model_Spectra.sg.iPLS and TMA_Vector are missing for the current spectra set, create them now ---
{ ###
if(!file.exists(paste0(Spectra_Set, '_Model_Spectra.sg.iPLS.RData'))) {
Model_Spectra_Meta <- Read_OPUS_Spectra(Spectra_Set, Spectra_Path = Spectra_Path, Max_N_Spectra = 300, Meta_Path = paste0(Spectra_Set, "_NIRS_Scanning_Session_Report.xlsx"),
verbose = verbose, plot = plot, htmlPlotFolder = paste0('Figures/', Spectra_Set, '_Spectra_Sample_of_300'))
# filenames X8000 X7992 X3952 project sample_year pacfin_code_id sequence_number age_structure_id specimen_id TMA sex structure_weight_g NWFSC_NIR_Project
# 1 SABL_COMBO2022_NIR0022A_PRD_1_102157421_O1 0.2202285 0.2201835 0.5198408 COMBO 2022 SABL 1 102157421-SABL-O 102157421 14 2 0.0228 PRD
# 2 SABL_COMBO2022_NIR0022A_PRD_10_102157430_O1 0.2037776 0.2037497 0.5039832 COMBO 2022 SABL 10 102157430-SABL-O 102157430 6 2 0.0173 PRD
# 3 SABL_COMBO2022_NIR0022A_PRD_100_102157520_O1 0.1761716 0.1760852 0.4924470 COMBO 2022 SABL 100 102157520-SABL-O 102157520 6 2 0.0196 PRD
# 4 SABL_COMBO2022_NIR0022A_PRD_11_102157431_O1 0.1911490 0.1911127 0.5683330 COMBO 2022 SABL 11 102157431-SABL-O 102157431 16 1 0.0265 PRD
# 5 SABL_COMBO2022_NIR0022A_PRD_12_102157432_O1 0.1880359 0.1880160 0.5052297 COMBO 2022 SABL 12 102157432-SABL-O 102157432 6 1 0.0200 PRD
# NWFSC_NIR_Scan_Session age_structure_side_scan crystallized_scan percent_crystallized_scan broken_scan tip_only_scan anterior_tip_missing posterior_tip_missing percent_missing_scan tissue_present_scan
# 1 NIR0022A L <NA> 0 <NA> <NA> <NA> <NA> 0 <NA>
# 2 NIR0022A L <NA> 0 <NA> <NA> <NA> <NA> 0 <NA>
# 3 NIR0022A L <NA> 0 <NA> <NA> <NA> <NA> 0 <NA>
# 4 NIR0022A R <NA> 0 <NA> <NA> <NA> <NA> 0 <NA>
# 5 NIR0022A L <NA> 0 <NA> <NA> <NA> <NA> 0 <NA>
# tissue_level_scan oil_clay_contamination_scan stained_scan contamination_other_scan notes_scan unscannable_BB unscannable_Broken_MissingPieces unscannable_Crystalized unscannable_sample_mixed unscannable_no_otolith
# 1 <NA> <NA> NA NA <NA> <NA> <NA> <NA> <NA> <NA>
# 2 <NA> <NA> NA NA <NA> <NA> <NA> <NA> <NA> <NA>
# 3 <NA> <NA> NA NA <NA> <NA> <NA> <NA> <NA> <NA>
# 4 <NA> <NA> NA NA <NA> <NA> <NA> <NA> <NA> <NA>
# 5 <NA> <NA> NA NA <NA> <NA> <NA> <NA> <NA> <NA>
# Length_cm Weight_kg Month_Scaled length_prop_max structure_weight_dg shortName
# 1 51.5 1.40 0.4166667 0.5885714 0.228 SABL_1_Combo
# 2 48.5 1.04 0.4166667 0.5542857 0.173 SABL_10_Combo
# 3 56.0 1.96 0.4166667 0.6400000 0.196 SABL_100_Combo
# 4 55.0 1.66 0.4166667 0.6285714 0.265 SABL_11_Combo
# 5 50.5 1.20 0.4166667 0.5771429 0.200 SABL_12_Combo
#
# Total number of oties read in: 1557. Number rejected based on metadata (including missing TMA, when asked for): 8. Number kept: 1549.
#
#
#
# (L) only one otolith in the cell (L) Only one otolith in the cell . (L) only one otolith in the cell.
# 1 1 3
# (L) Only one otolith in the cell. (L) only one otolith in the cell. (L) Only one otolith in the cell.
# 4 5 2
# 10% missing from the posterior end. 5% missing from the posterior end. Anterior portion missing from the otolith
# 1 1 1
# anterior portion missing from the otolith. Anterior portion missing of the otolith Anterior tip missing
# 1 1 1
# Both otoliths missing >30%, so did not weigh. Did scan, otolith missing anterior portion. L: Only one otolith in the cell. Left ololith missing anterior portion. Right otolith BB for TMA
# 1 2 1
# Left otolith was scanned, might had some clay residue on it. Otolith broken in two pieces. Otolith missing posterior end.
# 2 1 1
# tiny <NA>
# 2 1525
# # These are not matched to the scans, since they are unscannable
# Model_Spectra_Meta$unscannable_BB <- Model_Spectra_Meta$unscannable_Broken_MissingPieces <- Model_Spectra_Meta$unscannable_Crystalized <- Model_Spectra_Meta$unscannable_sample_mixed <- Model_Spectra_Meta$unscannable_no_otolith <- NULL
#
# Model_Spectra_Meta$sex <- recode.simple(Model_Spectra_Meta$sex, cbind(c(1, 2, 3), c('M', 'F', 'U'))) # Wow, sex still in numbers!!
# # xyplot(length_cm ~ age_best, group = sex, data = Model_Spectra_Meta, auto = TRUE)
#
# Model_Spectra_Meta$crystallized_scan <- !is.na(Model_Spectra_Meta$crystallized_scan)
# Table(Model_Spectra_Meta$crystallized_scan)
#
# Table(Model_Spectra_Meta$percent_crystallized_scan, Model_Spectra_Meta$crystallized_scan) # All NA percent_crystallized_scan's are zeros
# Model_Spectra_Meta$percent_crystallized_scan[is.na(Model_Spectra_Meta$percent_crystallized_scan)] <- 0 # Change NA to zero so that a numerical test can be done (see below).
# Table(Model_Spectra_Meta$percent_crystallized_scan, Model_Spectra_Meta$crystallized_scan)
#
# Table(Model_Spectra_Meta$broken_scan) # Do all of these broken pieces fit together well? What about entering the number of pieces the otie is broken into - zero for an unbroken ototlith.
# # Are the oties ever broken during scanning or the handling of the otie for scanning?
#
# Table(Model_Spectra_Meta$tip_only_scan) # is there a difference between 'no' and an NA for this one?
#
# Table(Model_Spectra_Meta$anterior_tip_missing)
#
# Table(Model_Spectra_Meta$posterior_tip_missing)
#
# Table(Model_Spectra_Meta$percent_missing_scan)
# Model_Spectra_Meta$percent_missing_scan[is.na(Model_Spectra_Meta$percent_missing_scan)] <- 0 # Now a numerical test can be done (see below).
# Table(Model_Spectra_Meta$percent_missing_scan)
#
# Table(Model_Spectra_Meta$tissue_present_scan)
#
# Table(Model_Spectra_Meta$tissue_level_scan) # Change this to 'percent_tissue_level_scan'?
# Model_Spectra_Meta$tissue_level_scan[is.na(Model_Spectra_Meta$tissue_level_scan)] <- 0 # Now a numerical test can be done (see below).
# Table(Model_Spectra_Meta$tissue_level_scan)
#
# Table(Model_Spectra_Meta$oil_clay_contamination_scan) # No percentage for this one
#
# Table(Model_Spectra_Meta$stained_scan) # All NA's. Is this 'yes'/'no' or percentage?
#
# Table(Model_Spectra_Meta$contamination_other_scan) # All NA's. Is this 'yes'/'no' or percentage?
#
#
# names(Model_Spectra_Meta)[names(Model_Spectra_Meta) %in% 'age_best'] <- "TMA"
# Table(is.finite(Model_Spectra_Meta$TMA))
#
# rev(sort(Model_Spectra_Meta$TMA))[1:20]
#
# dim(Model_Spectra_Meta) # Sable Combo 2022: 1557 rows 535 cols
#
# TF <- !is.na(Model_Spectra_Meta$TMA) & Model_Spectra_Meta$percent_crystallized_scan <= 15 & Model_Spectra_Meta$percent_crystallized_scan <= 10 &
# Model_Spectra_Meta$tissue_level_scan <= 10 & !is.na(Model_Spectra_Meta$length_cm) & !is.na(Model_Spectra_Meta$structure_weight_g)
# c(sum(TF), sum(!TF), sum(TF) + sum(!TF))
#
# sort(fileNamesRemove <- Model_Spectra_Meta$filenames[!TF])
#
# file.remove(paste0(Spectra_Path, "/", fileNamesRemove, ".0"), recursive = TRUE) # Bad raw scans removed here
#
# Model_Spectra_Meta <- Model_Spectra_Meta[TF, ] # --- Doing an overwrite here!! --- Gettin rid of bad scans or ones with no metadata that is wanted
# dim(Model_Spectra_Meta) # Sable Combo 2022: 1528 rows
#
# Model_Spectra_Meta$shortName <- apply(Model_Spectra_Meta[, 'filenames', drop = FALSE], 1, function(x) paste(get.subs(x, sep = "_")[c(1, 5)], collapse = "_"))
#
#
# # Look at the data with plotly and remove rogue oties if needed#
# plotly.Spec(Model_Spectra_Meta, 'all', htmlPlotFolder = paste0(Figures, '/Spectra Figure by TMA'))
# # Model_Spectra_Meta <- Model_Spectra_Meta[!Model_Spectra_Meta$shortName %in% 'HAKE_48', ] # Example of removing a rogue otie for Hake 2019
# # plotly.Spec(Model_Spectra_Meta, 'all') # Decide to save figure with rogue otie or the figure without the rogue otie, or both.
#
save(Model_Spectra_Meta, file = paste0(Spectra_Set, '_Model_Spectra_Meta_ALL_GOOD_DATA.RData')) # 1528
# load(file = paste0(Spectra_Set, '_Model_Spectra_Meta_ALL_GOOD_DATA.RData'))
# TMA only
TMA_Vector <- Model_Spectra_Meta$TMA
length(TMA_Vector) # 1528 After bad scans or missing dat - before saving out oties for final model check
# Save out 15 oties for final model check.
set.seed(Seed_Fold)
TMA_Tab <- Table(TMA_Vector)
(Low_strata <- sum(TMA_Tab[1:3]))
(Mid_strata <- sum(TMA_Tab[4:20]))
(High_strata <- sum(TMA_Tab[21:length(TMA_Tab)]))
(SaveOutOties <- c(sample(order(TMA_Vector)[1:Low_strata], 5), sample(order(TMA_Vector)[Low_strata + 1:Mid_strata], 5), sample(order(TMA_Vector)[Low_strata + Mid_strata + 1:High_strata], 5)) )
sort(TMA_Vector[SaveOutOties]) # Check the results
save(SaveOutOties, file = paste0(Spectra_Set, '_SaveOutOties_Seed_', Seed_Fold, '.RData'))
# TMA_Vector_SaveOutOties <- TMA_Vector[SaveOutOties]
# save(TMA_Vector_SaveOutOties, file = paste0(Spectra_Set, '_TMA_Vector_SaveOutOties.RData'))
#
# Model_Spectra_Meta_SaveOutOties <- Model_Spectra_Meta[SaveOutOties, ]
# save(Model_Spectra_Meta_SaveOutOties, file = paste0(Spectra_Set, '_Model_Spectra_Meta_SaveOutOties.RData'))
dim(Model_Spectra_Meta) # 1528 536
Model_Spectra_Meta <- Model_Spectra_Meta[-SaveOutOties, ] # --- Doing an overwrite here!! ---
dim(Model_Spectra_Meta) # 1513 536
# Now recreate the spectra only file Model_Spectra so that bad rows and saved out oties are removed
Model_Spectra <- cbind(Model_Spectra_Meta[, 2:((1:ncol(Model_Spectra_Meta))[names(Model_Spectra_Meta) %in% 'project'] - 1)]) # --- Overwrite of the spectra only file: Model_Spectra ---
dim(Model_Spectra_Meta) # 1513 536
dim(Model_Spectra) # 1513 507
Model_Spectra[1:3, c(1:2, 505:507)]
# TMA only vector that matches the recreated Model_Spectra above
TMA_Vector <- Model_Spectra_Meta$TMA # --- Doing another overwrite here!! ---
length(TMA_Vector) # 1513
# Use full file names - with '.0' at the end
fileNames.0 <- dir(path = Spectra_Path) # Need new list of filenames after removals above
length(fileNames.0)
fileNames.0[1:5]
# These are the oties that are not used in the NN model and are saved out for testing
sort(fileNames.0[SaveOutOties])
dir.create(paste0(Spectra_Set, '_Saved_Out'), showWarnings = FALSE)
file.copy(paste0(Spectra_Path, "/", fileNames.0[SaveOutOties]), paste0(Spectra_Set, '_Saved_Out'), recursive = TRUE, copy.date = TRUE)
file.remove(paste0(Spectra_Path, "/", fileNames.0[SaveOutOties]), recursive = TRUE) # Leave out raw scans removed here - number of scans left should match Model_Spectra_Meta, Model_Spectra, and TMA_Vector
}
# Savitzky-Golay smoothing
{ ###
###################################################################################################################
### Perform Savitzky-Golay 1st derivative with 17 point window smoothing 2rd order polynomial fit and visualize ###
### Intro: http://127.0.0.1:30354/library/prospectr/doc/prospectr.html
###################################################################################################################
### NOTE ### If there are multiple years of data, all subsequent transformations should be applied to the whole data set, then re-subset
Model_Spectra.sg <- data.frame(prospectr::savitzkyGolay(Model_Spectra, m = 1, p = 2, w = 15))
####################################################
### iPLS algorithm in mdatools ###
####################################################
# Maximum number of components to calculate.
nComp <- c(10, 15)[2]
Model_Spectra.iPLS.F <- mdatools::ipls(Model_Spectra.sg, TMA_Vector, glob.ncomp = nComp, center = TRUE, scale = TRUE, cv = 100,
int.ncomp = nComp, int.num = nComp, ncomp.selcrit = "min", method = "forward", silent = FALSE)
summary(Model_Spectra.iPLS.F)
# iPLS variable selection results
# Method: forward
# Validation: random with 100 segments
# Number of intervals: 15
# Number of selected intervals: 9
# RMSECV for global model: 2.964359 (15 LVs)
# RMSECV for optimized model: 2.880144 (14 LVs)
#
# Summary for selection procedure:
# n start end selected nComp RMSE R2
# 1 0 1 493 FALSE 15 2.964359 0.920
# 2 15 462 493 TRUE 12 3.437861 0.893
# 3 8 232 264 TRUE 15 3.066425 0.915
# 4 6 166 198 TRUE 14 3.037084 0.916
# 5 5 133 165 TRUE 12 3.017657 0.917
# 6 3 67 99 TRUE 14 2.941591 0.921
# 7 13 397 429 TRUE 15 2.927269 0.922
# 8 12 364 396 TRUE 14 2.907818 0.923
# 9 4 100 132 TRUE 15 2.897542 0.924
# 10 11 331 363 TRUE 14 2.883531 0.925
# plot the newly selected spectra regions
browsePlot('plot(Model_Spectra.iPLS.F)')
Model_Spectra.iPLS.F$int.selected
sort(Model_Spectra.iPLS.F$var.selected)
# dev.new() - With a main title
# plot(Model_Spectra.iPLS.F, main = NULL)
# plot predictions before and after selection
browsePlot('
par(mfrow = c(2, 1))
mdatools::plotPredictions(Model_Spectra.iPLS.F$gm) # gm = global PLS model with all variables included
mdatools::plotPredictions(Model_Spectra.iPLS.F$om) # om = optimized PLS model with selected variables
')
browsePlot('mdatools::plotRMSE(Model_Spectra.iPLS.F)')
# RMSE before and after selection
# Visually find the ylim to apply to both figures and over all areas and WB
browsePlot('
par(mfrow = c(2, 1))
mdatools::plotRMSE(Model_Spectra.iPLS.F$gm)
mdatools::plotRMSE(Model_Spectra.iPLS.F$om)
')
# Use the ylim for both plots
browsePlot('
par(mfrow = c(2, 1))
mdatools::plotRMSE(Model_Spectra.iPLS.F$gm, ylim = c(2.4, 6.5))
mdatools::plotRMSE(Model_Spectra.iPLS.F$om, ylim = c(2.4, 6.5))
')
# Select iPLS vars and add metadata wanted
# (p <- length(Model_Spectra.iPLS.F$var.selected)) # 380 freq selected out of a total of 1140
# Model_Spectra.sg.iPLS <- data.frame(Model_Spectra.sg[, sort(Model_Spectra.iPLS.F$var.selected)], length_prop_max = Model_Spectra_Meta$length_cm/max(Model_Spectra_Meta$length_cm),
# structure_weight_dg = 10 * Model_Spectra_Meta$structure_weight_g) # dg = decigram
Model_Spectra.sg.iPLS <- data.frame(Model_Spectra.sg[, sort(Model_Spectra.iPLS.F$var.selected)], Model_Spectra_Meta[, c('length_prop_max', 'structure_weight_dg', 'Month_Scaled')]) # dg = decigram
save(Model_Spectra.sg.iPLS, file = paste0(Spectra_Set, '_Model_Spectra.sg.iPLS.RData'))
save(TMA_Vector, file = paste0(Spectra_Set, '_TMA_Vector.RData'))
if(FALSE) {
Model_Spectra.Age.sg.iPLS <- data.frame(Age = TMA_Vector, Model_Spectra.sg.iPLS)
dim(Model_Spectra.Age.sg.iPLS)
# 2D plot
# Model_Spectra.sg.iPLS.PLOT <- cbind(Model_Spectra_Meta[, 1, drop = FALSE], Model_Spectra.sg.iPLS, Model_Spectra_Meta[, ncol(Model_Spectra):ncol(Model_Spectra_Meta)])
# plotly.Spec(Model_Spectra.sg.iPLS.PLOT, 'all')
# Plot the transformed spectra by age using only variables selected using iPLS
(Model_Spectra.Age.sg.iPLS.Long <- reshape2::melt(Model_Spectra.Age.sg.iPLS, id = 'Age', variable.name = 'Freq', value.name = 'Absorbance'))[1:4, ]
Model_Spectra.Age.sg.iPLS.Long$Freq <- as.numeric(substring(Model_Spectra.Age.sg.iPLS.Long$Freq, 2))
Model_Spectra.Age.sg.iPLS.Long <- sort.f(Model_Spectra.Age.sg.iPLS.Long, 'Freq')
Model_Spectra.Age.sg.iPLS.Agg <- aggregate(list(Absorbance = Model_Spectra.Age.sg.iPLS.Long$Absorbance),
list(Freq = Model_Spectra.Age.sg.iPLS.Long$Freq, Age = Model_Spectra.Age.sg.iPLS.Long$Age), mean, na.rm = TRUE)
Model_Spectra.Age.sg.iPLS.Agg$Age <- ordered(Model_Spectra.Age.sg.iPLS.Agg$Age, sort(unique(Model_Spectra.Age.sg.iPLS.Agg$Age)))
plotly::ggplotly(ggplot2::ggplot(data = Model_Spectra.Age.sg.iPLS.Agg, aes(x = Freq, y = Absorbance, z = Age)) + geom_line(aes(colour = Age), size = 0.2) +
scale_color_manual(values=rainbow(length(unique(Model_Spectra.Age.sg.iPLS.Agg$Age)), alpha = 1)))
# --------------- Try ipls() with smoothed spectra data and metadata - NO METADATA WAS SELECTED HERE ------------------------
# Remove NA's with predictors and response together - then re-split
Model_Spectra.sg.META <- na.omit(cbind(Model_Spectra.sg, Model_Spectra_Meta[, c("latitude", "longitude", "length", "weight", "sex")], TMA = TMA_Vector))
Ncol <- ncol(Model_Spectra.sg.META)
Model_Spectra.sg.META[1:3, c(1:2, (Ncol - 4):Ncol)]
TMA.META <- Model_Spectra.sg.META[, Ncol]
Model_Spectra.sg.META <- Model_Spectra.sg.META[, -Ncol]
Model_Spectra.iPLS.META.F <- mdatools::ipls(Model_Spectra.sg.META, TMA.META, glob.ncomp = nComp, center = TRUE, scale = TRUE, cv = 100,
int.ncomp = nComp, int.num = nComp, ncomp.selcrit = "min", method = "forward", silent = FALSE)
summary(Model_Spectra.iPLS.META.F)
# Plot the newly selected spectra regions
dev.new()
plot(Model_Spectra.iPLS.META.F)
Model_Spectra.iPLS.META.F$int.selected
sort(Model_Spectra.iPLS.META.F$var.selected)
Model_Spectra.sg.META[, Model_Spectra.iPLS.F$var.selected][1:3, c(1:3, 373:380)]
names(Model_Spectra.sg.META[, Model_Spectra.iPLS.F$var.selected])
}
}
} ###
# --- NN Model ---
{ ###
# Load the data if needed
base::load(paste0(Spectra_Set, '_Model_Spectra.sg.iPLS.RData')); print(dim(Model_Spectra.sg.iPLS))
# base::load(paste0(Spectra_Set, '_TMA_Vector.RData')); print(length(TMA_Vector))
base::load(paste0(Spectra_Set, '_Model_Spectra_Meta_ALL_GOOD_DATA.RData')) # Model_Spectra_Meta with SaveOutOties removed is only needed for TMA_Vector and the 'filenames' below
base::load(paste0(Spectra_Set, '_SaveOutOties_Seed_727.RData')); print(length(SaveOutOties))
Model_Spectra_Meta <- Model_Spectra_Meta[-SaveOutOties, ]; print(dim(Model_Spectra_Meta))
print(Model_Spectra_Meta[1:3, c(1, (grep('project', names(Model_Spectra_Meta))):ncol(Model_Spectra_Meta))])
TMA_Vector <- Model_Spectra_Meta$TMA
print(length(TMA_Vector))
fileNames = Model_Spectra_Meta$filenames
print(length(fileNames))
# ----- Remove both metadata columns for testing -----
# Model_Spectra.sg.iPLS$length_prop_max <- Model_Spectra.sg.iPLS$structure_weight_dg <- NULL
# ----- Leave only the fish length for testing -----
# Model_Spectra.sg.iPLS$structure_weight_dg <- NULL
# ----- Leave only the otie weight for testing -----
# Model_Spectra.sg.iPLS$length_prop_max <- NULL
print(dim(Model_Spectra.sg.iPLS))
# print(Model_Spectra.sg.iPLS$length_prop_max[1:4])
# print(Model_Spectra.sg.iPLS$structure_weight_dg[1:4])
print(headTail(Model_Spectra.sg.iPLS, 3, 0, 3, 5))
# --------- Special code to test 'Month_Scaled', 'Depth_m', 'Sex', 'Weight_kg', 'Days_into_Year', and reduced model size in the NN Model with the same scans in Model_Spectra.sg.iPLS ------------------------------
base::load("C:\\ALL_USR\\JRW\\SIDT\\Get Otie Info from Data Warehouse\\selectSpAgesFramFeb2024.RData") # From NWFSC Data Warehouse
# ===> Fish length and Otie Wgt: # SAD: 2050; RMSE: 2.7280
# Model_Spectra.sg.iPLS <- match.f(data.frame(Model_Spectra.sg.iPLS, specimen_id = as.character(Model_Spectra_Meta$specimen_id)), selectSpAgesFramFeb2024, "specimen_id", "AgeStr_id", c('Month_Scaled', 'Depth_m', 'Sex', 'Weight_kg')) # Very poor results
# Model_Spectra.sg.iPLS <- match.f(data.frame(Model_Spectra.sg.iPLS, specimen_id = as.character(Model_Spectra_Meta$specimen_id)), selectSpAgesFramFeb2024, "specimen_id", "AgeStr_id", c('Month_Scaled', 'Weight_kg', 'Depth_m')) # SAD: 2029; RMSE: 2.7678
Model_Spectra.sg.iPLS <- match.f(data.frame(Model_Spectra.sg.iPLS, specimen_id = as.character(Model_Spectra_Meta$specimen_id)), selectSpAgesFramFeb2024, "specimen_id", "AgeStr_id", c('Weight_kg', 'Depth_m')) # SAD: 2002; RMSE: 2.6742
# Model_Spectra.sg.iPLS <- match.f(data.frame(Model_Spectra.sg.iPLS, filenames = Model_Spectra_Meta$filenames, specimen_id = as.character(Model_Spectra_Meta$specimen_id)), selectSpAgesFramFeb2024, "specimen_id", "AgeStr_id", c('Weight_kg', 'Depth_m', 'Length_cm', 'Age')) # Stratified Random
# Model_Spectra.sg.iPLS <- match.f(data.frame(Model_Spectra.sg.iPLS, specimen_id = as.character(Model_Spectra_Meta$specimen_id)), selectSpAgesFramFeb2024, "specimen_id", "AgeStr_id", 'Weight_kg') # SAD: 2088; RMSE: 2.7389
# Model_Spectra.sg.iPLS <- match.f(data.frame(Model_Spectra.sg.iPLS, specimen_id = as.character(Model_Spectra_Meta$specimen_id)), selectSpAgesFramFeb2024, "specimen_id", "AgeStr_id", 'Depth_m') # SAD: 2042; RMSE: 2.7404
# Model_Spectra.sg.iPLS <- match.f(data.frame(Model_Spectra.sg.iPLS, specimen_id = as.character(Model_Spectra_Meta$specimen_id)), selectSpAgesFramFeb2024, "specimen_id", "AgeStr_id", 'Month_Scaled') # SAD: ????; RMSE: ????
# Model_Spectra.sg.iPLS <- match.f(data.frame(Model_Spectra.sg.iPLS, specimen_id = as.character(Model_Spectra_Meta$specimen_id)), selectSpAgesFramFeb2024, "specimen_id", "AgeStr_id", c('Weight_kg', 'Depth_m', 'Days_into_Year')) # SAD: 2090; RMSE: 2.8047
Model_Spectra.sg.iPLS$specimen_id <- NULL # specimen_id only needed for the matching above
# ---- Metadata only model run----
# Commented out the random selection code below so that the number oties is not reduced
Model_Spectra.sg.iPLS <- Model_Spectra.sg.iPLS[, (grep('length_prop_max', names(Model_Spectra.sg.iPLS))):ncol(Model_Spectra.sg.iPLS)]
headTail(Model_Spectra.sg.iPLS, 3, 2, 3, 5)
# Check for missing data
print(dim(Model_Spectra.sg.iPLS))
print(dim(na.omit(Model_Spectra.sg.iPLS)))
################ OLD ###############
# These 3 oties in the metadata were missing from the Data WareHouse: AgeStr_id %in% 102133144:102133146 ????????????????
# Model_Spectra.sg.iPLS$Month_Scaled[is.na(Model_Spectra.sg.iPLS$Month_Scaled)] <- 6:8/12
# Model_Spectra.sg.iPLS$Depth_m[is.na(Model_Spectra.sg.iPLS$Depth_m)] <- mean(Model_Spectra.sg.iPLS$Depth_m, na.rm = TRUE)
# Model_Spectra.sg.iPLS$Weight_kg[is.na(Model_Spectra.sg.iPLS$Weight_kg)] <- mean(Model_Spectra.sg.iPLS$Weight_kg, na.rm = TRUE)
# Model_Spectra.sg.iPLS$Sex[is.na(Model_Spectra.sg.iPLS$Sex)] <- c('M','F', 'M')
# print(dim(na.omit(Model_Spectra.sg.iPLS)))
# print(headTail(Model_Spectra.sg.iPLS, 3, 2, 3, 5))
################################
if(!is.null(Model_Spectra.sg.iPLS$Sex)) {
Model_Spectra.sg.iPLS$Sex_prop_max <- as.numeric(recode.simple(Model_Spectra.sg.iPLS$Sex, data.frame(c('F','M', 'U'), 0:2)))/2 # ** All variables have to be numeric **
Model_Spectra.sg.iPLS$Sex <- NULL
}
if(!is.null(Model_Spectra.sg.iPLS$Depth_m)) {
Model_Spectra.sg.iPLS$Depth_prop_max <- (Model_Spectra.sg.iPLS$Depth_m - min(Model_Spectra.sg.iPLS$Depth_m))/(max(Model_Spectra.sg.iPLS$Depth_m) - min(Model_Spectra.sg.iPLS$Depth_m))
Model_Spectra.sg.iPLS$Depth_m <- NULL
}
if(!is.null(Model_Spectra.sg.iPLS$Weight_kg)) {
Model_Spectra.sg.iPLS$Weight_prop_max <- (Model_Spectra.sg.iPLS$Weight_kg - min(Model_Spectra.sg.iPLS$Weight_kg))/(max(Model_Spectra.sg.iPLS$Weight_kg) - min(Model_Spectra.sg.iPLS$Weight_kg))
Model_Spectra.sg.iPLS$Weight_kg <- NULL
}
if(!is.null(Model_Spectra.sg.iPLS$Days_into_Year)) {
Model_Spectra.sg.iPLS$Days_into_Year_prop_max <- (Model_Spectra.sg.iPLS$Days_into_Year - min(Model_Spectra.sg.iPLS$Days_into_Year))/(max(Model_Spectra.sg.iPLS$Days_into_Year) - min(Model_Spectra.sg.iPLS$Days_into_Year))
Model_Spectra.sg.iPLS$Days_into_Year <- NULL
}
headTail(Model_Spectra.sg.iPLS, 3, 2, 3, 5)
# = = = = = = = = = = = = = = = = = Intial setup = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
# Special seed setting for model testing
Seed_Fold <- 787 # Seed_Fold = 787 for Run 3. Seed 747 used for Fish_Len_Otie_Wgt_Run_2 . Using a different seed starting here, to test main run of Sable_2022 with fish length and otie weight (and other metadata runs)
# Seed_Fold = 727 used in the code above and for previous runs (Fish_Len_Otie_Wgt Run 1) of Sable_2022 before 28 Dec 2023
# ------- Reduce model size to see the change in prediction ability ----------------------
set.seed(Seed_Fold)
# --- Random selection of a reduced number of oties ---
# Rdm_Oties <- sample(1:nrow(Model_Spectra.sg.iPLS), 750) # nrow(Model_Spectra.sg.iPLS) for Sablefish 2022 is 1,513
#
# Model_Spectra.sg.iPLS <- Model_Spectra.sg.iPLS[Rdm_Oties, ]
# print(dim(Model_Spectra.sg.iPLS))
# print(headTail(Model_Spectra.sg.iPLS, 3, 2, 3, 5))
#
# # Model_Spectra_Meta <- Model_Spectra_Meta[Rdm_Oties, ]
# # print(Model_Spectra_Meta[1:3, c(1, (grep('project', names(Model_Spectra_Meta))):ncol(Model_Spectra_Meta))])
#
# TMA_Vector <- TMA_Vector[Rdm_Oties]
# print(length(TMA_Vector))
#
# fileNames = Model_Spectra_Meta$filenames[Rdm_Oties]
# print(length(fileNames))
# --- Stratified random selection of a reduced number of oties---
# print(Bin_Num <- Table(factor.f(Model_Spectra.sg.iPLS$Length_cm, breaks = c(0, 25, 45, 65, Inf))))
# print(Mid_Split <- (500 - Bin_Num[1] - Bin_Num[4])/2)
#
# Model_Spectra.sg.iPLS <- rbind(Model_Spectra.sg.iPLS[Model_Spectra.sg.iPLS$Length_cm <= 25 | Model_Spectra.sg.iPLS$Length_cm > 65, ],
# Model_Spectra.sg.iPLS[Model_Spectra.sg.iPLS$Length_cm > 25 & Model_Spectra.sg.iPLS$Length_cm <= 45, ][sample(1:Bin_Num[2], floor(Mid_Split)), ],
# Model_Spectra.sg.iPLS[Model_Spectra.sg.iPLS$Length_cm > 45 & Model_Spectra.sg.iPLS$Length_cm <= 65, ][sample(1:Bin_Num[2], ceiling(Mid_Split)), ])
# print(dim(Model_Spectra.sg.iPLS))
#
# TMA_Vector <- Model_Spectra.sg.iPLS$Age
# fileNames <- Model_Spectra.sg.iPLS$filenames
#
# Model_Spectra.sg.iPLS$Length_cm <- NULL
# Model_Spectra.sg.iPLS$Age <- NULL
# Model_Spectra.sg.iPLS$filenames <- NULL
#
# print(headTail(Model_Spectra.sg.iPLS, 3, 2, 3, 5))
# --- Setup graphic windows ---
graphics.off()
dev.new(width = 14, height = 6) #2
dev.new() # 3
dev.new(width = 11, height = 8) # 4
dev.new(width = 11, height = 8) # 5
dev.new(width = 10, height = 10) # 6
dev.new(width = 10, height = 10) # 7
# = = = = = = Pick number of random reps (Rdm_reps), number of folds (num_folds), and iteration number (Iter_Num), then run the NN code to the next '= = =' line and expect long run times = = = = = = = = =
Rdm_reps <- 20 # j loop
num_folds <- 20 # i loop # Checking how many folds work best for metadata only model
Iter_Num <- 8 # Iter while() loop
# (Rdm_reps <- ifelse(model_Name == 'FCNN_model_ver_1', 20, 10))
Seed_Main <- Seed_Fold + 20 # Seed_Fold 747 used for Fish_Len_Otie_Wgt_Run_2. Seed_Main <- 707 used for previous runs of Sable_2022 before 28 Dec 2023 # Reducing the number of seeds will be considered later
set.seed(Seed_Main)
Seed_reps <- sample(1e7, Rdm_reps)
# Start fresh or continue by loading a file with model iterations already finished (see the commented line with an example model file).
Rdm_models <- list()
Rdm_folds_index <- list()
# base::load("Sable_Combo_2022_FCNN_model_ver_1_1_Rdm_model_11_Mar_2024_12_38_45.RData")
file.create('Run_NN_Model_Flag', showWarnings = TRUE) # Stopping the model with this flag is broken by the nested loops, but left for now in a hope that it can prehaps be fixed.
# Note that errors from plot.loess() are trapped by try() and are normal early in the iteration loop since there is not enough data to smooth.
for(j in (length(Rdm_folds_index) + 1):Rdm_reps) {
cat(paste0("\n\nStart of Random Rep = ", j , "\n\n"))
Seed_Data <- Seed_reps[j]
# Split the data into folds, spitting the remainder of an un-even division into the first folds, one otie per fold until finished.
# The split is based on the current seed which is dictated by Seed_Main (see above).
set.seed(Seed_Data)
index_org <- 1:nrow(Model_Spectra.sg.iPLS)
(fold_size_min <- floor(length(index_org)/num_folds))
(num_extra <- num_folds * dec(length(index_org)/num_folds))
index <- index_org
folds_index <- list()
for(i in 1:(num_folds - 1)) {
print(c(fold_size_min, i, num_extra, i <= num_extra, fold_size_min + ifelse(i <= num_extra, 1, 0), i - num_extra))
folds_index[[i]] <- sample(index, fold_size_min + ifelse(i < (num_extra + 0.1), 1, 0)) # Finite math - grr!
index <- index[!index %in% folds_index[[i]]]
}
folds_index[[num_folds]] <- index # Remainder from the above for() loop goes into the last fold index
print(lapply(folds_index, length)) # Check the binning result
print(c(sum(unlist(lapply(folds_index, length))), length(index_org)))
Fold_models <- list()
for (i in 1:num_folds) {
Model_Spectra.sg.iPLS.F <- Model_Spectra.sg.iPLS[-folds_index[[i]], ]
TMA_Vector.F <- TMA_Vector[-folds_index[[i]]]
# Split the data into training set (2/3) and test set (1/3)
set.seed(Seed_Data)
index <- 1:nrow(Model_Spectra.sg.iPLS.F)
testindex <- sample(index, trunc(length(index)/3))
x.test <- 1000 * Model_Spectra.sg.iPLS.F[testindex, ]
x.train <- 1000 * Model_Spectra.sg.iPLS.F[-testindex, ]
y.test <- TMA_Vector.F[testindex]
y.train <- TMA_Vector.F[-testindex]
cat(paste0("\n\nDimension of x.train = ", paste(dim(x.train), collapse = ' '), '\n\n')) # 906 380; 905 380 with crystallized otie removed
# Same learning rate for all models
learningRate <- c(0.00088, 0.0009)[2]
layer_dropout_rate <- NULL
# layer_dropout_rate <- 0.2
if(model_Name == 'FCNN_model_ver_1') model <- FCNN_model_ver_1(layer_dropout_rate = layer_dropout_rate)
if(model_Name == 'CNN_model_ver_5') model <- CNN_model_ver_5()
if(model_Name == 'CNN_model_2D') model <- CNN_model_2D()
# -- Don't reset Iter, Cor, CA_diag, SAD, or .Random.seed when re-starting the same run ---
tensorflow::set_random_seed(Seed_Model, disable_gpu = Disable_GPU); Seed_Model # Trying to this here and above (see the help for: tensorflow::set_random_seed)
set.seed(Seed_Data); Seed_Data # Re-setting the 'data' seed here to know where the model starts, also the Keras backend needs to cleared and the model reloaded - see above.
Iter <- 0
Cor <- RMSE <- CA_diag <- SAD <- saveModels <- NULL
saveModels_List <- list()
while(file.exists('Run_NN_Model_Flag')) { # The multiple full fold version breaks the stop by removing the file flag, but it remains for now
# R memory garbage collection
gc()
# Clear TensorFlow's session
k_clear_session()
(Iter <- Iter + 1)
cat(paste0("\n\nRandom Replicates = ", j, ": Fold number = ", i, ": Iter = ", Iter,"\n"))
if(Iter > 1) {
Iter_Loop_Time_Min <- as.numeric(difftime(Sys.time(), Loop_Start_Time, units = "mins"))
cat("\nThe last 500 epochs took", format(Iter_Loop_Time_Min, digits = 4), "minutes. ") # 500 epochs is hardwired - see below
Time_Left_Min <- ((Rdm_reps - j + 1) * num_folds * Iter_Num + (num_folds - i + 1) * Iter_Num + (Iter_Num - Iter + 1)) * Iter_Loop_Time_Min
if(Time_Left_Min < 60) cat("Around", format(Time_Left_Min, digits = 4), "minutes left.\n\n")
if(Time_Left_Min >= 60 & Time_Left_Min < 60 * 24) cat("Around", format(Time_Left_Min/60, digits = 4), "hours left.\n\n")
if(Time_Left_Min >= 60 * 24) cat("Around", format(Time_Left_Min/60/24, digits = 4), "days left.\n\n")
}
Loop_Start_Time <- Sys.time()
# config <- tf$compat.v1.ConfigProto(intra_op_parallelism_threads = 2L, inter_op_parallelism_threads = 2L)
# session <- tf$Session(config = config)
# k_set_session(session)
# blas_set_num_threads(4)
# blas_get_num_procs()
# FCNN model
if(model_Name == 'FCNN_model_ver_1') {
x.train.array <- as.matrix(x.train)
# callback_tensorboard() writes a log for TensorBoard, which allows you to visualize dynamic graphs of your training and test metrics.
history <- fit(model, x.train.array, y.train, epochs = 1, batch_size = 32, validation_split = 0.2, verbose = 2,
callbacks = if(file.exists('NN_Verbose_Flag.txt')) list(callback_tensorboard(histogram_freq = 1, profile_batch = 2)) else NULL, view_metrics = FALSE)
history <- fit(model, x.train.array, y.train, epochs = 198, batch_size = 32, validation_split = 0.2, verbose = ifelse(file.exists('NN_Verbose_Flag.txt'), 2, 0), view_metrics = ifelse(file.exists('NN_Verbose_Flag.txt'), TRUE, FALSE))
history <- fit(model, x.train.array, y.train, epochs = 1, batch_size = 32, validation_split = 0.2, verbose = 2, view_metrics = FALSE)
history <- fit(model, x.train.array, y.train, epochs = 99, batch_size = 32, validation_split = 0.2, verbose = 0, view_metrics = FALSE)
history <- fit(model, x.train.array, y.train, epochs = 1, batch_size = 32, validation_split = 0.2, verbose = 2, view_metrics = FALSE)
history <- fit(model, x.train.array, y.train, epochs = 200, batch_size = 32, validation_split = 0.2, verbose = 0, view_metrics = FALSE)
x.test.array <- as.matrix(x.test)
}
viewMetrics <- c(TRUE, FALSE)[2]
# CNN_model ver 1,3,4,5
if(model_Name == 'CNN_model_ver_5') {
x.train.array <- array(as.matrix(x.train), c(nrow(x.train), ncol(x.train), 1))
history <- fit(model, x.train.array, y.train, epochs = 50, batch_size = 32, validation_split = 0.2, verbose = 2,
view_metrics = viewMetrics)
# view_metrics = viewMetrics, callbacks = list(callback_tensorboard(histogram_freq = 1, profile_batch = 2))) # profile_batch = c(1, 5)
x.test.array <- array(as.matrix(x.test), c(nrow(x.test), ncol(x.test), 1))
}
# CNN_model ver 2
# x.train.array <- array(as.matrix(x.train), c(nrow(x.train), ncol(x.train), 1))
# history <- fit(model, x.train.array, y.train, epochs = 1, batch_size = 32, validation_split = 0.2, verbose = 2, view_metrics = viewMetrics)
# history <- fit(model, x.train.array, y.train, epochs = 99, batch_size = 32, validation_split = 0.2, verbose = 0, view_metrics = viewMetrics)
# history <- fit(model, x.train.array, y.train, epochs = 1, batch_size = 32, validation_split = 0.2, verbose = 2, view_metrics = viewMetrics)
# history <- fit(model, x.train.array, y.train, epochs = 199, batch_size = 32, validation_split = 0.2, verbose = 0, view_metrics = viewMetrics)
# x.test.array <- array(as.matrix(x.test), c(nrow(x.test), ncol(x.test), 1))
if(model_Name == 'CNN_model_2D') {
x.train.array <- array(as.matrix(x.train), c(nrow(x.train), ncol(x.train), 1))
history <- fit(model, x.train.array, y.train * diag(length(y.train)), epochs = 50, batch_size = 32, validation_split = 0.2, verbose = 2, view_metrics = viewMetrics)
x.test.array <- array(as.matrix(x.test), c(nrow(x.test), ncol(x.test), 1))
}
evaluate(model, x.test.array, y.test, verbose = 0)
cat("\n")
print(summary(history))
dev.set(3)
print(plot(history))
if(file.exists('NN_Verbose_Flag.txt'))
browsePlot('print(plot(history))', file = paste0("NN_History_Iter_", Iter, ".png")) # Save NN History figures
# Predict using the test set; plot, create statistics, and create an agreement table
y.test.pred <- predict(model, x.test.array)
if(model_Name == 'FCNN_model_ver_1' & is.null(layer_dropout_rate)) Delta <- -0.05 # Delta is a previous estimate or guess for now, which varies by species.
if(model_Name == 'FCNN_model_ver_1' & !is.null(layer_dropout_rate)) Delta <- -0.3
if(model_Name == 'CNN_model_ver_5') Delta <- -0.2
if(model_Name == 'CNN_model_2D') Delta <- 0
y.test.pred.rd <- round(y.test.pred + Delta) # Rounding with a added delta (which is a negative number)
dev.set(4)
# plot(y.test, y.test.pred)
# abline(0, 1, col = 'green', lty = 2)
print(predicted_observed_plot(y.test, y.test.pred, xlab = 'y.test', ylab = 'y.test.pred'))
# SAD vector the Sum of absolute differences plot
# SAD <- c(SAD, sqrt(sum((y.test - y.test.pred.rd)^2)/(length(y.test) - 1))) # RMSE
SAD <- c(SAD, sum(abs(y.test - y.test.pred.rd)))
# Correlation vector for the iterations plot
Cor <- c(Cor, cor(y.test, y.test.pred))
# RMSE vector for the iterations plot
RMSE <- c(RMSE, sqrt(mean((y.test - y.test.pred)^2, na.rm = TRUE)))
# e1071::classAgreement diagonal
CA_diag <- c(CA_diag, e1071::classAgreement(Table(y.test.pred.rd, y.test), match.names = FALSE)$diag)
cat("\nclassAgreement Diagonal =", rev(CA_diag)[1], "\n")
cat("\n\n")
# print(e1071::classAgreement(Table(y.test.pred.rd, y.test), match.names = TRUE)$diag) # match.names = TRUE option
# Correlation Between Sum of Absolute Differences and the classAgreement diagonal
if(length(SAD) >= 10)
# cat("\nCorrelation between sum of Absolute Differences and the classAgreement Diagonal =", signif(cor(SAD[5:length(SA)], CA_diag[5:length(CA_diag)]), 6), "\n")
cat("\nCorrelation between sum of Absolute Differences and the classAgreement Diagonal =", signif(cor(SAD, tail(CA_diag, length(SAD))), 6), "\n")
# dev.new(width = 14, height = 10)
# agreementFigure(y.test, y.test.pred, Delta, full = TRUE)
dev.set(5) # agreementFigure() also prints out the Correlation, R_squared, RMSE, MAE, SAD (Sum of Absolute Differences)
agreementFigure(y.test, y.test.pred, Delta, main = paste0("Random Reps = ", j, ": Fold Num = ", i, ": Iter = ", Iter))
dev.set(2)
par(mfrow = c(3, 1))
plot(1:length(RMSE), RMSE, col = 'green', type = 'b', ylab = "RMSE (green)", xlab = "Iteration Number")
abline(h = 4, lty = 2, col ='grey39', lwd = 1.25)
if(Iter < 5)
try(plot(1:length(CA_diag), CA_diag, col = 'red', type = 'b', ylab = "Diagonal of Class Agreement (red)", xlab = "Iteration Number"))
else
try(plot.loess(1:length(CA_diag), CA_diag, col = 'red', line.col = 'deeppink', type = 'b', ylab = "Diagonal of Class Agreement (red)", xlab = "Iteration Number"))
abline(h = 0.2, lty = 2, col ='grey39', lwd = 1.25)
# Avoiding high SAD values at the beginning, and rarely, during a run.
SAD_plot <- SAD
SAD_plot[SAD_plot > 1400] <- NA # Extreme model runs can, on a very rare occasion, put the value of SAD above 1,400 beyond the initial runs
if(Iter < 5)
try(plot(1:length(SAD_plot), SAD_plot, col = 'blue', type = 'b', ylab = "Sum of Absolute Differences (blue)", xlab = "Iteration Number"))
else
try(plot.loess(1:length(SAD_plot), SAD_plot, col = 'blue', line.col = 'dodgerblue', type = 'b', ylab = "Sum of Absolute Differences (blue)", xlab = "Iteration Number"))
abline(h = 950, lty = 2, col ='grey39', lwd = 1.25)
# Save all the iteration models until the best one is found
print(saveName <- paste0(Spectra_Set, '_', paste(get.subs(model_Name, "_")[-2], collapse = "_"), '_SM_', Seed_Model, '_RI_', j, '_LR_',
format(learningRate, sci = FALSE), '_LD_', ifelse(is.null(layer_dropout_rate), 0, layer_dropout_rate), '_It_', length(SAD),
'_SAD_', rev(SAD)[1], '_', timeStamp()))
assign(saveName, keras::serialize_model(model, include_optimizer = TRUE))
# save(Iter, Cor, CA_diag, SAD, learningRate, layer_dropout_rate, .Random.seed, list = saveName, file = paste0(saveName, '.RData')) # For debugging
saveModels <- c(saveModels, saveName)
saveModels_List[[saveName]] <- keras::serialize_model(model, include_optimizer = TRUE)
if(Iter == Iter_Num)
break
} # Iter while() loop
if(!file.exists('Run_NN_Model_Flag'))
break
Iter_Best_Model <- sort.f(data.frame(SAD, RMSE, CA_diag, Iter = 1:Iter_Num), c(1, 2))[1, 4] # Best model is when SAD is lowest, with ties broken by RMSE
print(sort.f(data.frame(SAD, RMSE, CA_diag, Iter = 1:Iter_Num), c(1, 3)))
cat(paste0('\n\nBest_Model Number = ', Iter_Best_Model, '\n\n'))
Fold_models[[i]] <- saveModels_List[[Iter_Best_Model]]
cat(paste0('\nBest Model Name = ', saveModels[Iter_Best_Model], "\n\n"))
rm(list = saveModels)
x.fold.test <- as.matrix(1000 * Model_Spectra.sg.iPLS[folds_index[[i]], ])
y.fold.test <- TMA_Vector[folds_index[[i]]]
y.fold.test.pred <- predict(keras::unserialize_model(Fold_models[[i]], custom_objects = NULL, compile = TRUE), x.fold.test)
dev.set(6)
agreementFigure(y.fold.test, y.fold.test.pred, Delta = Delta, full = TRUE, main = paste0("Random Rep = ", j, ": Fold Num = ", i))
dev.set(7)
agreementFigure(y.fold.test, y.fold.test.pred, Delta = Delta, full = FALSE, main = paste0("Random Rep = ", j, ": Fold Num = ", i))
} # j Fold loop
if(!file.exists('Run_NN_Model_Flag'))
break
Rdm_models[[j]] <- Fold_models # List of lists being assigned to an element of a list - the best model for each fold (10 or other used) within the jth random rep
Rdm_folds_index[[j]] <- folds_index # List of vectors being assigned to an element of a list - the index for each fold (10 or other used) within the jth random rep
x.fold.test.ALL <- NULL
y.fold.test.ALL <- NULL
y.fold.test.pred.ALL <- NULL
for (k in 1:length(Fold_models)) {
x.fold.test <- as.matrix(1000 * Model_Spectra.sg.iPLS[folds_index[[k]], ])
x.fold.test.ALL <- rbind(x.fold.test.ALL, x.fold.test)
y.fold.test.ALL <- c(y.fold.test.ALL, TMA_Vector[folds_index[[k]]])
print(length(predict(keras::unserialize_model(Fold_models[[k]], custom_objects = NULL, compile = TRUE), x.fold.test)))
y.fold.test.pred.ALL <- c(y.fold.test.pred.ALL, predict(keras::unserialize_model(Fold_models[[k]], custom_objects = NULL, compile = TRUE), x.fold.test))
}
browsePlot('agreementFigure(y.fold.test.ALL, y.fold.test.pred.ALL, Delta = Delta, full = TRUE, main = paste0("Random Rep = ", j))')
SG_Variables_Selected <- names(Model_Spectra.sg.iPLS)
roundingDelta <- Delta # This Delta is only the previous estimate or guess for now (see above). The best rounding Delta is again tested for in the predict script.
save(Iter, i, j, Cor, CA_diag, SAD, learningRate, layer_dropout_rate, Seed_Fold, Seed_Model, Seed_Main, Rdm_models,
Rdm_folds_index, SG_Variables_Selected, roundingDelta, file = paste0(Spectra_Set, '_', model_Name, '_', length(Rdm_folds_index), '_Rdm_model_', timeStamp(), '.RData'))
} # k Random Replicate loop
# = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = = =
} ###
# --- Find Median over all Rdm_reps Models and create figures ---
{ ###
# Only 2 loads needed to redo this section with new data - the Model_Spectra.sg.iPLS has to, of course, match the Rdm_model and Rdm_folds_index and the Conda eniv needs to be loaded properly using the code above.
# base::load("C:\\ALL_USR\\JRW\\SIDT\\Sablefish 2022 Combo\\Sable_Combo_2022_NN_Fish_Len_Otie_Wgt_GPU_Machine\\Sable_Combo_2022_FCNN_model_ver_1_5_Rdm_model_21_Dec_2023_08_14_19.RData")
# base::load("C:\\ALL_USR\\JRW\\SIDT\\Sablefish 2022 Combo\\Sable_Combo_2022_NN_Fish_Len_Otie_Wgt\\Sable_Combo_2022_Model_Spectra.sg.iPLS.RData")
# A generic Model_Spectra.sg.iPLS may need metadata added to the scans - compare to the end of SG_Variables_Selected (found within e.g. ...FCNN_model_ver_1_20_Pred_Median_TMA.RData).
# If the model has a reduced number of otoliths, then the correct Run number's pseudo random number seed has to set.
# cor(Sable_Combo_2022_NN_Pred_Median_TMA$TMA, TMA_Vector) needs to be 1 (one).
# ----------------------- Put the fitted results for each random reps (Rdm_reps) full fold model into a data frame: y.fold.test.pred_RDM ------------------------
(Rdm_reps <- length(Rdm_folds_index))
y.fold.test.pred_RDM <- NULL
for (j in 1:Rdm_reps) {
folds_index <- Rdm_folds_index[[j]]
Fold_models <- Rdm_models[[j]]
y.fold.test.pred.ALL <- NULL
for (i in 1:length(Fold_models)) {
if(verbose)
cat(paste0("\nRdm_reps ", j, ": Fold_model ", i, "\n"))
x.fold.test <- as.matrix(1000 * Model_Spectra.sg.iPLS[folds_index[[i]], ])
y.fold.test.pred <- as.vector(predict(keras::unserialize_model(Fold_models[[i]], custom_objects = NULL, compile = TRUE), x.fold.test))
if(verbose)
print(c(length(folds_index[[i]]), length(y.fold.test.pred)))
y.fold.test.pred.ALL <- rbind(y.fold.test.pred.ALL, cbind(Index = folds_index[[i]], y.test.fold.pred = y.fold.test.pred))
}
cat(paste0("\nFold_model ", j, "\n"))
print(dim(y.fold.test.pred.ALL ))
y.test.pred <- sort.f(data.frame(y.fold.test.pred.ALL))[, 2] # Sort on the Index to match back to the order of the full TMA_Vector and Model_Spectra.sg.iPLS
y.fold.test.pred_RDM <- rbind(y.fold.test.pred_RDM, y.test.pred)
cat(paste0("\nRdm_reps ", j, "\n"))
print(dim(y.fold.test.pred_RDM))
# dev.new(width = 11, height = 8)
# agreementFigure(TMA_Vector, y.test.pred, Delta = -0.05, full = TRUE, main = paste0("Random Rep = ", j))
# if(verbose)
# browsePlot('agreementFigure(TMA_Vector, y.test.pred, Delta = -0.05, full = TRUE, main = paste0("Random Rep = ", j))') # Delta is a previous estimate or guess for now
# Full figure only needed for a long-lived species like Sablefish
# dev.new(width = 11, height = 8)
# agreementFigure(TMA_Vector, y.test.pred, Delta = -0.25, full = FALSE, main = paste0("Random Rep = ", j))
}
# ----------------------- Median over all Rdm_reps Models ------------------------
# Look to see if all random reps fit well and didn't have an issue with good fitting (only seen in the metadata only models). Also compare the agreement figures.
renum(t(apply(y.fold.test.pred_RDM, 1, function(x) unlist(Correlation_R_squared_RMSE_MAE_SAD(x, TMA_Vector)))))
y.fold.test.pred_RDM_median <- apply(y.fold.test.pred_RDM, 2, median)
# y.fold.test.pred_RDM_median <- apply(y.fold.test.pred_RDM[1, , drop = FALSE], 2, median) # Select only those random runs which show good fits # SAD = 3300. R2 = 0.8432
# Delta <- -0.05 # Previous estimate or guess
data.frame(Delta = Delta, Correlation_R_squared_RMSE_MAE_SAD(TMA_Vector, round(y.fold.test.pred_RDM_median + Delta)))
# What is the best Delta (by SAD, with ties broken by RMSE) on the median over all, Rdm_reps, full k-folds
Delta_Table <- NULL
for (Delta. in seq(0, -0.45, by = -0.05)) {
# cat("\n\n")
# print(c(Delta = Delta., Correlation_R_squared_RMSE_MAE_SAD(TMA_Vector, round(y.fold.test.pred_RDM_median + Delta.))))
Delta_Table <- rbind(Delta_Table, c(Delta = Delta., unlist(Correlation_R_squared_RMSE_MAE_SAD(TMA_Vector, round(y.fold.test.pred_RDM_median + Delta.)))))
}
print(Delta_Table <- data.frame(Delta_Table))
# Best Delta from table above
(Delta <- Delta_Table$Delta[order(Delta_Table$SAD, Delta_Table$RMSE)[1]])
SG_Variables_Selected <- names(Model_Spectra.sg.iPLS)
roundingDelta <- Delta
# Do a final save after the best rounding Delta is official found for this spectra set - the best rounding Delta is again tested for in the predict script.
save(Iter, i, j, Cor, CA_diag, SAD, learningRate, layer_dropout_rate, Seed_Fold, Seed_Model, Seed_Main, Rdm_models,
Rdm_folds_index, SG_Variables_Selected, roundingDelta, file = paste0(Spectra_Set, '_', model_Name, '_', length(Rdm_folds_index), '_Rdm_model_', timeStamp(), '.RData'))
# Agreement Figures (standard and zoomed) using the best delta from above
# dev.new(width = 11, height = 8) # R plot window version
# agreementFigure(TMA_Vector, y.fold.test.pred_RDM_median, Delta = Delta, full = TRUE, main = paste0("Median over ", Rdm_reps, ' Full k-Fold Models'), cex = 1.25) # R plot window version
# browsePlot('agreementFigure(TMA_Vector, y.fold.test.pred_RDM_median, Delta = Delta, full = TRUE, main = paste0("Median over ", Rdm_reps, " Full k-Fold Models"), cex = 1.25)', file = 'Figures/Sable_2022_Combo_20_Rdm_Final.pdf', pdf = TRUE) # PDF version
browsePlot('agreementFigure(TMA_Vector, y.fold.test.pred_RDM_median, Delta = Delta, full = TRUE, main = paste0("Median over ", Rdm_reps, " Full k-Fold Models"))', file = paste0('Figures/', Spectra_Set, '_', length(Rdm_folds_index), '_Rdm_Final.png'))
browsePlot('agreementFigure(TMA_Vector, y.fold.test.pred_RDM_median, Delta = Delta, full = FALSE, main = paste0("Median over ", Rdm_reps, " Full k-Fold Models"))', file = paste0('Figures/', Spectra_Set, '_', length(Rdm_folds_index), '_Rdm_Final_Zoomed.png'))
# Apply that best Delta (from above) to all Rdm_reps models individually
Stats_RDM_median_by_model <- NULL
for(numRdmModels in 1:Rdm_reps) {
y.fold.test.pred_RDM_median_one_rep <- apply(y.fold.test.pred_RDM[numRdmModels, ,drop = FALSE], 2, median)
Stats_RDM_median_by_model <- rbind(Stats_RDM_median_by_model, data.frame(t(unlist(Correlation_R_squared_RMSE_MAE_SAD(TMA_Vector, round(y.fold.test.pred_RDM_median_one_rep + Delta))))))
}
print(Stats_RDM_median_by_model)
# An additional full k-fold added to the total number of models at each step in turn
# dev.new(width = 11, height = 8)
{ # matplot of Various stats vs nunber of complete Folds
browsePlot("
par(mfrow = c(3,2))
# Delta <- -0.05 # Reset Delta if recreating this figure as an old Delta may linger.
Stats_RDM_median_by_model_added <- NULL
for(numRdmModels in 1:Rdm_reps) {
y.fold.test.pred_RDM_median <- apply(y.fold.test.pred_RDM[1:numRdmModels, ,drop = FALSE], 2, median)
Stats_RDM_median_by_model_added <- rbind(Stats_RDM_median_by_model_added, data.frame(t(unlist(Correlation_R_squared_RMSE_MAE_SAD(TMA_Vector, round(y.fold.test.pred_RDM_median + Delta))))))
}
print(Stats_RDM_median_by_model_added)
min.stats <- apply(Stats_RDM_median_by_model_added[, c(3,5)], 2, min)
minAdj <- sweep(data.matrix(Stats_RDM_median_by_model_added[, c(3,5)]), 2, min.stats)
max.of.Adj <- apply(minAdj, 2, max)
print(Stats_0_1_interval <- cbind(Stats_RDM_median_by_model_added[, 1:2], t(t(minAdj)/max.of.Adj)))
matplot(1:Rdm_reps, Stats_0_1_interval, type = 'o', col = c(1:3, 6), xlab = 'Number of Complete Folds', ylab = 'Various Stats', main = 'Original Order')
# Add 5 more Randomized order figures
set.seed(Seed_Main)
(Seed_reps <- round(runif(6, 0, 1e8)))
for (i in 1:5) {
set.seed(Seed_reps[i])
(Rdm_Vec <- sample(1:Rdm_reps))
Stats_RDM_median_by_model_added <- NULL
for(numRdmModels in 1:Rdm_reps) {
y.fold.test.pred_RDM_median <- apply(y.fold.test.pred_RDM[Rdm_Vec[1:numRdmModels], , drop = FALSE], 2, median)
Stats_RDM_median_by_model_added <- rbind(Stats_RDM_median_by_model_added, data.frame(t(unlist(Correlation_R_squared_RMSE_MAE_SAD(TMA_Vector, round(y.fold.test.pred_RDM_median + Delta))))))
}
min.stats <- apply(Stats_RDM_median_by_model_added[, c(3,5)], 2, min)
minAdj <- sweep(data.matrix(Stats_RDM_median_by_model_added[, c(3,5)]), 2, min.stats)
max.of.Adj <- apply(minAdj, 2, max)
(Stats_0_1_interval <- cbind(Stats_RDM_median_by_model_added[, 1:2], t(t(minAdj)/max.of.Adj)))
matplot(1:Rdm_reps, Stats_0_1_interval, type = 'o', col = c(1:3, 6), xlab = 'Number of Complete Folds', ylab = 'Various Stats', main = 'Randomized Order')
}
", width = 11, height = 8, file = paste0('Figures/Full_k-fold_models_added_sequentially.png'))
}
# --- NN prediction for each otie in the NN model ---
Pred_median <- r(data.frame(NN_Pred_Median = apply(y.fold.test.pred_RDM, 2, median),
Lower_Quantile_0.025 = apply(y.fold.test.pred_RDM, 2, quantile, probs = 0.025, na.rm = TRUE),
Upper_Quantile_0.975 = apply(y.fold.test.pred_RDM, 2, quantile, probs = 0.975, na.rm = TRUE)), 4)
cat(paste0("\n\n--- Note: The quantiles are a reflection of the NN models precision based on ", length(Rdm_models), " full 10-fold randomized models, not the accuracy to a TMA Age ---\n\n"))
assign(paste0(Spectra_Set, '_NN_Pred_Median_TMA'), data.frame(filenames = fileNames, Pred_median, TMA = TMA_Vector), pos = 1)
save(list = paste0(Spectra_Set, '_NN_Pred_Median_TMA'), file = paste0(Spectra_Set, '_', model_Name, '_', length(Rdm_folds_index), '_Pred_Median_TMA_', timeStamp(), '.RData'))
# This agreementFigure() already produced above
# (y.fold.test.pred_RDM_median <- apply(y.fold.test.pred_RDM, 2, median))[1:10]
# browsePlot('agreementFigure(TMA_Vector, y.fold.test.pred_RDM_median, Delta = Delta, full = TRUE, main = paste0("Median over ", Rdm_reps, " Full k-Fold Models"), cex = 1.25)')
# Copy the spectra set prediction to a generic name and add a rounded prediction by adding the best delta found above
Model_Ages <- get(paste0(Spectra_Set, '_NN_Pred_Median_TMA'))
Model_Ages$Pred_Age_Rounded <- round(Model_Ages$NN_Pred_Median + Delta)
Model_Ages[1:5,]
# -- Plot by sorted difference --
# g <- ggplot(Model_Ages_Sub, aes(jitter(TMA, 1.25), TMA - NN_Pred_Median)) +
# geom_point()
# browsePlot('print(g)', file = paste0('Figures/TMA_minus_NN_Pred_vs_TMA.png'))
# Jitter TMA; vertical line for each unique TMA - without standard grid - all the data used for the training (not a subset like below).
xlim <- c(min(Model_Ages$TMA) - 1.25, max(Model_Ages$TMA) + 1.25)
Model_Ages$TMA_Minus_Pred_Age_Rounded <- Model_Ages$TMA - Model_Ages$Pred_Age_Rounded
browsePlot('set.seed(707); gPlot(Model_Ages, "TMA", "TMA_Minus_Pred_Age_Rounded", ylab = "TMA - Pred_Age_Rounded", xFunc = jitter, ylim = c(-xlim[2], xlim[2]), xlim = xlim,
grid = FALSE, vertLineEachPoint = TRUE)', file = paste0('Figures/TMA_minus_round_NN_Pred_vs_TMA_Jitter.png'))
# ====== Using a SAMPLE of 100 ages so the figures are not too crowded =====
set.seed(Seed_Fold)
Model_Ages_Sub <- Model_Ages[sample(1:nrow(Model_Ages), 100), ]
Model_Ages_Sub$Index <- 1:nrow(Model_Ages_Sub)
# - Plot by order implied by the spectra file names - ggplotly() changes how scale_color_manual() works ?????????????????
cols <- c('green', 'red')
g <- ggplot(Model_Ages_Sub, aes(Index, NN_Pred_Median)) +
geom_point() +
geom_errorbar(aes(ymin = Lower_Quantile_0.025, ymax = Upper_Quantile_0.975)) +
geom_point(aes(Index, Pred_Age_Rounded, col = cols[1])) +
geom_point(aes(Index + 0.1, TMA, col = cols[2])) +
scale_color_manual(labels = c('Rounded Age', 'TMA'), values = cols, name = ' ')
browsePlot('print(g)', file = paste0('Figures/Predicted_Ages_Order_by_File_Names_Subset.png'))
# -- Plot by sorted NN predicted ages --
Model_Ages_Sub_Sorted <- sort.f(Model_Ages_Sub, 'NN_Pred_Median') # Sort Model_Ages_Sub by NN_Pred_Median, except for "Index" (see the next line below)
Model_Ages_Sub_Sorted$Index <- sort(Model_Ages_Sub_Sorted$Index) # Reset Index for graphing
if(verbose) head(Model_Ages_Sub_Sorted, 10)
cols <- c('green', 'red')
g <- ggplot(Model_Ages_Sub_Sorted, aes(Index, NN_Pred_Median)) +
# xlim(0, 65) + ylim(0, 20) +
geom_point() +
geom_errorbar(aes(ymin = Lower_Quantile_0.025, ymax = Upper_Quantile_0.975)) +
geom_point(aes(Index, Pred_Age_Rounded, col = cols[1])) +
geom_point(aes(Index + 0.1, TMA, col = cols[2])) +
scale_color_manual(labels = c('Rounded Age', 'TMA'), values = cols, name = ' ')
browsePlot('print(g)', file = paste0('Figures/Predicted_Ages_Sorted_Subset.png'))
# -- Plot by sorted TMA --
Model_Ages_Sub_Sorted <- sort.f(Model_Ages_Sub, 'TMA') # Sort Model_Ages_Sub by TMA, except for "Index" (see the next line below)
Model_Ages_Sub_Sorted$Index <- sort(Model_Ages_Sub_Sorted$Index) # Reset Index for graphing
if(verbose) head(Model_Ages_Sub_Sorted, 10)
cols <- c('green', 'red')
g <- ggplot(Model_Ages_Sub_Sorted, aes(Index, NN_Pred_Median)) +
# xlim(0, 65) + ylim(0, 20) +
geom_point() +
geom_errorbar(aes(ymin = Lower_Quantile_0.025, ymax = Upper_Quantile_0.975)) +
geom_point(aes(Index, TMA, col = cols[2])) +
geom_point(aes(Index + 0.1, Pred_Age_Rounded, col = cols[1])) +
scale_color_manual(labels = c('Rounded Age', 'TMA'), values = cols, name = ' ')
browsePlot('print(g)', file = paste0('Figures/TMA_Sorted_Subset.png'))
# How many TMA ages are 3 or under
print(Table(TMA_Vector <= 3)/length(TMA_Vector))
# How many TMA ages are 15 or under
print(Table(TMA_Vector <= 15)/length(TMA_Vector))
# How many TMA ages are 20 or under
print(Table(TMA_Vector <= 20)/length(TMA_Vector))
}
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