.Rhistory

View(tmp)
?ordered
x <- readr@@read_csv("/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Mesh.Inch.csv")
x <- readr::read_csv("/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Mesh.Inch.csv")
x <- x |>
# dplyr::mutate(ycentred = y - mean(y)) |> # make mean column
# The above exists already in gbm.auto L843
# Also it uses preset colname y produced by gbm.auto.
dplyr::rename("Category" = tidyselect::last_col(offset = 2), # no first_col option
"ycentred" = tidyselect::last_col()) |>
# 2023-08-30 quoted Category to hopefully address gbm.factorplot: no visible binding for global variable ‘Category’
# also need to do for ycentred
dplyr::arrange(ycentred) # re-order the x axis for categorical variables in order from high to low value
View(x)
x <- readr::read_csv("/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year.csv")
View(x)
x <- x |>
# dplyr::mutate(ycentred = y - mean(y)) |> # make mean column
# The above exists already in gbm.auto L843
# Also it uses preset colname y produced by gbm.auto.
dplyr::rename("Category" = tidyselect::last_col(offset = 2), # no first_col option
"ycentred" = tidyselect::last_col()) |> # attempt to address no visible binding for global variable ‘Category’
# 2023-08-30 quoted Category to hopefully address gbm.factorplot: no visible binding for global variable ‘Category’
# also need to do for ycentred
dplyr::arrange("ycentred") # re-order the x axis for categorical variables in order from high to low value
View(x)
x <- x |>
# dplyr::mutate(ycentred = y - mean(y)) |> # make mean column
# The above exists already in gbm.auto L843
# Also it uses preset colname y produced by gbm.auto.
dplyr::rename("Category" = tidyselect::last_col(offset = 2), # no first_col option
"ycentred" = tidyselect::last_col()) |> # attempt to address no visible binding for global variable ‘Category’
# 2023-08-30 quoted Category to hopefully address gbm.factorplot: no visible binding for global variable ‘Category’
# also need to do for ycentred
dplyr::arrange(ycentred) # re-order the x axis for categorical variables in order from high to low value
devtools::document()
devtools::check()
data("iris")
tmp <- iris |> dplyr::mutate("Category" = dplyr::ordered(Sepal.Length))
tmp <- iris |> dplyr::mutate("Category" = ordered(Sepal.Length))
View(tmp)
tmp <- iris |> dplyr::mutate("Category" = ordered(Sepal.Length)) |> arrange(Category)
tmp <- iris |> dplyr::mutate("Category" = ordered(Sepal.Length)) |> dplyr::arrange(Category)
View(tmp)
tmp <- iris |> dplyr::mutate("Category" = ordered(Sepal.Length)) |> dplyr::arrange("Category")
rm(tmp)
tmp <- iris |> dplyr::mutate("Category" = ordered(Sepal.Length)) |> dplyr::arrange("Category")
View(tmp)
rm(tmp)
tmp <- iris |> dplyr::mutate("Category" = ordered("Sepal.Length")) |> dplyr::arrange(Category)
View(tmp)
# cran tests
# attempt to address no visible binding for global variable ‘Category’ and ycentred
mydata <- read.csv("/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year.png")
# cran tests
# attempt to address no visible binding for global variable ‘Category’ and ycentred
mydata <- read.csv("/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year.csv")
View(mydata)
gbm.auto::gbm.factorplot(x = mydata, ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST")
gbm.auto::gbm.factorplot(x = mydata, ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
gsavewidth = 4*480,
ggsaveheight = 4*480,
ggsaveunits = "px")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
gsavewidth = (4*480),
ggsaveheight = (4*480),
ggsaveunits = "px")
4*480
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
gsavewidth = 1920,
ggsaveheight = 1920,
ggsaveunits = "px")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
gsavewidth = 1920,
ggsaveheight = 1920,
ggsaveunits = "cm")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
gsavewidth = 19,
ggsaveheight = 19,
ggsaveunits = "cm")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
gsavewidth = 30,
ggsaveheight = 19,
ggsaveunits = "cm")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
gsavewidth = 50,
ggsaveheight = 19,
ggsaveunits = "cm")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
gsavewidth = 5,
ggsaveheight = 19,
ggsaveunits = "cm")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
# gsavewidth = 5,
ggsaveheight = 19,
ggsaveunits = "cm")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
# gsavewidth = 5,
ggsaveheight = 9,
ggsaveunits = "cm")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
# gsavewidth = 5,
ggsaveheight = 4*480,
ggsaveunits = "px")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
# gsavewidth = 5,
ggsaveheight = 3*480,
ggsaveunits = "px")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
# gsavewidth = 5,
ggsaveheight = 1*480,
ggsaveunits = "px")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
# gsavewidth = 5,
ggsaveheight = 240,
ggsaveunits = "px")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
ggsavewidth = 4*480,
ggsaveheight = 4*480,
ggsaveunits = "px")
source("~/Dropbox/Galway/Analysis/R/gbm.auto/R/gbm.factorplot.R")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
ggsavewidth = 4*480,
ggsaveheight = 4*480,
ggsaveunits = "px")
source("~/Dropbox/Galway/Analysis/R/gbm.auto/R/gbm.factorplot.R")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
ggsavewidth = 4*480,
ggsaveheight = 4*480,
ggsaveunits = "px")
factorplotlevels = NULL
ggplot2guideaxisangle = 0
ggplot2labsx = ""
ggplot2labsy = "Marginal Effect"
ggplot2axistext = 1.5
ggplot2axistitle = 2
ggplot2legendtext = 1
ggplot2legendtitle = 1.5
ggplot2legendtitlealign = 0
ggplot2plotbackgroundfill = "white"
ggplot2plotbackgroundcolour = "grey50"
ggplot2striptextx = 2
ggplot2panelbordercolour = "black"
ggplot2panelborderfill = NA
ggplot2panelborderlinewidth = 1
ggplot2legendspacingx = grid::unit(0, "cm")
ggplot2legendbackground = ggplot2::element_blank()
ggplot2panelbackgroundfill = "white"
ggplot2panelbackgroundcolour = "grey50"
ggplot2panelgridcolour = "grey90"
ggplot2legendkey = ggplot2::element_blank()
ggsavefilename = paste0(lubridate::today(), "_Categorical-variable.png")
ggsaveplot = ggplot2::last_plot()
ggsavedevice = "png"
ggsavepath = ""
ggsavescale = 2
ggsavewidth = 10
ggsaveheight = 4
ggsaveunits = "in"
ggsavedpi = 300
ggsavelimitsize = TRUE
x = mydata
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png"
ggsavewidth = 4*480
ggsaveheight = 4*480
ggsaveunits = "px"
is.character(x)
if (is.character(x)) {
x <- readr::read_csv(x) # readr::read_csv("/home/simon/Documents/Si Work/PostDoc Work/Gbmauto help/2022-03_Frances_Naomi/2023-02-21 categorical variables issue/count_elasmo/Gaus_Best_line_isl_grp.csv")
} else {
x <- x
}
tmp <- x
View(x)
x <- x |>
# dplyr::mutate(ycentred = y - mean(y)) |> # make mean column
# The above exists already in gbm.auto L843
# Also it uses preset colname y produced by gbm.auto.
dplyr::rename("Category" = tidyselect::last_col(offset = 2), # no first_col option
"ycentred" = tidyselect::last_col()) |> # attempt to address no visible binding for global variable ‘Category’
# 2023-08-30 quoted Category to hopefully address gbm.factorplot: no visible binding for global variable ‘Category’
# also need to do for ycentred
dplyr::arrange(ycentred) # re-order the x axis for categorical variables in order from high to low value
is.null(factorplotlevels)
# re-reorder by factorplotlevels if present
if (!is.null(factorplotlevels)) {
# check level number matches x categories
if (length(factorplotlevels) != length(x[, "Category"])) stop("number of factorplotlevels doesn't match number of categories in x") # x$Category
# check names match
if (!all(factorplotlevels %in% x[, "Category"])) stop(paste0("The following level names not present in categories in x: ", # x$Category
factorplotlevels[!factorplotlevels %in% x[, "Category"]])) # x$Category
x <- x |>
dplyr::mutate(Category = ordered(Category, levels = factorplotlevels)) |> # recreate Category as ordered factor with factorplotlevels. Can't quote "Category" in ordered
dplyr::arrange(Category) # arrange by labels (implicit). Can't quote "Category"
} else {
if (is.integer(x$Category)) x <- x |> dplyr::mutate(Category = ordered(Category)) # make integers ordered factor to avoid defaulting to continuous
}
View(x)
ggplot2::ggplot(x) +
ggplot2::geom_col(ggplot2::aes(x = Category, # x[, "Category"]
y = ycentred)) + # x[, "ycentred"]
# rotate x axis labels
ggplot2::guides(x =  ggplot2::guide_axis(angle = ggplot2guideaxisangle)) +
# alter axis labels
ggplot2::labs(x = "",
y = "Marginal Effect") +
# change theme elements
ggplot2::theme_minimal() %+replace% ggplot2::theme(
axis.text = ggplot2::element_text(size = ggplot2::rel(ggplot2axistext)),
axis.title = ggplot2::element_text(size = ggplot2::rel(ggplot2axistitle)),
legend.text = ggplot2::element_text(size = ggplot2::rel(ggplot2legendtext)),
legend.title = ggplot2::element_text(size = ggplot2::rel(ggplot2legendtitle)),
legend.title.align = ggplot2legendtitlealign, # otherwise effect type title centre aligned for some reason
plot.background = ggplot2::element_rect(fill = ggplot2plotbackgroundfill,
colour = ggplot2plotbackgroundcolour), # white background
strip.text.x = ggplot2::element_text(size = ggplot2::rel(ggplot2striptextx)),
panel.border = ggplot2::element_rect(colour = ggplot2panelbordercolour,
fill = ggplot2panelborderfill,
linewidth = ggplot2panelborderlinewidth),
legend.spacing.x = ggplot2legendspacingx, # compress spacing between legend items, this is min
legend.background = ggplot2legendbackground,
panel.background = ggplot2::element_rect(fill = ggplot2panelbackgroundfill,
colour = ggplot2panelbackgroundcolour),
panel.grid = ggplot2::element_line(colour = ggplot2panelgridcolour),
legend.key = ggplot2legendkey)
library(ggplot2)
ggplot2::ggplot(x) +
ggplot2::geom_col(ggplot2::aes(x = Category, # x[, "Category"]
y = ycentred)) + # x[, "ycentred"]
# rotate x axis labels
ggplot2::guides(x =  ggplot2::guide_axis(angle = ggplot2guideaxisangle)) +
# alter axis labels
ggplot2::labs(x = "",
y = "Marginal Effect") +
# change theme elements
ggplot2::theme_minimal() %+replace% ggplot2::theme(
axis.text = ggplot2::element_text(size = ggplot2::rel(ggplot2axistext)),
axis.title = ggplot2::element_text(size = ggplot2::rel(ggplot2axistitle)),
legend.text = ggplot2::element_text(size = ggplot2::rel(ggplot2legendtext)),
legend.title = ggplot2::element_text(size = ggplot2::rel(ggplot2legendtitle)),
legend.title.align = ggplot2legendtitlealign, # otherwise effect type title centre aligned for some reason
plot.background = ggplot2::element_rect(fill = ggplot2plotbackgroundfill,
colour = ggplot2plotbackgroundcolour), # white background
strip.text.x = ggplot2::element_text(size = ggplot2::rel(ggplot2striptextx)),
panel.border = ggplot2::element_rect(colour = ggplot2panelbordercolour,
fill = ggplot2panelborderfill,
linewidth = ggplot2panelborderlinewidth),
legend.spacing.x = ggplot2legendspacingx, # compress spacing between legend items, this is min
legend.background = ggplot2legendbackground,
panel.background = ggplot2::element_rect(fill = ggplot2panelbackgroundfill,
colour = ggplot2panelbackgroundcolour),
panel.grid = ggplot2::element_line(colour = ggplot2panelgridcolour),
legend.key = ggplot2legendkey)
devtools::document()
source("~/Dropbox/Galway/Analysis/R/gbm.auto/R/gbm.factorplot.R")
rm(list = c("gbm.factorplot"))
devtools::document()
# cran tests
# attempt to address no visible binding for global variable ‘Category’ and ycentred
remotes::install_github("SimonDedman/gbm.auto")
# ctrl shift F10
library(gbm.auto)
mydata <- read.csv("/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year.csv")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
ggsavewidth = 4*480,
ggsaveheight = 4*480,
ggsaveunits = "px")
source("~/Desktop/gbm.factorplot-BKUP.R")
devtools::document()
rm(list = c("gbm.factorplot"))
devtools::document()
devtools::check()
# cran tests
# attempt to address no visible binding for global variable ‘Category’ and ycentred
remotes::install_github("SimonDedman/gbm.auto")
# ctrl shift F10
library(gbm.auto)
mydata <- read.csv("/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year.csv")
gbm.auto::gbm.factorplot(x = mydata,
ggsavefilename = "/home/simon/Documents/Si Work/PostDoc Work/Kroetz & Dedman Sawfish BRT/P.Pectinata.CPUE.m2/AllExpvars/P.Pectinata.CPUE.m2/Bin_Best_line_Year_ggTEST.png",
ggsavewidth = 4*480,
ggsaveheight = 4*480,
ggsaveunits = "px")
devtools::build()
devtools::check()
devtools::build()
devtools::release()
devtools::document()
devtools::check()
devtools::check_win_devel()
devtools::release()
devtools::document()
devtools::release()
devtools::document()
drumline <- readRDS("/home/simon/Documents/Si Work/PostDoc Work/Saving The Blue/Data/2023-12-18_drumline_reefs_dropoff.rds")
drumline %<>% tidyr::drop_na(CaribbeanReef_CPUE)
library(magrittr) # %<>%
library(dplyr) # %>% matches last filter mutate case_when relocate everything rename across last_col bind_cols group_by tally pull summarise n_distinct left_join arrange select bind_rows # %>% matches last filter mutate case_when relocate everything rename across last_col bind_cols group_by tally pull summarise n_distinct left_join arrange select bind_rows
library(lubridate) # minute yday month is.POSIXt today
library(tidyverse) # "No used functions found" # "No used functions found"
library(tidylog) # filter mutate relocate pivot_wider rename replace_na group_by tally summarise left_join drop_na select pivot_longer # filter mutate relocate pivot_wider rename replace_na group_by tally summarise left_join drop_na select pivot_longer
library(gbm.auto)
source("~/Dropbox/Galway/Analysis/R/My Misc Scripts/lognegs.R")
drumline <- readRDS("/home/simon/Documents/Si Work/PostDoc Work/Saving The Blue/Data/2023-12-18_drumline_reefs_dropoff.rds")
drumline %<>% tidyr::drop_na(CaribbeanReef_CPUE)
samples = as.data.frame(drumline |> filter(CaribbeanReef_CPUE != 0) |> select(CaribbeanReef_CPUE, all_of(expvars))),
samples = as.data.frame(drumline |> filter(CaribbeanReef_CPUE != 0) |> select(CaribbeanReef_CPUE, all_of(expvars)))
drumline <- readRDS("/home/simon/Documents/Si Work/PostDoc Work/Saving The Blue/Data/2023-12-18_drumline_reefs_dropoff.rds")
drumline %<>% tidyr::drop_na(CaribbeanReef_CPUE)
expvars = c(
"Habitat", # Site3 Habitat Substrate2 all similar
"Tide",
"Season",
"LunarPhase",
"Depth_m",
"Temperature_C",
"Yearday",
"DtDropOff"
)
samples = as.data.frame(drumline |> filter(CaribbeanReef_CPUE != 0) |> select(CaribbeanReef_CPUE, all_of(expvars)))
expvar = expvars
# expvar = c("Habitat", "Tide", "LunarPhase", "Depth_m", "Temperature_C", "Yearday", "DtDropOffLogNeg"),
# expvar = c("DtDropOffLogNeg"),
resvar = "CaribbeanReef_CPUE"
# expvarnames = NULL,
# resvarname = NULL,
savedir = paste0("../../Projects/2021-10_Drumline_Reefshark/LMplots PairPlots/")
expvarnames = NULL
resvarname = NULL
plotname = NULL
pngtype = c("cairo-png", "quartz", "Xlib")
r2line = TRUE
pointtext = FALSE
pointlabs = resvar
pointcol = "black"
expvar
i <- "Tide"
print(paste0("plotting ", which(expvar %in% i), "/", length(expvar), ": ", i))
# overwrite xname if expvarnames present
xname <- ifelse(test = is.null(expvarnames),
yes = i,
no = expvarnames[which(expvar %in% i)])
# overwrite plotname if plotname present
plotname <- ifelse(test = is.null(plotname),
yes = xname,
no = plotname[which(expvar %in% i)])
# overwrite yname if resvarname present
yname <- ifelse(test = is.null(resvarname),
yes = resvar,
no = resvarname)
# run plot
gbm.auto::lmplot(
x = samples[, i],
y = samples[, resvar],
xname = xname,
yname = yname,
savedir = savedir,
pngtype = c("cairo-png", "quartz", "Xlib"),
# xlab = xname, # x axis label, parsed from xname unless specified
# ylab = yname, # y axis label, parsed from yname unless specified
plotname = plotname, # filename for png, parsed from xname unless specified
r2line = r2line, # plot rsquared trendline, default TRUE
pointtext = pointtext, # label each point? Default false
pointlabs = pointlabs, # point labels, defaults to resvar value
pointcol = pointcol, # points colour
)
savedir
getwd()
# expvarnames = NULL,
# resvarname = NULL,
savedir = "/home/simon/Documents/Si Work/PostDoc Work/Saving The Blue/Projects/2021-10_Drumline_Reefshark/LMplots PairPlots"
# run plot
gbm.auto::lmplot(
x = samples[, i],
y = samples[, resvar],
xname = xname,
yname = yname,
savedir = savedir,
pngtype = c("cairo-png", "quartz", "Xlib"),
# xlab = xname, # x axis label, parsed from xname unless specified
# ylab = yname, # y axis label, parsed from yname unless specified
plotname = plotname, # filename for png, parsed from xname unless specified
r2line = r2line, # plot rsquared trendline, default TRUE
pointtext = pointtext, # label each point? Default false
pointlabs = pointlabs, # point labels, defaults to resvar value
pointcol = pointcol, # points colour
)
# expvarnames = NULL,
# resvarname = NULL,
savedir = "/home/simon/Documents/Si Work/PostDoc Work/Saving The Blue/Projects/2021-10_Drumline_Reefshark/LMplots PairPlots/"
# run plot
gbm.auto::lmplot(
x = samples[, i],
y = samples[, resvar],
xname = xname,
yname = yname,
savedir = savedir,
pngtype = c("cairo-png", "quartz", "Xlib"),
# xlab = xname, # x axis label, parsed from xname unless specified
# ylab = yname, # y axis label, parsed from yname unless specified
plotname = plotname, # filename for png, parsed from xname unless specified
r2line = r2line, # plot rsquared trendline, default TRUE
pointtext = pointtext, # label each point? Default false
pointlabs = pointlabs, # point labels, defaults to resvar value
pointcol = pointcol, # points colour
)
plotname
plotname = NULL
expvar
for (i in expvar) { # i <- "Tide"
print(paste0("plotting ", which(expvar %in% i), "/", length(expvar), ": ", i))
# overwrite xname if expvarnames present
xname <- ifelse(test = is.null(expvarnames),
yes = i,
no = expvarnames[which(expvar %in% i)])
# overwrite plotname if plotname present
plotnameFun <- ifelse(test = is.null(plotname),
yes = xname,
no = plotname[which(expvar %in% i)])
# overwrite yname if resvarname present
yname <- ifelse(test = is.null(resvarname),
yes = resvar,
no = resvarname)
# run plot
gbm.auto::lmplot(
x = samples[, i],
y = samples[, resvar],
xname = xname,
yname = yname,
savedir = savedir,
pngtype = c("cairo-png", "quartz", "Xlib"),
# xlab = xname, # x axis label, parsed from xname unless specified
# ylab = yname, # y axis label, parsed from yname unless specified
plotname = plotnameFun, # filename for png, parsed from xname unless specified
r2line = r2line, # plot rsquared trendline, default TRUE
pointtext = pointtext, # label each point? Default false
pointlabs = pointlabs, # point labels, defaults to resvar value
pointcol = pointcol, # points colour
)
rm(list("xname", "plotname"))
}
for (i in expvar) { # i <- "Tide"
print(paste0("plotting ", which(expvar %in% i), "/", length(expvar), ": ", i))
# overwrite xname if expvarnames present
xname <- ifelse(test = is.null(expvarnames),
yes = i,
no = expvarnames[which(expvar %in% i)])
# overwrite plotname if plotname present
plotnameFun <- ifelse(test = is.null(plotname),
yes = xname,
no = plotname[which(expvar %in% i)])
# overwrite yname if resvarname present
yname <- ifelse(test = is.null(resvarname),
yes = resvar,
no = resvarname)
# run plot
gbm.auto::lmplot(
x = samples[, i],
y = samples[, resvar],
xname = xname,
yname = yname,
savedir = savedir,
pngtype = c("cairo-png", "quartz", "Xlib"),
# xlab = xname, # x axis label, parsed from xname unless specified
# ylab = yname, # y axis label, parsed from yname unless specified
plotname = plotnameFun, # filename for png, parsed from xname unless specified
r2line = r2line, # plot rsquared trendline, default TRUE
pointtext = pointtext, # label each point? Default false
pointlabs = pointlabs, # point labels, defaults to resvar value
pointcol = pointcol, # points colour
)
}
samples <- read.csv("~/Downloads/catchdata_2001-2020_USETHISONEforBRT.csv", header=FALSE)
View(samples)
library(gbm.auto)
gbm.auto(samples=samples,expvar=c(10:26),resvar=27,lr=c(0.01,0.001),savedir = "/home/simon/Downloads/")
library(tidyverse)
samples <- read_csv("/home/simon/Downloads/data.csv")
gbm.auto(samples=samples,expvar=c(10:26),resvar=27,lr=c(0.01,0.001),savedir = "/home/simon/Downloads/")
usethis::use_mit_license()
document()
devtools::document()
devtools::check
devtools::check()
devtools::document()
devtools::check()
citation("movegroup")
install.packages("GWalkR")
library(GWalkR)
library(tidyverse)
mpg_tbl <- read_csv("083_gwalkr/data/mpg.csv")