Package 'martelosim'

Build Samsara txt files from xlsx inventory

Description

Build Samsara txt files from xlsx inventory

Usage

build_samsa2_files(
  file = file.path("data", sprintf("Data_Marteloscope_%s.xlsx", getOption("mart_site"))),
  verbose = TRUE
)

Arguments

file	inventory file in xlsx, by default Data_marteloscope_<site>.xlsx
verbose	Allow to print messages. False by default.

---

Check tinytex

Description

Check tinytex

Usage

check_tinytex_dep(verbose = FALSE)

Arguments

verbose

sho messages

---

Open or message marking file

Description

Open or message marking file

Usage

find_marking(open = TRUE, verbose = TRUE)

Arguments

open	Open files with sheet editor. TRUE by default
verbose	Write nice messages, TRUE by default

---

Sapplings height classes

Description

Sapplings height classes

Usage

HClasses

Format

An object of class data.frame with 4 rows and 3 columns.

Source

Benoit Courbaud

---

iplus traduction for martelage

Description

iplus traduction for martelage

Usage

iplus_action

Format

An object of class data.frame with 4 rows and 3 columns.

Source

Benoit Courbaud

---

iplus traduction for martelage

Description

iplus traduction for martelage

Usage

iplus_reason

Format

An object of class data.frame with 11 rows and 3 columns.

Source

Benoit Courbaud

---

Plots color scales for reports

Description

Plots color scales for reports

Usage

mart_scales

Format

An object of class list of length 9.

Source

Benoit Courbaud

---

Render maps for field identification of interesting trees

Description

Render maps for field identification of interesting trees

Usage

martelo_maps()

Value

Create a pdf file.

---

Render report for one group

Description

Render report for one group

Usage

martelo_report(
  marking_groups = "X",
  dendrometry = TRUE,
  regeneration = TRUE,
  light = TRUE,
  harvest = TRUE,
  carbon = TRUE,
  biodiversity = TRUE,
  rockfall = TRUE,
  snow = TRUE,
  economy = TRUE,
  multi = FALSE
)

Arguments

marking_groups	Group Name. Must be a group present.
dendrometry	Print the page about this subject. TRUE by default.
regeneration	Print the page about this subject. TRUE by default.
light	Print the page about this subject. TRUE by default.
harvest	Print the page about this subject. TRUE by default.
carbon	Print the page about this subject. TRUE by default.
biodiversity	Print the page about this subject. TRUE by default.
rockfall	Print the page about this subject. TRUE by default.
snow	Print the page about this subject. TRUE by default.
economy	Print the page about this subject. TRUE by default.
multi	Render a different report with only comparative plots

Value

Create a pdf file.

---

martelosim

Description

Report production from marteloscopes with Capsis

Details

The goal of this package is to help users in using Capsis softawre and compile reports for field workshops. The workshop consist in predicting management effects on forest stand within the capsis platform.

Author(s)

Maintainer: Maxime Jaunatre [email protected] (ORCID) [translator]

Authors:

• Benoit Courbaud [email protected] (ORCID)

Other contributors:

• INRAE [copyright holder]

See Also

Useful links:

• https://forge.inrae.fr/lessem/rpackages/martelosim

---

Plot the map of a marteloscope

Description

Choose with what column you need to fill the tree points

Usage

martelosim_evol(data, y_col, fill_col, fill_scale, ...)

Arguments

data	data.frame with columns Year.
y_col	column to use for y axis of the plot. Col is because it's geom_area
fill_col	column on which to fill. Write as ggplot input in aes()
fill_scale	manual fill scale to be given as values in scale_fill_manual()
...	scales for action shape and color. color_scale and shape_scale values are set

---

Plot the map of a marteloscope

Description

Choose with what column you need to fill the tree points

Usage

martelosim_hist(data, x, y, fill, fill_scale, ...)

Arguments

data	data.frame with columns Year.
x	column to plot in x
y	column to plot in y
fill	column on which to fill. Write as ggplot input in aes()
fill_scale	manual fill scale to be given as values in scale_fill_manual()
...	scales for action shape and color. color_scale and shape_scale values are set

---

Plot the map of a marteloscope

Description

Choose with what column you need to fill the tree points

Usage

martelosim_map(
  data,
  fill_col,
  fill_scale,
  poly,
  label = FALSE,
  action = FALSE,
  limits = NULL,
  ...
)

Arguments

data	data.frame with columns X_m, Y_m, D_cm, Id. Two first are the position of trees, Id a label, D_cm the diameter.
fill_col	column on which to fill. Write as ggplot input in aes()
fill_scale	manual fill scale to be given as values in scale_fill_manual()
poly	polygon of the marteloscope. From inventory
label	TRUE FALSE add labels to trees
action	TRUE FALSE add action shape and color to plot.
limits	NULL by default. Recompute x and y scales
...	scales for action shape and color. color_scale and shape_scale values are set

---

Log some options for the project.

Description

Log some options for the project.

Usage

martelosim_options(
  capsis_exe_path,
  site,
  date,
  animateur,
  mail_animateur,
  lang = c("en", "fr"),
  verbose = TRUE
)

Arguments

capsis_exe_path	capsis executable path
site	Name of the marteloscope site
date	Date of the marteloscope exercise
animateur	Name of the site animateur
mail_animateur	Contact for the animateur
lang	Language, still in development
verbose	Print nice messages. TRUE by default

---

Plot the map of a marteloscope with pixels

Description

Choose with what column you need to fill the tree points

Usage

martelosim_pixelmap(
  data,
  treedata,
  fill_col,
  fill_scale,
  poly,
  action = FALSE,
  limits = NULL,
  ...
)

Arguments

data	data.frame with columns X_m, Y_m, Cell_Id. Intended for polygons plots
treedata	data.frame with X_m, Y_m, D_cm and Action columns Two first are the position of trees, Id a label, D_cm the diameter.
fill_col	column on which to fill. Write as ggplot input in aes()
fill_scale	manual fill scale to be given as values in scale_fill_manual()
poly	polygon of the marteloscope. From inventory
action	TRUE FALSE add action shape and color to plot.
limits	NULL by default. Recompute x and y scales
...	scales for action shape and color. color_scale and shape_scale values are set

---

Create a new inventory from previous marteloscope

Description

Create a new inventory from previous marteloscope

Usage

new_inventory(
  inv_site = c("new", "copy", "Prelenfrey", "Soteska", "Bouges", "Brauze_1", "Crocq",
    "LaChaume", "Brin", "Rindbach", "Nevegal", "Sailershausen1", "Schneidersrangen",
    "ColDePorte", "ColDeLEpine", "Krivoklat", "Collemeluccio", "Haugimont"),
  inv_file = NULL,
  lang = c("en", "fr"),
  open = TRUE,
  verbose = FALSE
)

Arguments

inv_site	name of the site. If the site exist, it will initiate xlsx file for the users. If not, it propose a new empty file (default).
inv_file	NULL by default. If copy, the file to copy in active directory
lang	language, default is "en" but "fr" can be selected. "fr" option is not fully developped.
open	boolean, allow to lauch excell or libre office if available
verbose	Allow to print messages. False by default.

Details

The file name is always Data_Marteloscope_<inv_site>.xlsx and is stored in data/

---

Prepare Samsara

Description

Write command file for launching samsara2 software and prepare plot

Usage

prepare_samsara(
  create_periphery = TRUE,
  create_virtual_saplings = TRUE,
  range_dbh = c(as.numeric(getOption("mart_recdbh")), 92.5),
  inv_year = as.numeric(getOption("mart_year")),
  inv_mindbh = as.numeric(getOption("mart_recdbh")),
  simulation_year_step = 1,
  memory_perc = 75,
  verbose = FALSE
)

Arguments

create_periphery	Creation of the periphery of the plot. TRUE by default. Must be TRUE for the first simulation, and FALSE later to speed up simulations
create_virtual_saplings	Creation of the saplings of the plot. TRUE by default. Must be TRUE for the first simulation, and FALSE later to speed up simulations
range_dbh	range of dbh for tree diameter classes.
inv_year	year of the inventory. Used to define the starting year of simulations. Value retrievedfrom inventory file.
inv_mindbh	inventory minimum dbh. Value retrieved from inventory file.
simulation_year_step	Simulation year step, value by default is 1.
memory_perc	Percentage of computer RAM affected to CAPSIS. default is 75%.
verbose	Print messages or not.

---

Write a random marking file

Description

Write a random marking file

Usage

random_marking(name = "Random", verbose = TRUE, open = FALSE)

Arguments

name	name of the marking. Default is "Random"
verbose	Print nice messages. TRUE by default
open	Open the file. FALSE by default

---

Run Samsara software

Description

Run Samsara software

Usage

run_samsara(
  commandFile = sprintf("%s_Martelo_CommandFile.txt", getOption("mart_site")),
  combineOutputs = TRUE,
  memory_perc = 75,
  verbose = TRUE
)

Arguments

commandFile	Default command file to use is the one with the site name.
combineOutputs	Not used yet, if needs to combine outputs
memory_perc	75 percentage of RAM is used by default if memory > 4Gb.
verbose	print logs in terminal or not. TRUE by default

---

Write command file for launching samsara2 software and prepare plot

Description

Write command file for launching samsara2 software and prepare plot

Usage

write_prep_samsara_cmd(
  create_periphery = TRUE,
  create_virtual_saplings = TRUE,
  range_dbh = c(as.numeric(getOption("mart_recdbh")), 92.5),
  inv_year = as.numeric(getOption("mart_year")),
  inv_mindbh = as.numeric(getOption("mart_recdbh")),
  simulation_year_step = 1,
  verbose = FALSE
)

Arguments

create_periphery	Creation of the periphery of the plot. TRUE by default. Must be TRUE for the first simulation, and FALSE later to speed up simulations
create_virtual_saplings	Creation of the saplings of the plot. TRUE by default. Must be TRUE for the first simulation, and FALSE later to speed up simulations
range_dbh	range of dbh for tree diameter classes.
inv_year	year of the inventory. Used to define the starting year of simulations. Value retrievedfrom inventory file.
inv_mindbh	inventory minimum dbh. Value retrieved from inventory file.
simulation_year_step	Simulation year step, value by default is 1.
verbose	Print messages or not.

---

Write command file for launching samsara2 software

Description

Write command file for launching samsara2 software

Usage

write_samsara_cmd(
  marking_groups,
  thinning_time,
  evolution_time,
  create_periphery = FALSE,
  create_virtual_saplings = FALSE,
  range_dbh = c(as.numeric(getOption("mart_recdbh")), 92.5),
  inv_year = as.numeric(getOption("mart_year")),
  inv_mindbh = as.numeric(getOption("mart_recdbh")),
  simulation_year_step = 1,
  silviculture = c("auto", "expert"),
  verbose = FALSE
)

Arguments

marking_groups	list of marking_groups to build the command file for. Under development so it use all marking_groups at this time
thinning_time	Time between management actions
evolution_time	Total duration of the simulation
create_periphery	Creation of the periphery of the plot. TRUE by default. Must be TRUE for the first simulation, and FALSE later to speed up simulations
create_virtual_saplings	Creation of the saplings of the plot. TRUE by default. Must be TRUE for the first simulation, and FALSE later to speed up simulations
range_dbh	range of dbh for tree diameter classes.
inv_year	year of the inventory. Used to define the starting year of simulations. Value retrievedfrom inventory file.
inv_mindbh	inventory minimum dbh. Value retrieved from inventory file.
simulation_year_step	Simulation year step, value by default is 1.
silviculture	Choice between "auto" and "expert", for building data/Silviculture file.
verbose	Print messages or not.

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