Merge pull request #54 from sylvainschmitt/main

0.1.1

.Rbuildignore

@@ -23,3 +23,5 @@ inst/figures/lidr_fig.R
 inst/gsl
 LICENSE.md
 .covrignore
+.vscode
+.lintr

.github/workflows/R-CMD-check.yaml

@@ -29,7 +29,6 @@ jobs:
       matrix:
         config:
           - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: '3.6'}
           - {os: macos-latest,   r: 'release'}
 
     env:

.github/workflows/lint.yaml

@@ -0,0 +1,32 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.gitignore

@@ -18,3 +18,4 @@ config.status
 simulations
 supplementary.html
 inst/gsl
+*.las

.lintr

@@ -0,0 +1,2 @@
+linters: linters_with_defaults() # see vignette("lintr")
+encoding: "UTF-8"

.vscode/.env

@@ -0,0 +1,24 @@
+LD_LIBRARY_PATH=/usr/lib/R/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/default-java/lib/server
+R_ARCH=
+R_BROWSER=xdg-open
+R_BZIPCMD=/bin/bzip2
+R_DOC_DIR=/usr/share/R/doc
+R_GZIPCMD=/bin/gzip -n
+R_HOME=/usr/lib/R
+R_INCLUDE_DIR=/usr/share/R/include
+R_LIBS_SITE=/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library
+R_LIBS_USER=~/R/x86_64-pc-linux-gnu-library/4.1
+R_PAPERSIZE=letter
+R_PAPERSIZE_USER=a4
+R_PDFVIEWER=/usr/bin/xdg-open
+R_PLATFORM=x86_64-pc-linux-gnu
+R_PRINTCMD=/usr/bin/lpr
+R_RD4PDF=times,inconsolata,hyper
+R_SESSION_TMPDIR=/tmp/RtmpKdLxpi
+R_SHARE_DIR=/usr/share/R/share
+R_STRIP_SHARED_LIB=strip --strip-unneeded
+R_STRIP_STATIC_LIB=strip --strip-debug
+R_SYSTEM_ABI=linux,gcc,gxx,gfortran,gfortran
+R_TEXI2DVICMD=/usr/bin/texi2dvi
+R_UNZIPCMD=/usr/bin/unzip
+R_ZIPCMD=/usr/bin/zip

.vscode/c_cpp_properties.json

@@ -0,0 +1,17 @@
+{
+    "configurations": [
+        {
+            "name": "Linux",
+            "includePath": [
+                "${workspaceFolder}/**",
+                "${env:HOME}/R/x86_64-pc-linux-gnu-library/4.1/Rcpp/include",
+                "/usr/share/R/include"
+            ],
+            "defines": [],
+            "compilerPath": "/usr/bin/gcc",
+            "cStandard": "c11",
+            "cppStandard": "c++17"
+        }
+    ],
+    "version": 4
+}

.vscode/debug.R

@@ -0,0 +1,9 @@
+env <- Sys.getenv()
+envnames <- names(env)
+rnames <- envnames[startsWith(envnames, "R_")]
+cached_names <- rnames
+ld_lib_path <- Sys.getenv("LD_LIBRARY_PATH")
+if (ld_lib_path != "") {
+  cached_names <- c("LD_LIBRARY_PATH", rnames)
+}
+writeLines(paste0(cached_names, "=", env[cached_names]), ".vscode/.env")

.vscode/launch.json

@@ -0,0 +1,32 @@
+{
+    // Use IntelliSense to learn about possible attributes.
+    // Hover to view descriptions of existing attributes.
+    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+    "version": "0.2.0",
+    "configurations": [
+      {
+        "name": "(gdb) Launch",
+        "type": "cppdbg",
+        "request": "launch",
+        "program": "/usr/lib/R/bin/exec/R",
+        "args": [
+          "--vanilla",
+          "-e",
+          "devtools::test(filter = 'cpp')"
+        ],
+        "stopAtEntry": false,
+        "envFile": "${workspaceFolder}/.vscode/.env",
+        "cwd": "${workspaceFolder}",
+        "externalConsole": false,
+        "MIMode": "gdb",
+        "setupCommands": [
+          {
+            "description": "Enable pretty-printing for gdb",
+            "text": "-enable-pretty-printing",
+            "ignoreFailures": true
+          }
+        ],
+        "preLaunchTask": "debug"
+      }
+    ]
+  }

.vscode/tasks.json

@@ -0,0 +1,14 @@
+{
+    // See https://go.microsoft.com/fwlink/?LinkId=733558
+    // for the documentation about the tasks.json format
+    "version": "2.0.0",
+    "tasks": [
+      {
+        "label": "debug",
+        "type": "shell",
+        "command": "Rscript ${workspaceFolder}/.vscode/debug.R",
+        "problemMatcher": []
+      }
+    ]
+  }
+

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rcontroll
 Type: Package
 Title: Individual-Based Forest Growth Simulator 'TROLL'
-Version: 0.1.0
+Version: 0.1.1
 Authors@R: c(
     person("Sylvain", "Schmitt", email="[email protected]", role=c("aut", "cre"), comment = c(ORCID = "0000-0001-7759-7106")),
     person("Guillaume", "Salzet", email="[email protected]", role="aut", comment = c(ORCID = "0000-0003-4548-5673")),
@@ -52,6 +52,7 @@ Suggests:
     rmarkdown,
     testthat,
     covr
+Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Collate: 
     'RcppExports.R'
@@ -75,12 +76,13 @@ Collate:
     'generate_lidar.R'
     'generate_parameters.R'
     'get_forest.trollsim.R'
+    'get_log.trollsim.R'
     'load_stack.R'
+    'load_sim.trollsim.R'
     'print.trollsim.R'
     'rcontroll-package.R'
     'rcontroll.R'
     'stack.R'
-    'summary.trollsim.R'
     'update_parameters.trollsim.R'
 VignetteBuilder: knitr
 Depends: 

NAMESPACE

@@ -8,7 +8,9 @@ export(generate_lidar)
 export(generate_parameters)
 export(get_chm)
 export(get_forest)
+export(get_log)
 export(load_output)
+export(load_sim)
 export(load_stack)
 export(stack)
 export(troll)
@@ -21,6 +23,8 @@ exportClasses(trollstack)
 exportMethods(autoplot)
 exportMethods(get_chm)
 exportMethods(get_forest)
+exportMethods(get_log)
+exportMethods(load_sim)
 exportMethods(print)
 exportMethods(show)
 exportMethods(summary)

NEWS.md

@@ -1,3 +1,31 @@
+# rcontroll 0.1.0.9004
+
+- merging and cleaning before CRAN fix
+
+# rcontroll 0.1.0.9003
+
+- TROLL version 3.1.8 following discussion with IM, updating treefall time normalisation and carbon starvation to match TROLL4, a clean merge with main and dev will be needed
+
+# rcontroll 0.1.1.9002
+
+- lidr fig
+
+# rcontroll 0.1.1.9001
+
+- extended documentation following review
+
+# rcontroll 0.1.0.9065
+
+- new stack in tmp fix & TROLLV3_output update
+
+# rcontroll 0.1.0.9064
+
+- improving memory usage
+
+# rcontroll 0.1.0.9063
+
+- fixed stack with batch foreach 
+
 # rcontroll 0.1.0.9062
 
 - fixes after CRAN 3rd submission (see cran-comments.md)

R/TROLLv3_climatedaytime12.R

@@ -1,18 +1,25 @@
-#' TROLL climate parameters over months
+#' `TROLL` climate parameters over months
 #'
-#' Climate parameters used by TROLL model over months.
+#' Climate parameters used by `TROLL` model over months.
 #'
 #' @format A data frame with 12 rows and 12 variables: \describe{
-#'   \item{Temperature}{temperature (degree C)}
-#'   \item{DaytimeMeanTemperature}{mean day temperature (degree C)}
-#'   \item{NightTemperature}{night temperature (degree C)}
-#'   \item{Rainfall}{rainfall (mm)} \item{WindSpeed}{wind speed (km/h)}
-#'   \item{DaytimeMeanIrradiance}{daytime mean irradiance}
-#'   \item{MeanIrradiance}{mean irradiance}
-#'   \item{SaturatedVapourPressure}{saturated vapour pressure (Pa)}
-#'   \item{VapourPressure}{vapour pressure (Pa)}
-#'   \item{VaporPressureDeficit}{vapour pressure deficit (VPD, Pa)}
-#'   \item{DayTimeVapourPressureDeficitVPDbasic}{daytime basic VPD (Pa)}
-#'   \item{DaytimeMeanVapourPressureDeficit}{daytime mean VPF (Pa)} }
+#'   \item{Temperature}{monthly average of temperature (degree C)}
+#'   \item{DaytimeMeanTemperature}{the monthly average of daytime temperature
+#'   (degree C, 7am-7pm)} \item{NightTemperature}{the monthly average of
+#'   temperature at night  (degree C, 8pm-6am)} \item{Rainfall}{monthly average
+#'   of cumulative rainfall (cm)} \item{WindSpeed}{monthly average of wind speed
+#'   (m/s)} \item{DaytimeMeanIrradiance}{monthly average of cumulative solar
+#'   irradiance averaged over one day (W/m2, 7am-7pm)}
+#'   \item{MeanIrradiance}{monthly average of cumulative solar irradiance over
+#'   24 hours (W/m2)} \item{SaturatedVapourPressure}{monthly average of
+#'   saturation vapour pressure (hPa)} \item{VapourPressure}{monthly average of
+#'   vapour pressur (hPa)} \item{VaporPressureDeficit}{monthly average of vapour
+#'   pressure deficit (VPD, hPa)}
+#'   \item{DayTimeVapourPressureDeficitVPDbasic}{monthly average of daytime
+#'   vapour pressure deficit (7am-7pm) according to basic formula (hPa)}
+#'   \item{DaytimeMeanVapourPressureDeficit}{monthly average of daytime vapour
+#'   pressure deficit (7am-7pm) according to advanced formula (hPa)} }
+#'
+#' @seealso [generate_climate()], [TROLLv3_daytimevar]
 #'
 "TROLLv3_climatedaytime12"

R/TROLLv3_daytimevar.R

@@ -1,11 +1,14 @@
-#' TROLL daytime variation parameters
+#' `TROLL` daytime variation parameters
 #'
-#' Daytime variation parameters used by TROLL models.
+#' Daytime variation parameters used by `TROLL`s models.
 #'
 #' @format A data frame with 24 rows and 5 variables: \describe{
 #'   \item{starttime}{starting time} \item{endtime}{ending time}
-#'   \item{vardaytime_light}{daytime variation in light}
-#'   \item{vardaytime_vpd}{daytime variation in vapour pressure deficit}
-#'   \item{vardaytime_T}{daytime variation in temperature}}
+#'   \item{vardaytime_light}{daily variation in irradiance relative to the mean
+#'   value of the day} \item{vardaytime_vpd}{daily variation in vapour pressure
+#'   deficit relative to the mean value of the day} \item{vardaytime_T}{daily
+#'   variation in temperature relative to the mean value of the day}}
+#'
+#' @seealso [generate_climate()], [TROLLv3_climatedaytime12]
 #'
 "TROLLv3_daytimevar"

R/TROLLv3_input.R

@@ -1,12 +1,14 @@
-#' TROLL global parameters
+#' `TROLL` global parameters
 #'
-#' Global parameters definition used by TROLL model.
+#' Global parameters definition used by `TROLL` model.
 #'
 #' @format A data frame with 61 rows and 3 variables: \describe{
 #'   \item{param}{global parameter} \item{value}{value of the parameter}
 #'   \item{description}{description of the parameter} }
 #'
+#' @seealso [generate_parameters()]
+#'
 "TROLLv3_input"
 
-# TROLLv3_input <- readr::read_tsv("inst/extdata/TROLLv3_input.txt")
-# usethis::use_data(TROLLv3_input, overwrite = T)
+# TROLLv3_input <- readr::read_tsv("inst/extdata/TROLLv3_input.txt") # nolint
+# usethis::use_data(TROLLv3_input, overwrite = T) # nolint

R/TROLLv3_output.R

@@ -1,19 +1,23 @@
-#' TROLL output
+#' `TROLL` output
 #'
-#' TROLL outputs from a 100-year simulation on a 100x100 grid with the other
+#' `TROLL` outputs from a 100-year simulation on a 100x100 grid with the other
 #' default parameters and using TROLLv3_species, TROLLv3_climatedaytime12, and
 #' TROLLv3_daytimevar for use in tests and examples. Ecosystem level output has
 #' been thinned and species output has been removed to save disk space.
 #'
-#' @format A trollsim object.
+#' @format A [trollsim()] object.
+#'
+#' @seealso [TROLLv3_species()], [TROLLv3_climatedaytime12()],
+#'   [TROLLv3_daytimevar()], [troll()]
 #'
 "TROLLv3_output"
 
+# nolint start
 # data("TROLLv3_species")
 # data("TROLLv3_climatedaytime12")
 # data("TROLLv3_daytimevar")
 # TROLLv3_output <- troll(name = "test",
-#                         path = "/home/sylvain/Documents/ECOFOG/",
+#                         path = "/home/sschmitt/Documents/",
 #                         global = generate_parameters(
 #                           rows = 100,
 #                           cols = 100,
@@ -30,3 +34,4 @@
 # forest <- TROLLv3_output@forest
 # autoplot(TROLLv3_output, "temporal")
 # usethis::use_data(TROLLv3_output, overwrite = T)
+# nolint end

R/TROLLv3_pointcloud.R

@@ -1,12 +1,14 @@
-#' TROLL lidar parameters
+#' `TROLL` lidar parameters
 #'
-#' Lidar parameters definition used by TROLL model for lidar simulations.
+#' Lidar parameters definition used by `TROLL` for lidar simulations.
 #'
 #' @format A data frame with 5 rows and 3 variables: \describe{
-#'   \item{param}{global parameter} \item{value}{value of the parameter}
+#'   \item{param}{lidar parameter} \item{value}{value of the parameter}
 #'   \item{description}{description of the parameter} }
 #'
+#' @seealso [generate_lidar()]
+#'
 "TROLLv3_pointcloud"
 
-# TROLLv3_pointcloud <- readr::read_tsv("inst/extdata/TROLLv3_pointcloud.txt")
-# usethis::use_data(TROLLv3_pointcloud, overwrite = T)
+# TROLLv3_pointcloud <- readr::read_tsv("inst/extdata/TROLLv3_pointcloud.txt") # nolint
+# usethis::use_data(TROLLv3_pointcloud, overwrite = T) # nolint

R/TROLLv3_species.R

@@ -1,6 +1,6 @@
-#' TROLL species parameters
+#' `TROLL` species parameters
 #'
-#' Functional traits used by TROLL model for 45 species in French Guiana.
+#' Functional traits used by `TROLL` model for 45 species in French Guiana.
 #'
 #' @format A data frame with 45 rows and 12 variables: \describe{
 #'   \item{s_name}{Species name genus_species} \item{s_LMA}{leaf mass per area}
@@ -10,4 +10,6 @@
 #'   coefficient} \item{s_regionalfreq}{regional frequency} \item{s_tlp}{Turgor
 #'   loss point} \item{s_drymass}{leaf dry mass} \item{s_seedmass}{seed mass} }
 #'
+#' @seealso [troll()], [stack()]
+#'
 "TROLLv3_species"