diff --git a/README.Rmd b/README.Rmd index 662528a..b83d4c9 100644 --- a/README.Rmd +++ b/README.Rmd @@ -28,11 +28,8 @@ library(SticsRFiles) [![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip) - [![R build status](https://github.com/SticsRPacks/SticsOnR/workflows/R-CMD-check/badge.svg)](https://github.com/SticsRPacks/SticsOnR/actions) - [![Codecov test coverage](https://codecov.io/gh/SticsRPacks/SticsOnR/branch/master/graph/badge.svg)](https://codecov.io/gh/SticsRPacks/SticsOnR?branch=master) - [![DOI](https://zenodo.org/badge/166790380.svg)](https://zenodo.org/badge/latestdoi/166790380) diff --git a/README.md b/README.md index ac24827..745e150 100644 --- a/README.md +++ b/README.md @@ -13,14 +13,10 @@ library(SticsRFiles) [![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip) - [![R build status](https://github.com/SticsRPacks/SticsOnR/workflows/R-CMD-check/badge.svg)](https://github.com/SticsRPacks/SticsOnR/actions) - [![Codecov test coverage](https://codecov.io/gh/SticsRPacks/SticsOnR/branch/master/graph/badge.svg)](https://codecov.io/gh/SticsRPacks/SticsOnR?branch=master) - - [![DOI](https://zenodo.org/badge/166790380.svg)](https://zenodo.org/badge/latestdoi/166790380) @@ -86,10 +82,10 @@ be installed. One can use either `devtools` or For `devtools`, installation requires system dependent tools. They must be installed first. - - For Windows + - For Windows RTools must be installed using the last installer from [here](https://cran.r-project.org/bin/windows/Rtools) - - For linux + - For linux Development tools must be installed first, like the `build-essentials` package for a Debian like distribution for example. @@ -184,7 +180,7 @@ function. # Specifying the JavaStics folder javastics_path <- "/path/to/JavaSTICS-1.41-stics-9.1" -# Specifying a workspace as a subfolder of JavaStics +# Specifying a workspace as a subfolder of JavaStics workspace_path <- "example" # or an absolute path to an external folder @@ -199,7 +195,7 @@ run_javastics(javastics_path, workspace_path, usms_list = c("banana","wheat")) #> [1] "wheat" #> v All usms ran successfully! -# Running all usms contained in the workspace +# Running all usms contained in the workspace run_javastics(javastics_path, workspace_path) #> v Using stics 'modulostics' (exe: 'stics_modulo.exe') #> [1] "SugarCane" @@ -251,21 +247,21 @@ runs_info #> [[1]] #> [[1]]$name #> [1] "banana" -#> +#> #> [[1]]$error #> [1] FALSE -#> +#> #> [[1]]$message #> [1] "0" -#> -#> +#> +#> #> [[2]] #> [[2]]$name #> [1] "wheat" -#> +#> #> [[2]]$error #> [1] FALSE -#> +#> #> [[2]]$message #> [1] "0" ``` @@ -325,53 +321,6 @@ run_stics(stics_path, output_path, usm_dir_names = c("banana","wheat")) # Running all the usms defined in the sub-directories of output_path run_stics(stics_path, output_path, usm_dir_names = "all") -#> Warning in system2(command = command, args = com_args, stderr = TRUE, stdout -#> = TRUE): l'exécution de la commande '"D:/Home/sbuis/Documents/WORK/STICS/ -#> JavaSTICS-1.41-stics-9.0/bin/stics_modulo" ' renvoie un statut 9 - -#> Warning in system2(command = command, args = com_args, stderr = TRUE, stdout -#> = TRUE): l'exécution de la commande '"D:/Home/sbuis/Documents/WORK/STICS/ -#> JavaSTICS-1.41-stics-9.0/bin/stics_modulo" ' renvoie un statut 9 - -#> Warning in system2(command = command, args = com_args, stderr = TRUE, stdout -#> = TRUE): l'exécution de la commande '"D:/Home/sbuis/Documents/WORK/STICS/ -#> JavaSTICS-1.41-stics-9.0/bin/stics_modulo" ' renvoie un statut 9 - -#> Warning in system2(command = command, args = com_args, stderr = TRUE, stdout -#> = TRUE): l'exécution de la commande '"D:/Home/sbuis/Documents/WORK/STICS/ -#> JavaSTICS-1.41-stics-9.0/bin/stics_modulo" ' renvoie un statut 9 - -#> Warning in system2(command = command, args = com_args, stderr = TRUE, stdout -#> = TRUE): l'exécution de la commande '"D:/Home/sbuis/Documents/WORK/STICS/ -#> JavaSTICS-1.41-stics-9.0/bin/stics_modulo" ' renvoie un statut 9 - -#> Warning in system2(command = command, args = com_args, stderr = TRUE, stdout -#> = TRUE): l'exécution de la commande '"D:/Home/sbuis/Documents/WORK/STICS/ -#> JavaSTICS-1.41-stics-9.0/bin/stics_modulo" ' renvoie un statut 9 - -#> Warning in system2(command = command, args = com_args, stderr = TRUE, stdout -#> = TRUE): l'exécution de la commande '"D:/Home/sbuis/Documents/WORK/STICS/ -#> JavaSTICS-1.41-stics-9.0/bin/stics_modulo" ' renvoie un statut 9 - -#> Warning in system2(command = command, args = com_args, stderr = TRUE, stdout -#> = TRUE): l'exécution de la commande '"D:/Home/sbuis/Documents/WORK/STICS/ -#> JavaSTICS-1.41-stics-9.0/bin/stics_modulo" ' renvoie un statut 9 - -#> Warning in system2(command = command, args = com_args, stderr = TRUE, stdout -#> = TRUE): l'exécution de la commande '"D:/Home/sbuis/Documents/WORK/STICS/ -#> JavaSTICS-1.41-stics-9.0/bin/stics_modulo" ' renvoie un statut 9 - -#> Warning in system2(command = command, args = com_args, stderr = TRUE, stdout -#> = TRUE): l'exécution de la commande '"D:/Home/sbuis/Documents/WORK/STICS/ -#> JavaSTICS-1.41-stics-9.0/bin/stics_modulo" ' renvoie un statut 9 - -#> Warning in system2(command = command, args = com_args, stderr = TRUE, stdout -#> = TRUE): l'exécution de la commande '"D:/Home/sbuis/Documents/WORK/STICS/ -#> JavaSTICS-1.41-stics-9.0/bin/stics_modulo" ' renvoie un statut 9 - -#> Warning in system2(command = command, args = com_args, stderr = TRUE, stdout -#> = TRUE): l'exécution de la commande '"D:/Home/sbuis/Documents/WORK/STICS/ -#> JavaSTICS-1.41-stics-9.0/bin/stics_modulo" ' renvoie un statut 9 # Getting returned information about stics runs runs_info <- run_stics(stics_path, output_path, usm_dir_names = c("banana","wheat")) @@ -380,24 +329,24 @@ runs_info #> [[1]] #> [[1]]$name #> [1] "banana" -#> +#> #> [[1]]$error #> [1] FALSE -#> +#> #> [[1]]$message -#> [1] " numcult = 1" +#> [1] " numcult = 1" #> [2] " The execution has been successfully accomplished." -#> -#> +#> +#> #> [[2]] #> [[2]]$name #> [1] "wheat" -#> +#> #> [[2]]$error #> [1] FALSE -#> +#> #> [[2]]$message -#> [1] " numcult = 1" +#> [1] " numcult = 1" #> [2] " The execution has been successfully accomplished." ``` @@ -430,22 +379,22 @@ A template is returned by the function when called with no arguments: stics_wrapper_options() #> $javastics_path #> [1] "unknown" -#> +#> #> $stics_exe #> [1] "unknown" -#> +#> #> $data_dir #> [1] "unknown" -#> +#> #> $parallel #> [1] FALSE -#> +#> #> $cores #> [1] NA -#> +#> #> $time_display #> [1] FALSE -#> +#> #> $verbose #> [1] TRUE ``` @@ -455,7 +404,7 @@ with JavaStics and the directory where individual usms input directories have been generated: ``` r -sim_options <- stics_wrapper_options(javastics_path = javastics_path, +sim_options <- stics_wrapper_options(javastics_path = javastics_path, data_dir = output_path, verbose = FALSE) ``` @@ -588,7 +537,7 @@ obs_list$wheat #> 19 258.38 plant_1 #> 20 258.45 plant_1 -sim_options <- stics_wrapper_options(javastics_path = javastics_path, +sim_options <- stics_wrapper_options(javastics_path = javastics_path, data_dir = output_path, verbose = TRUE) #> v Using stics: 'D:/OneDrive - cirad.fr/Travail_Postdoc/SticsRPacks/JavaSTICS-1.41-stics-9.1/bin/stics_modulo.exe' @@ -600,7 +549,7 @@ results <- stics_wrapper(model_options = sim_options, sit_var_dates_mask = obs_l head(results) #> $error #> [1] TRUE -#> +#> #> $sim_list #> $maize #> Date lai_n masec_n mafruit AZnit_1 AZnit_2 AZnit_3 QNplante @@ -639,51 +588,51 @@ head(results) #> 15 plant_1 #> 16 plant_1 #> 17 plant_1 -#> +#> #> $wheat -#> Date lai_n masec_n HR_1 HR_2 HR_3 resmes AZnit_1 AZnit_2 AZnit_3 -#> 1 1995-01-30 0.705 0.158 24.5 24.5 21.5 192 0.391 0.444 3.250 -#> 2 1995-02-03 0.777 0.227 24.5 24.5 21.5 192 0.408 0.378 2.670 -#> 3 1995-02-07 0.849 0.270 23.9 24.4 21.5 191 0.389 0.319 2.400 -#> 4 1995-02-16 1.080 0.496 24.5 24.5 21.5 192 0.521 0.297 1.540 -#> 5 1995-02-24 1.320 0.739 24.5 24.5 21.5 192 23.700 6.400 2.080 -#> 6 1995-03-06 1.880 1.340 24.3 24.4 21.5 192 8.800 4.830 1.640 -#> 7 1995-03-16 2.370 2.120 23.4 23.2 21.3 187 2.020 3.940 1.580 -#> 8 1995-03-23 2.570 2.640 22.1 23.8 21.4 186 75.900 2.940 1.900 -#> 9 1995-04-03 2.990 3.750 19.7 21.8 21.0 176 62.300 2.640 1.400 -#> 10 1995-04-11 3.250 5.120 14.7 20.2 20.4 161 47.100 2.500 1.100 -#> 11 1995-04-18 3.000 5.830 19.7 18.9 19.6 163 42.500 2.440 0.901 -#> 12 1995-04-26 2.470 6.660 24.5 24.5 21.3 191 18.800 11.500 2.790 -#> 13 1995-05-02 2.060 7.430 21.7 23.8 21.4 185 84.400 14.900 3.320 -#> 14 1995-05-05 1.920 8.260 18.3 23.0 21.2 177 75.600 13.000 3.110 -#> 15 1995-05-09 1.680 9.240 14.9 21.9 20.8 166 67.300 11.100 2.840 -#> 16 1995-05-12 1.450 9.630 24.5 24.5 21.5 192 38.500 25.700 11.300 -#> 17 1995-05-15 1.360 9.970 22.4 24.1 21.4 187 29.100 26.500 14.700 -#> 18 1995-05-19 1.130 10.500 22.9 23.9 21.4 188 18.700 25.800 18.900 -#> 19 1995-05-29 0.512 11.700 18.5 22.7 21.1 176 9.880 21.500 17.700 -#> 20 1995-07-17 0.000 11.700 21.8 24.3 21.5 187 11.700 19.500 30.200 -#> QNplante Plant -#> 1 5.61 plant_1 -#> 2 6.26 plant_1 -#> 3 6.91 plant_1 -#> 4 8.65 plant_1 -#> 5 15.20 plant_1 -#> 6 33.60 plant_1 -#> 7 43.10 plant_1 -#> 8 46.70 plant_1 -#> 9 63.50 plant_1 -#> 10 80.80 plant_1 -#> 11 87.10 plant_1 -#> 12 102.00 plant_1 -#> 13 117.00 plant_1 -#> 14 129.00 plant_1 -#> 15 141.00 plant_1 -#> 16 148.00 plant_1 -#> 17 154.00 plant_1 -#> 18 162.00 plant_1 -#> 19 180.00 plant_1 -#> 20 182.00 plant_1 -#> +#> Date lai_n masec_n HR_1 HR_2 HR_3 resmes AZnit_1 +#> 1 1995-01-30 0.31003 0.09153 24.50000 24.50000 21.49999 192.3000 0.41713 +#> 2 1995-02-03 0.31242 0.11221 24.50000 24.50000 21.49999 192.3000 0.42380 +#> 3 1995-02-07 0.31354 0.12467 23.84483 24.37532 21.49294 190.8271 0.41926 +#> 4 1995-02-16 0.32451 0.18564 24.50000 24.50000 21.49999 192.3000 0.56208 +#> 5 1995-02-24 0.35891 0.24260 24.50000 24.50000 21.49999 192.3000 26.41268 +#> 6 1995-03-06 0.44264 0.34755 24.14648 24.38064 21.49236 191.3786 20.30915 +#> 7 1995-03-16 0.65818 0.52581 22.89588 23.60845 21.41254 187.1468 10.44319 +#> 8 1995-03-23 0.92638 0.71555 21.59650 24.01906 21.45064 185.8416 83.97830 +#> 9 1995-04-03 1.52201 1.52236 19.84414 22.49030 21.22817 178.4759 67.59111 +#> 10 1995-04-11 2.07250 2.53152 15.95694 21.11659 20.85113 166.8974 55.87930 +#> 11 1995-04-18 2.29059 3.10799 20.66066 19.72960 20.35101 170.2009 51.30755 +#> 12 1995-04-26 3.07941 3.93828 24.50000 24.50000 21.49999 192.3000 21.52207 +#> 13 1995-05-02 3.94086 4.88480 22.22058 23.73749 21.37783 186.0460 84.98852 +#> 14 1995-05-05 4.52523 5.91712 18.70683 22.44921 21.10305 175.7793 75.39217 +#> 15 1995-05-09 4.72279 7.23955 14.63764 20.44039 20.41699 161.1490 64.17078 +#> 16 1995-05-12 4.67417 7.84193 24.50000 24.50000 21.49999 192.3000 33.96954 +#> 17 1995-05-15 4.62342 8.42934 22.93225 23.99567 21.40491 187.9911 23.10137 +#> 18 1995-05-19 4.46845 9.30616 23.36981 23.80873 21.37116 188.2342 12.41579 +#> 19 1995-05-29 3.88449 11.50751 19.07685 20.87937 20.71562 171.4053 5.17826 +#> 20 1995-07-17 0.00000 16.69752 21.79237 24.26819 21.48919 186.8908 8.98478 +#> AZnit_2 AZnit_3 QNplante Plant +#> 1 0.41585 3.28942 5.03274 plant_1 +#> 2 0.33597 2.67066 5.75932 plant_1 +#> 3 0.26660 2.37828 6.46400 plant_1 +#> 4 0.25005 1.48598 8.32339 plant_1 +#> 5 6.94052 2.16342 11.53375 plant_1 +#> 6 7.23958 2.09553 18.91107 plant_1 +#> 7 6.40922 2.43523 31.03929 plant_1 +#> 8 5.19814 3.35878 39.28777 plant_1 +#> 9 3.25693 2.44714 60.99855 plant_1 +#> 10 2.77037 1.89108 75.65481 plant_1 +#> 11 2.51856 1.50726 82.47911 plant_1 +#> 12 13.37259 4.31289 101.03638 plant_1 +#> 13 16.14248 4.74810 120.17694 plant_1 +#> 14 13.88273 4.42838 133.52654 plant_1 +#> 15 11.35942 4.01791 149.24533 plant_1 +#> 16 24.80969 11.06544 160.28954 plant_1 +#> 17 24.04470 14.10819 169.77567 plant_1 +#> 18 21.51919 18.25439 179.93832 plant_1 +#> 19 16.92093 17.07984 196.65919 plant_1 +#> 20 14.76355 20.99991 212.83035 plant_1 +#> #> attr(,"class") #> [1] "cropr_simulation" ``` @@ -756,14 +705,14 @@ successions usm1.1-\>usm1.2 and usm2.1-\>usm2.2). ``` r -sim_options <- stics_wrapper_options(javastics_path = javastics_path, +sim_options <- stics_wrapper_options(javastics_path = javastics_path, data_dir = output_path, time_display = TRUE, verbose = FALSE) results <- stics_wrapper(model_options = sim_options) #> Warning in e$fun(obj, substitute(ex), parent.frame(), e$data): already exporting #> variable(s): force_param_values -#> Time difference of 26.52565 secs +#> Time difference of 25.78408 secs ``` - Activating parallel execution @@ -771,7 +720,7 @@ results <- stics_wrapper(model_options = sim_options) On may specify the number of cores to use with the cores argument. ``` r -sim_options <- stics_wrapper_options(javastics_path = javastics_path, +sim_options <- stics_wrapper_options(javastics_path = javastics_path, data_dir = output_path, parallel =TRUE, time_display = TRUE, cores = 2, verbose = FALSE) @@ -779,7 +728,7 @@ sim_options <- stics_wrapper_options(javastics_path = javastics_path, results <- stics_wrapper(model_options = sim_options) #> Warning in e$fun(obj, substitute(ex), parent.frame(), e$data): already exporting #> variable(s): force_param_values -#> Time difference of 15.16197 secs +#> Time difference of 16.0054 secs ``` If cores is not given, parallel execution is performed over machine @@ -790,16 +739,16 @@ library(parallel) # Used cores number detectCores() - 1 -#> [1] 3 +#> [1] 11 -sim_options <- stics_wrapper_options(javastics_path = javastics_path, +sim_options <- stics_wrapper_options(javastics_path = javastics_path, data_dir = output_path, parallel =TRUE, time_display = TRUE, verbose = FALSE) results <- stics_wrapper(model_options = sim_options) #> Warning in e$fun(obj, substitute(ex), parent.frame(), e$data): already exporting #> variable(s): force_param_values -#> Time difference of 9.150996 secs +#> Time difference of 7.891811 secs ``` ## Citation