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Commit fd0c5449 authored by Nauta, Lisanne's avatar Nauta, Lisanne
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Removed rgdal dependency. Added renv lockfile to install all dependencies... 

Removed rgdal dependency. Added renv lockfile to install all dependencies required to run the model. Lockfile does not include packages required to run the plumber api. Updated Readme.
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.Rprofile 0 → 100644
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source("renv/activate.R")
Model scripts/plotter.R
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library(rgdal)
library(sp)
library(khroma)
......
README.md
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......@@ -18,8 +18,16 @@ git checkout mapping-tool
dependencies for model:
```R
install.packages("raster","sf","sp","rgdal","logger","dplyr","tictoc","parallel","khroma")
install.packages("raster","sf","sp","logger","dplyr","tictoc","parallel","khroma")
```
Note that the raster package is deprecated since October 2023, but can be installed in R 4.3.3 on Windows systems.
dependencies for pathogenflows:
```R
install.packages("jsonlite")
```
additional dependencies for api:
```R
install.packages("jsonlite","plumber","rnaturalearth","rnaturalearthdata")
......@@ -36,7 +44,7 @@ git submodule update
```
The git repository of the submodule is now cloned in the submodule directory. Now open the GloWPa.Rproj file R studio.
Install the folowing R packages from the R console: `devtools::install_local('./libs/pathogenflows')`
Install the Pathogenflows library from the source code: `install.packages('./libs/pathogenflows', repos = NULL, type = 'source')`
## Updating code in submodules
In case anything needs to be changed in the submodule code make sure you make changes in the repository of the submodule. So:
......
local_env.R
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# SET LOCAL SETTINGS
model_dir <- "/home/nauta/Data/Software/GloWPa/"
model_input_dir <- "/home/nauta/Data/Projects/2020/K2P/02_Experiment/02_Runs/Run0/Input/kla_online/"
model_output_dir <- "/home/nauta/Data/Projects/2020/K2P/02_Experiment/02_Runs/Run0/Output/"
model_dir <- "C:/Users/nauta008/Data/Software/glowpa_fix/glowpa-model"
model_input_dir <- "C:/Users/nauta008/Data/Data/glowpa/mapping_tool_fix"
model_output_dir <- "C:/Users/nauta008/Data/Data/glowpa/mapping_tool_fix/output"
csv_sep <- ";"
# ----
renv.lock 0 → 100644
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renv/.gitignore 0 → 100644
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library/
local/
cellar/
lock/
python/
sandbox/
staging/
renv/activate.R 0 → 100644
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renv/settings.json 0 → 100644
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