traits4models

.github/CONTRIBUTING.md

@@ -7,7 +7,7 @@ R package **medfate** and its associated R packages should be viewed as an ongoi
 Contributions to the development of **medfate** can be done in different aspects:
 
  1. **Model design and formulation**: If your expertise includes any of the processes that are modelled in the package and you feel that your expertise could be helpful to improve the package, you are more than welcome to contact us! If you are familiarized with Git, GitHub and R package development, you can fork the package, make changes and then a pull request (see below). Otherwise, other forms of collaboration can be established. While contributions are welcome, we do not want to have multiple, diverging, versions of the simulation models. Hence, we want to centralize and review modifications, so that former package functionality is not lost.
- 2. **Model parameterization**: Finding suitable parameter values for trait-based models is hard, and requires gathering data from multiple databases. Efforts to find species parameter values required for **medfate** can be made available to others by including new species parameter tables, such as `SpParamsMED`. We are currently developing on a companion package called [**medfatetraits**](https://github.com/emf-creaf/medfatetraits/) that should be helpful to define and populate new species parameter tables.
+ 2. **Model parameterization**: Finding suitable parameter values for trait-based models is hard, and requires gathering data from multiple databases. Efforts to find species parameter values required for **medfate** can be made available to others by including new species parameter tables, such as `SpParamsMED`. We are currently developing on a companion package called [**traits4models**](https://github.com/emf-creaf/traits4models/) that should be helpful to define and populate new species parameter tables.
  3. **Model evaluation**: Simulation models should be tested extensively, and there is a lot to be done in this respect in the case of **medfate**. Hence, we will appreciate help in this area, for example pointing at interesting validation data sets. They should lead to new package vignettes showing the performance of the model in different situations.
 
 ## Reporting bugs and suggesting enchancements

R/dataset_documentation.R

@@ -42,7 +42,7 @@ NULL
 #' }
 #' @details
 #' \code{SpParamsMED} was the official species parameter for package versions up to v.4.0.0, but will not be maintained in the future. Additional 
-#' species parameter tables for different countries are distributed via package \code{medfatetraits}, available from GitHub (https://emf-creaf.github.io/medfatetraits/).
+#' species parameter tables for different countries are distributed via package \code{traits4models}, available from GitHub (https://emf-creaf.github.io/traits4models/).
 #' 
 #' @examples
 #' data(SpParamsDefinition)

README.Rmd

@@ -47,7 +47,7 @@ During the development of **medfate** some functions have been originally placed
 
  + Package [**medfateland**](https://emf-creaf.github.io/medfateland) extends **medfate** by allowing simulations to be performed in a spatially explicit context.
  + Package [**meteoland**](https://emf-creaf.github.io/meteoland) allows generating daily weather input for simulation models in **medfate** and **medfateland**.
- + Package [**medfatetraits**](https://emf-creaf.github.io/medfatetraits) provides functions to help creating species parameter inputs for **medfate** and **medfateland** simulation functions [*under development*].
+ + Package [**traits4models**](https://emf-creaf.github.io/traits4models) provides functions to help creating species parameter inputs for **medfate** and **medfateland** simulation functions [*under development*].
 
 ```{r, out.width='60%', fig.align="center", echo=FALSE}
 knitr::include_graphics("man/figures/packages.png")

README.md

@@ -62,7 +62,7 @@ which evolve together with **medfate**:
 - Package [**meteoland**](https://emf-creaf.github.io/meteoland) allows
  generating daily weather input for simulation models in **medfate**
  and **medfateland**.
-- Package [**medfatetraits**](https://emf-creaf.github.io/medfatetraits)
+- Package [**traits4models**](https://emf-creaf.github.io/traits4models)
  provides functions to help creating species parameter inputs for
  **medfate** and **medfateland** simulation functions \[*under
  development*\].

data-raw/ReloadParameters.R

@@ -54,7 +54,7 @@ SpParamsMED = medfate::modifySpParams(SpParamsMED, resproutingParamsSpecies, sub
 # Add bark thickness parameters
 bt_models <- openxlsx::read.xlsx(paste0(MFWdir,"MedfateSpeciesParametrization/AllometryDatabases/TreeAllometries/TreeAllometries.xlsx"), 
  sheet= "Tree_BT_models", rowNames = TRUE)
-SpParamsMED <- medfatetraits::populate_tree_allometries(SpParamsMED, bt_models, "barkthickness")
+SpParamsMED <- traits4models::populate_tree_allometries(SpParamsMED, bt_models, "barkthickness")
 
 # Manual tuning
 tree_all_cols = 30:42

vignettes/intro/PackageOverview.Rmd

@@ -111,6 +111,6 @@ During the development of **medfate** some functions have been originally placed
 
  + Package [**meteoland**](https://emf-creaf.github.io/meteoland) allows generating daily weather input for simulation models in **medfate**.
  + Package [**medfateland**](https://emf-creaf.github.io/medfateland) extends **medfate** by allowing simulations to be performed in a spatially explicit context.
- + Package [**medfatetraits**](https://emf-creaf.github.io/medfatetraits) provides functions to help creating species parameter inputs for **medfate** and **medfateland** simulation functions [*under development*].
+ + Package [**traits4models**](https://emf-creaf.github.io/traits4models) provides functions to help creating species parameter inputs for **medfate** and **medfateland** simulation functions [*under development*].
 
 The set of R packages are developed and maintained by the [*Ecosystem Modelling Facility*](https://emf.creaf.cat) at CREAF (Spain).

vignettes/intro/UnderstandingInputs.Rmd

@@ -35,7 +35,7 @@ data("SpParamsDefinition")
 knitr::kable(SpParamsDefinition[,-2])
 ```
 
-In order to understand the role of parameters in the model, you should read the details of model design and formulation included in the [**medfatebook**](https://emf-creaf.github.io/medfatebook/index.html). Details regarding how the species parameter tables are build can be found in [**medfatetraits**](https://emf-creaf.github.io/medfatetraits/index.html). 
+In order to understand the role of parameters in the model, you should read the details of model design and formulation included in the [**medfatebook**](https://emf-creaf.github.io/medfatebook/index.html). Details regarding how the species parameter tables are build can be found in [**traits4models**](https://emf-creaf.github.io/traits4models/index.html). 
 
 ## Vegetation