Merge branch 'Documentation'

RBBGCMuso/R/musoRand.R

@@ -1,10 +1,10 @@
 #' musoRand
 #'
-#' This funtion samples uniformly from the choosen parameters of the BiomeBGC-Muso model, which parameters are constrained by the model logic.
+#' This funtion samples uniformly from the chosen parameters of the Biome-BGCMuSo model, where the parameters are constrained by the model logic.
 #' @author Roland Hollos
-#' @param parameters This is a dataframe (heterogen data-matrix), which first column is the name of the parameters, the second is a numeric vector of the rownumbers of the given variable in the input-file, the last two column consist the endpont of the parameter-ranges, where the parameters will be randomized.
+#' @param parameters This is a dataframe (heterogeneous data-matrix), where first column is the name of the parameters, the second is a numeric vector of the rownumbers of the given variable in the input-file, the last two column consist the endpont of the parameter-ranges, where the parameters will be randomized.
 #' @param constrains This is a matrics wich specify the constrain rules for the sampling. Further informations coming son.
-#' @param iteration The number of sample-s. It is adviced to use at least 3000 iteration, because it is generally fast and it can be subsampled later at any time.
+#' @param iteration The number of samples. We propose to use at least 3000 iteration, because it is generally fast and it can be subsampled later at any time.
 #' @importFrom limSolve xsample
 #' @export
 

RBBGCMuso/R/quickeffect.R

@@ -1,13 +1,13 @@
 #' musoQuickEffect
 #'
-#' This function changes a choosen parameter, and visualize the effect of the change on a chosen variable.
+#' This function changes a chosen parameter from the INI or from the ecophysiological constants file (EPC) within a predefined range (defined by the user), and visualizes the effect of the change on the selected output variable. The user has to specify the parameter, the interval for the parameter effect test, and the number of steps. This function focuses only on one parameter. The so-called paramSweep function can manipulate multiple INI/EPC parameters and visualize the results. 
-#' @author Roland Hollos
+#' @author Roland HOLLOS
-#' @param settings The settings from setupMuso output
+#' @param settings RBBGCMuso uses variables that define the entire simulation environment. Those environment variables include the name of the INI files, the name of the meteorology files, the path to the model executable and its file name, the entire output list, the entire output variable matrix, the dependency rules for the EPC parameters etc. Using the runMuso function RBBGCMuso can automatically create those environment variables by inspecting the files in the working directory (this happens through the setupMuso function). It means that by default model setup is performed automatically in the background and the user has nothing to do. With this settings parameter we can force runMuso to skip automatic environment setup as we provide the environment settings to runMuso. In a typical situation the user can skip this option.
-#' @param startVal The oroginal parameterValue
+#' @param startVal The initial value of the given parameter. 
-#' @param endVal The goal value while the function pass 
+#' @param endVal The maximum of the given parameter. 
-#' @param nSteps How many steps 'till you reach the endVal
+#' @param nSteps Number of steps from startVal to endVal. It equals the number of simulations, and number of curves on the final plot. 
-#' @param fileTochange Please choose "epc" "ini" or "both". This is the place of the orininal variable.
+#' @param fileTochange Please choose "EPC", "INI" or "BOTH". This file will be used for the analysis, and the original parameter values will be changed according to the choice of the user. 
-#' @return An effect plot
+#' @return Graph showing the runs with the selected parameters with color coding. The graph will show data from the last simulation year. 
 #' @importFrom ggplot2 ggplot aes_string geom_line geom_point aes labs theme ggsave element_blank facet_wrap
 #' @importFrom dplyr filter group_by summarize mutate '%>%' tbl_df select
 #' @importFrom tibble rownames_to_column

README.org

@@ -169,6 +169,8 @@ In advanced mode there is possibility to select the parameters.csv file using th
 Advanced sensitivity analysis is possible with the musoSensi function of RBBGCMuso. [[http://agromo.agrar.mta.hu/files/musoSensi_usage_v6_FINAL.pdf][See this link to read the manual of the sensitivity analysis.]]
 Note that parameters.csv is provided in the hhs example dataset, so you don't have to create it manually. 
 
+*IMPORTANT NOTE: If the result file contains only NAs it means that none of the parameters affected the output variable of interest. In this case you need to adjust the output parameter selection or the EPC parameter list. A simple example for this is soil temperature which is not affected by some of the plant parameters. [[https://github.com/hollorol/RBBGCMuso/issues/3][See this link for further details.]]
+
 *** Contact
 
 E-mail: hollorol@gmail.com