update IGBP006 parameter

R/PML.R

@@ -2,7 +2,7 @@
 #' surface for each time step (16-day).
 #'
 #' This algorithm fits to high resolution data data in GEE.
-#' 
+#'
 #' @param data A data.frame with the columns of
 #' - `Prcp`   : Precipitation, mm
 #' - `Tavg`   : daily average temperature, deg C
@@ -30,7 +30,7 @@
 #' - `rou_a`   :
 #' - `gama`    :
 #' - `epsilon` :
-#' 
+#'
 #' @param par PML_V2 parameters (see Zhang 2019 for details).
 #' - `hc`      : canopy height (m)
 #' - `Alpha`   : initial photochemical efficiency, 0.02-0.08
@@ -49,7 +49,7 @@
 #' @param ratio land cover ratio
 #' @param return.Es Because `fval_soil` need moving average in temporal. We can't
 #' get it directly if the `data` is Spatial pixels.
-#' @param IGBPname IGBPname
+#' @param IGBPcode IGBP006 code
 #' @param scale one of c("site", "regional").
 #' @param ... ignored
 #' 
@@ -74,8 +74,8 @@
 #'
 #' @export
 PML <- function(
-  data, par = NULL, CO2 = NULL, IGBPname = NULL, ratio = 1, ..., 
-  scale = c("site", "regional"), V2 = TRUE, return.Es = TRUE) 
+  data, par = NULL, CO2 = NULL, IGBPcode = NULL, ratio = 1, ...,
+  scale = c("site", "regional"), V2 = TRUE, return.Es = TRUE)
 {
   scale <- match.arg(scale)
   # 380, 475, 570# umol mol-1,475; #data$CO2
@@ -88,8 +88,9 @@ PML <- function(
   kA <- 0.7 # extinction coefficient
   LAIref <- 5 # par[10);  # 1-5
 
-  ind <- match(IGBPname, options_param$IGBPname) # index of options_param
-
+  # ind <- match(IGBPname, options_param$IGBPname) # index of options_param
+  ind = IGBPcode
+
   if (is.null(par)) {
     Alpha  <- options_param$Alpha[ind] # initial photochemical efficiency, 0.02-0.08
     Thelta <- options_param$Thelta[ind] #

R/model_calib.R

@@ -3,9 +3,9 @@
 #' @inheritParams PML
 #' @inheritParams rtop::sceua
 #'
-#' @param IGBPcode (optional) If `hc_raw` specified in `par`, `IGBPcode` can be ignored.
+#' @param IGBPcode (optional) [IGBP_006] code. If `hc_raw` specified in `par`, `IGBPcode` can be ignored.
 #' Otherwise, `IGBPcode` should be provided.
-#'
+#' 
 #' @importFrom rtop sceua
 #' @export
 PML_calib <- function(data, IGBPcode = 1, of_gof = NSE, ..., verbose = TRUE, maxn = 1e3) {
@@ -29,7 +29,7 @@ PML_calib <- function(data, IGBPcode = 1, of_gof = NSE, ..., verbose = TRUE, max
   # par = sceua(PML_goal, par0, lb, ub, iprint = ifelse(verbose, 0, -1), maxn = maxn,
   #                 data = data, IGBPcode = IGBPcode, of_gof = of_gof)$par
   par <- set_names(par, parnames)
-  par["hc"] <- options_param$hc_raw[IGBPcode + 1]
+  par["hc"] <- options_param$hc_raw[IGBPcode]
 
   gof <- PML_goal(par, data, detailed = TRUE, of_gof = NSE)
   cat(str(gof))
@@ -109,6 +109,7 @@ PML_gof <- function(dat, of_gof = NSE, detailed = TRUE) {
 #' @import crayon
 PML_goal <- function(par, data, IGBPcode = NULL, ..., of_gof = NSE, detailed = FALSE) {
   dat <- PML_predict(data, par, IGBPcode = IGBPcode)
+
   # smaller, better
   PML_gof(dat, of_gof = of_gof, detailed = detailed)
 }

README.md

@@ -28,6 +28,9 @@ You can install the development version of `PMLV2` like so:
 
 ``` r
 remotes::install_github("gee-hydro/PMLV2")
+
+pak::pkg_install(c("phenofit"))
+pak::pkg_install(c("rpkgs/rfluxnet", "rpkgs/nctools"))
 ```
 
 ## Example

TODO.md

@@ -0,0 +1,10 @@
+<h1>TODO</h1>
+
+
+- [x] 1. 原本默认是`IGBP05`的参数类型，现在修正到`IGBP06`，由于前者已经淘汰。
+
+- [ ] 2. 参数率定考虑依然保持在R语言。但如果Julia能够胜任的话，则弃用R语言。
+
+- [ ] 3. R语言不适合做全球计算，栅格计算改为Julia语言。
+
+- [ ] 4. 数据预处理，保留使用R语言。dataframe数据处理，R语言最成熟。