version 0.2.1 released (#9)

* shinyapp: GPPobs and NDVI3g work
* unify examples and rename PhenoExtract to get_pheno
* add examples
* tidy getRealDate
* update plot_input function
* rename season_3y to season_mov
* rm parameter I_optimFUN in optim_pheno
* version 0.2.1 released
* finished gee_Whittaker evaluation

.Rbuildignore

@@ -22,4 +22,4 @@
 ^cran-comments\.md$
 ^Dockerfile$
 ^update 20181028/$
-^README\.Rmd$
+^README\.Rmd$

.gitignore

@@ -62,11 +62,14 @@ src-i386/
 src-x64/
 inst/doc
 temp/
-# test/
+test/
 
 # Office document
 notebook
 *.csv
 *.xlsx
 *.docx
 *.pdf
+
+# TIMESAT file
+*.set

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: phenofit
 Type: Package
 Title: Extract Remote Sensing Vegetation Phenology 
-Version: 0.1.9
+Version: 0.2.1
 Authors@R: c(
     person("Dongdong", "Kong", role = c("aut", "cre"), email = "kongdd.sysu@gmail.com"),
-    person("Yongqiang", "Zhang", role = c("aut"), email = "yongqiang.zhang2014@gmail.com"),
     person("Mingzhong", "Xiao", role = c("aut"), email = "xmingzh@mail2.sysu.edu.cn"),
+    person("Yongqiang", "Zhang", role = c("aut"), email = "yongqiang.zhang2014@gmail.com"),
     person("Xihui", "Gu", role = c("aut"), email = "guxh@cug.edu.cn"),
     person("Jianjian", "Cui", role = c("aut"), email = "cuijj6@mail2.sysu.edu.cn"))
 Description: 
@@ -36,6 +36,5 @@ Imports: Rcpp,
 Suggests: knitr,
     rmarkdown,
     testthat
-VignetteBuilder: knitr
 URL: https://github.com/kongdd/phenofit
 BugReports: https://github.com/kongdd/phenofit/issues

Dockerfile

@@ -81,6 +81,6 @@ RUN wget --no-verbose https://download3.rstudio.org/ubuntu-14.04/x86_64/VERSION
 EXPOSE 3838
 
 RUN installGithub.r kongdd/Ipaper \
-    && R -e "devtools::install_github('kongdd/phenofit', ref='debug-whittaker')" \
+    && R -e "devtools::install_github('kongdd/phenofit', ref='dev')" \
     && rm -rf /tmp/downloaded_packages/
     # kongdd/phenofit \

NAMESPACE

@@ -15,22 +15,19 @@ export(FitDL.Gu)
 export(FitDL.Klos)
 export(FitDL.Zhang)
 export(GOF)
-export(GOF_fFITs)
 export(I_optim)
 export(I_optimx)
 export(Logistic)
 export(PhenoDeriv)
-export(PhenoExtract)
-export(PhenoExtract.fFITs)
 export(PhenoGu)
 export(PhenoKl)
 export(PhenoTrs)
 export(R2_sign)
 export(add_HeadTail)
 export(add_dn)
 export(backval)
-export(check_fit)
 export(check_input)
+export(check_ylu)
 export(contain)
 export(curvature)
 export(curvefit)
@@ -47,10 +44,14 @@ export(findpeaks)
 export(fprintf)
 export(getBits)
 export(getRealDate)
+export(get_GOF)
+export(get_GOF.fFITs)
 export(get_fitting)
 export(get_fitting.fFITs)
 export(get_param)
 export(get_param.fFITs)
+export(get_pheno)
+export(get_pheno.fFITs)
 export(ifelse2)
 export(init_lambda)
 export(init_param)
@@ -77,7 +78,7 @@ export(reorder_name)
 export(rm_empty)
 export(runningId)
 export(season)
-export(season_3y)
+export(season_mov)
 export(skewness)
 export(tidyFitPheno)
 export(tidy_MOD13.gee)
@@ -114,6 +115,9 @@ importFrom(dplyr,left_join)
 importFrom(dplyr,nth)
 importFrom(grDevices,cairo_pdf)
 importFrom(grDevices,dev.off)
+importFrom(grid,grid.draw)
+importFrom(grid,pushViewport)
+importFrom(grid,viewport)
 importFrom(gridExtra,arrangeGrob)
 importFrom(lubridate,day)
 importFrom(lubridate,ddays)

NEWS.md

@@ -1,3 +1,40 @@
+# phenofit 0.2.1 (2019-03-11)    
+
+* fix point shape error of `plot_input`
+* make_legend supports 4 quality categories (MOD13A1) and 6 quality categories (MOD09A1) now.
+* wWHIT only adjusts time series of growing season. 
+
+
+# phenofit 0.2.1 (2019-02-18)    
+
+* release in CRAN
+
+
+# phenofit 0.1.8 (2019-01-06)    
+
+* `shiny` app `phenofit` released.
+* add `QC_flag` to the output of `check_input`.
+
+
+# phenofit 0.1.7 (2018-10-29)   
+* Add V-curve optimization in `season_mov` for Whittaker's parameter lambda.
+* Remove `check_ylu` and `upper envelope` in `wWHIT`.
+* Update `v-curve`.
+
+# phenofit 0.1.6 (2018-10-26)   
+
+* Melt parameters (i.e. `nptperyear` and `south`) into `INPUT`. `check_input`,
+ `season`, `season_mov` and `curvefits` are impacted.
+* Add `adj.param` parameter to `season`, which determine whether to automatically 
+adjust roughn curve fitting parameters.
+
+
+# phenofit 0.1.5 (2018-09-19)
+
+* shiny app `check_season` online now.
+* `season` can export rough curve fitting result, even no peaks or trough found.
+
+
 # phenofit 0.1.3 (2018-07-25)
 
 * fix `Init_param`   
@@ -11,21 +48,3 @@
 strategy.
 * `doubleLog.zhang` is still not as stable as others.
 * `wTSM_cpp` iter parameter is ignored now.
-
-# phenofit 0.1.5 (2018-09-19)
-
-* shiny app `check_season` online now.
-* `season` can export rough curve fitting result, even no peaks or trough found.
-
-# phenofit 0.1.6 (2018-10-26)
-
-* Melt parameters (i.e. `nptperyear` and `south`) into `INPUT`. `check_input`,
- `season`, `season_3y` and `curvefits` are impacted.
-* Add `adj.param` parameter to `season`, which determine whether to automatically 
-adjust roughn curve fitting parameters.
-
-# phenofit 0.1.7 (2018-10-29)
-
-* Add V-curve optimization in `season_3y` for Whittaker's parameter lambda.
-* Remove `check_fit` and `upper envelope` in `wWHIT`.
-* Update `v-curve`.

R/S3_fFITs.R

@@ -29,7 +29,7 @@ NULL
 #' plot curve fitting VI, gradient (first order difference D1), hessian (D2),
 #' curvature (k) and the change rate of curvature(der.k)
 #'
-#' @inheritParams PhenoExtract
+#' @inheritParams get_pheno
 #' @param x Fine curve fitting object \code{\link{fFITs}} returned by
 #' \code{\link{curvefit}}.
 #' @param ... ignored.
@@ -109,94 +109,3 @@ plot.fFITs <- function(x, method, ...){
     # diff <- der1 - der1_diff
     # der <- data.frame(der1_diff, der1 = der1, diff = diff)
 }
-
-
-#' GOF_fFITs
-#'
-#' Good-of-fitting (GOF) to fine curve fitting results.
-#' 
-#' @param fFITs \code{fFITs} object returned by \code{\link{curvefit}}.
-#'
-#' @return
-#' \describe{
-#'   \item{meth}{The name of fine curve fitting method}
-#'   \item{RMSE}{Root Mean Square Error}
-#'   \item{NSE}{Nash-Sutcliffe model efficiency coefficient}
-#'   \item{R}{Pearson-Correlation}
-#'   \item{pvalue}{pvalue of \code{R}}
-#'   \item{n}{The number of observations}
-#' }
-#'
-#' @references
-#' [1]. https://en.wikipedia.org/wiki/Nash-Sutcliffe_model_efficiency_coefficient \cr
-#' [2]. https://en.wikipedia.org/wiki/Pearson_correlation_coefficient
-#' 
-#' @seealso \code{\link{curvefit}}
-#' 
-#' @examples
-#' library(phenofit)
-#' # simulate vegetation time-series
-#' fFUN = doubleLog.Beck
-#' par  = c(
-#'     mn  = 0.1,
-#'     mx  = 0.7,
-#'     sos = 50,
-#'     rsp = 0.1,
-#'     eos = 250,
-#'     rau = 0.1)
-#' t    <- seq(1, 365, 8)
-#' tout <- seq(1, 365, 1)
-#' y <- fFUN(par, t)
-#'
-#' methods <- c("AG", "Beck", "Elmore", "Gu", "Zhang") # "Klos" too slow
-#' fFITs <- curvefit(y, t, tout, methods)
-#'
-#' GOF_fFITs(fFITs)
-#' @export
-GOF_fFITs <- function(fFITs){
-    methods <- names(fFITs$fFIT)
-    nmeth   <- length(methods)
-
-    t     <- fFITs$data$t
-    tout  <- fFITs$tout
-    ti    <- intersect(t, tout)
-    I_org <- match(ti, t)
-    I_sim <- match(ti, tout)
-
-    Y_obs  <- fFITs$data$y[I_org]
-    # Y_sim  <- map(x$fFIT, ~last(.$fits))
-
-    # The following script assume that tout in every method is equal length.
-    # calculate statistic for every meth
-    info <- ldply(fFITs$fFIT, function(fFIT){
-        Y_sim <- last(fFIT$zs)[I_sim]
-        I <- which(!(is.na(Y_obs) | is.na(Y_sim)))
-
-        # n_obs <- length(Y_obs)
-        Y_sim2 <- Y_sim[I]
-        Y_obs2 <- Y_obs[I]
-
-        R      <- NA
-        pvalue <- NA
-        n      <- length(I)
-
-        if (n < 2) return(c(RMSE = NA, NSE = NA, R = R, pvalue = pvalue, n = n))
-
-        tryCatch({
-            cor.obj <- cor.test(Y_obs, Y_sim, use = "complete.obs")
-            R       <- cor.obj$estimate[[1]]
-            pvalue  <- cor.obj$p.value
-        }, error = function(e){
-            message(sprintf('[statistic] %s', e$message))
-        })
-
-        RMSE <- sqrt(sum((Y_obs - Y_sim)^2)/n)
-        NSE  <- 1 - sum((Y_sim - Y_obs)^2) / sum((Y_obs - mean(Y_obs))^2)
-
-        c(RMSE = RMSE, NSE = NSE, R = R, pvalue = pvalue, n = n)
-    }, .id = "meth")
-    info
-}
-
-# GOFs_fFITs <- function(fit){
-# }

R/add_HeadTail.R

@@ -5,8 +5,8 @@
 #' (image date) column which are (\code{Date} variable).
 #' @inheritParams check_input
 #' @inheritParams season
-#' 
-#' @param trs If nmissing < trs*nptperyear (little missing), this year is 
+#'
+#' @param trs If nmissing < trs*nptperyear (little missing), this year is
 #' include to extract phenology; if \code{FALSE}, this year is excluded.
 #'
 #' @note \code{date} is image date; \code{t} is compositing date.
@@ -17,17 +17,17 @@
 #' @examples
 #' library(phenofit)
 #' data("MOD13A1")
-#' 
+#'
 #' dt <- tidy_MOD13.gee(MOD13A1$dt)
 #' st <- MOD13A1$st
-#' 
+#'
 #' sitename <- dt$site[1]
 #' d     <- dt[site == sitename, ] # get the first site data
 #' sp    <- st[site == sitename, ] # station point
-#' 
+#'
 #' nptperyear = 23
 #' dnew     <- add_HeadTail(d, nptperyear = nptperyear) # add one year in head and tail
-#' 
+#'
 #' @export
 add_HeadTail <- function(d, south = FALSE, nptperyear, trs = 0.45){
     if (missing(nptperyear)){