knfi 1.0.1 code change

SYOUNG9836 · Nov 19, 2024 · 7522e40 · 7522e40
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commit 7522e40
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -12,3 +12,4 @@
 ^Meta$
 ^TinyTeX\.zip$
 ^CRAN-SUBMISSION$
+^\.RDataTmp$
diff --git a/.gitignore b/.gitignore
@@ -2,6 +2,7 @@
 .Rhistory
 .RData
 .Ruserdata
+.RDataTmp
 *.zip
 inst/doc
 docs

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: knfi
 Title: Analysis of Korean National Forest Inventory Database
-Version: 1.0.0
+Version: 1.0.1
 Maintainer: Sinyoung Park <[email protected]>
 Authors@R: 
   c(person(given = "Sinyoung", family = "Park", role = c("aut", "cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-3658-0935")),
@@ -59,7 +59,9 @@ Imports:
     sp,
     cowplot,
     ggpubr,
-    drat
+    drat,
+    purrr,
+    scales
 Depends: 
     R (>= 3.6)
 Suggests: 

diff --git a/NAMESPACE b/NAMESPACE
@@ -24,10 +24,16 @@ import(vegan)
 importFrom(cowplot,plot_grid)
 importFrom(data.table,rbindlist)
 importFrom(magrittr,"%>%")
+importFrom(rlang,caller_env)
+importFrom(rlang,env)
+importFrom(rlang,env_parent)
+importFrom(rlang,eval_tidy)
 importFrom(rlang,parse_exprs)
 importFrom(rlang,sym)
 importFrom(rlang,syms)
+importFrom(scales,hue_pal)
 importFrom(stats,sd)
+importFrom(stats,setNames)
 importFrom(stats,var)
 importFrom(tidyr,spread)
 importFrom(utils,install.packages)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,14 @@
-# knfi 1.0.0
+# knfi 1.0.1
+## Bug fixes
+* Fixed a bug in `summary_nfi` and `biomass_nfi` where functions were not working when `largetree_area = FALSE`.
+* Fixed a filtering bug in `filter_nfi` where plots with the same subplot name in different cycles were not properly filtered at sublayers - resolved by implementing simultaneous filtering using both subplot and cycle.
+
+## Improvements
+* `read_nfi`: Added support for additional `list.files()` arguments (e.g., `pattern`, `recursive`) to provide more flexibility in file selection.
+* `summary_nfi`, `iv_nfi`, `diversity_nfi`, `biomass_nfi`, `cwd_biomass_nfi`: Added `continuousplot` parameter to filter for plots with measurements across all NFI cycles.
+* `tsvis_nfi`: Added layout control parameters (`ncol`, `nrow`) for customizing plot visualization  and `top` parameter for selecting number of top species to display.
+*`nfi_col`: Renamed from `col_name` to provide a more descriptive name
 
-* Initial CRAN submission.
+
+# knfi 1.0.0
+*  Initial CRAN submission(2024-10-10).
diff --git a/R/biomass_nfi.R b/R/biomass_nfi.R
@@ -46,12 +46,10 @@ bm_df <- function(data){
     (CONDEC_CLASS_CD ==0) ~ "OTHER_CON", # Other conifer species
     TRUE ~ as.character(NA)
 
-    # Bambusoideae (대나무) ?? 
-
   ))
 
 
-  output <- left_join(output, bio_coeff, by= c("species_bm" ="SPCD") )
+  output <- left_join(output, bio_coeff[,-1], by= c("species_bm" ="SPCD") )
 
   ## Calculating aboveground biomass--------------------------------------------------------------
   ## species ~ Volume*(Wood density)*(Biomass expansion factor)-------------------------------
@@ -98,6 +96,7 @@ bm_df <- function(data){
 #' @param byplot : A logical flag (default FALSE); if TRUE, calculates statistics for each plot separately. If FALSE, calculates for the entire dataset or groups specified by `plotgrp` and `treegrp`.
 #' @param plotgrp : A character vector; variables from 'plot' tables for grouping. Use \code{c()} to combine multiple variables.
 #' @param treegrp : A character vector; variables from 'tree' tables for grouping. Use \code{c()} to combine multiple variables.
+#' @param continuousplot : A logical flag (default TRUE); if TRUE, includes only plots that have been continuously measured in all NFI cycles (5th, 6th, etc.). If FALSE, includes plots regardless of missing cycle measurements.
 #' @param strat : A character vector; the variable used for post-stratification. In the National Forest Inventory of Korea, it is typically used by forest type.
 #' @param clusterplot : A logical flag (default FALSE); if TRUE, treats each cluster plot as a single unit. If FALSE, calculates for each subplot separately.
 #' @param largetreearea : A logical flag (default TRUE); if TRUE, includes large tree survey plots in the analysis. If FALSE, only uses standard tree plots.
@@ -119,10 +118,10 @@ bm_df <- function(data){
 #' data("nfi_donghae")
 #' 
 #' # Basic usage
-#' biomass <- biomass_nfi(nfi_donghae)
+#' biomass <- biomass_nfi(nfi_donghae, continuousplot = TRUE)
 #' 
 #' # Calculate biomass by administrative district
-#' district_biomass <- biomass_nfi(nfi_donghae, plotgrp = "SGG")
+#' district_biomass <- biomass_nfi(nfi_donghae, plotgrp = "SGG", continuousplot=TRUE)
 #' 
 #' # Calculate biomass for each plot
 #' plot_biomass <- biomass_nfi(nfi_donghae, byplot = TRUE)
@@ -134,7 +133,7 @@ bm_df <- function(data){
 #' @export 
 
 
-biomass_nfi <- function(data, byplot= FALSE, plotgrp=NULL, treegrp= NULL, strat="FORTYP_SUB", clusterplot=FALSE, largetreearea=TRUE, stockedland=TRUE, talltree=TRUE){
+biomass_nfi <- function(data, byplot= FALSE, plotgrp=NULL, treegrp= NULL, continuousplot=FALSE, strat="FORTYP_SUB", clusterplot=FALSE, largetreearea=TRUE, stockedland=TRUE, talltree=TRUE){
 
 
   ## error message-------------------------------------------------------------- 
@@ -147,10 +146,12 @@ biomass_nfi <- function(data, byplot= FALSE, plotgrp=NULL, treegrp= NULL, strat=
 
 
   if (clusterplot){
-    if(strat=="FORTYP_SUB"){
-      warning("When the param 'clusterplot' is set to TRUE, param 'strat' uses FORTYP_CLST (the forest type for the cluster plot) instead of FORTYP_SUB (the forest type for each subplot).")
+    if(!is.null(strat) && strat=="FORTYP_SUB"){
+      stop("When the param 'clusterplot' is set to TRUE, param 'strat' uses FORTYP_CLST (the forest type for the cluster plot) instead of FORTYP_SUB (the forest type for each subplot).")
+    }
 
-      strat <- c("FORTYP_CLST")
+    if(!is.null(plotgrp) && plotgrp=="FORTYP_SUB"){
+      stop("When the param 'clusterplot' is set to TRUE, param 'plotgrp' uses FORTYP_CLST (the forest type for the cluster plot) instead of FORTYP_SUB (the forest type for each subplot).")
     }
   }
 
@@ -202,6 +203,24 @@ biomass_nfi <- function(data, byplot= FALSE, plotgrp=NULL, treegrp= NULL, strat=
   if(talltree){
     data$tree <- data$tree %>% filter(WDY_PLNTS_TYP_CD == "1")
   }
+
+  if ("FORTYP_SUB" %in% names(data$plot)) {
+    data$plot <- data$plot %>% filter(!is.na(FORTYP_SUB))
+  }
+
+  if(continuousplot){
+
+    all_cycle <- unique(data$plot$CYCLE)
+    samples_with_all_cycle <- data$plot %>%
+      filter(!is.na(FORTYP_SUB)) %>%
+      group_by(SUB_PLOT) %>%
+      filter(all(all_cycle %in% CYCLE)) %>%
+      distinct(SUB_PLOT) %>%
+      pull(SUB_PLOT)
+
+    data <- filter_nfi(data, c("plot$SUB_PLOT %in% samples_with_all_cycle"))
+
+  }
 
   df <- left_join(data$tree[,c('CLST_PLOT', 'SUB_PLOT',"CYCLE", 'WDY_PLNTS_TYP_CD','SP', 'SPCD',
                                 'CONDEC_CLASS_CD', 'DECEVER_CD', 'DBH', 'VOL_EST',  'LARGEP_TREE', treegrp)], 
@@ -217,11 +236,12 @@ biomass_nfi <- function(data, byplot= FALSE, plotgrp=NULL, treegrp= NULL, strat=
 
   if(!largetreearea){ 
     df <- df %>% filter(df$LARGEP_TREE == "0")
+    df$largetree <- 0
   }else{
     df$largetree <- ifelse(df$DBH>=30, 1, 0)
-    df$largetree_area <- 0.08 - ((df$NONFR_INCL_AREA_LARGEP*10)/10000) # unit m2/10
   }
 
+  df$largetree_area <- 0.08 - ((df$NONFR_INCL_AREA_LARGEP*10)/10000) # unit m2/10
   df$tree_area <- 0.04 - ((df$NONFR_INCL_AREA_SUBP*10)/10000)
 
   df <- bm_df(df)
@@ -254,26 +274,25 @@ biomass_nfi <- function(data, byplot= FALSE, plotgrp=NULL, treegrp= NULL, strat=
       group_by(CYCLE, !!plot_id, INVYR) %>%
       summarise(largetree_area = sum(largetree_area, na.rm=TRUE),
                 tree_area= sum(tree_area, na.rm=TRUE),.groups = 'drop')
-    
+
     bm_temp <- df %>% 
-      group_by(CYCLE, !!plot_id, INVYR, largetree, !!!plotgrp, !!!treegrp, !!strat) %>% 
+      group_by(CYCLE, !!plot_id, INVYR, largetree, !!!plotgrp, SP, !!strat) %>% 
       summarise(volume_m3 = sum(VOL_EST, na.rm=TRUE),
                 biomass_ton = sum(T_biomass, na.rm=TRUE),
                 AG_biomass_ton = sum(AG_biomass, na.rm=TRUE),
                 carbon_stock_tC = sum(carbon_stock, na.rm=TRUE),
                 co2_stock_tCO2 = sum(co2_stock, na.rm=TRUE),.groups = 'drop')
-    
+
     bm_temp <- full_join(bm_temp, plot_area, by=c('CYCLE', 'INVYR', quo_name(plot_id)))
 
-    condition <- (names(bm_temp) %in% c("volume_m3","biomass_ton","AG_biomass_ton","carbon_stock_tC","co2_stock_tCO2"))
-
 
     if(!largetreearea){ # 1.1.1 Biomass calculation by cluster plots excluding large tree survey plots 
 
       condition_ha <- c("volume_m3_ha","biomass_ton_ha","AG_biomass_ton_ha","carbon_stock_tC_ha","co2_stock_tCO2_ha")
       bm_temp[condition_ha] <-  NA
       bm_temp <- as.data.frame(bm_temp)
 
+      condition <- (names(bm_temp) %in% c("volume_m3","biomass_ton","AG_biomass_ton","carbon_stock_tC","co2_stock_tCO2"))
       condition_ha <- (names(bm_temp) %in% c("volume_m3_ha","biomass_ton_ha","AG_biomass_ton_ha","carbon_stock_tC_ha","co2_stock_tCO2_ha"))
 
       bm_temp[condition_ha] <- 
@@ -284,11 +303,13 @@ biomass_nfi <- function(data, byplot= FALSE, plotgrp=NULL, treegrp= NULL, strat=
 
       bm_temp[condition] <- NULL
       bm_temp$tree_area <- NULL
-      bm_temp$largetreearea <- NULL
+      bm_temp$largetree_area <- NULL
 
 
     }else{ # 1.1.2 Biomass calculation by cluster plots including large tree survey plots 
 
+      condition <- (names(bm_temp) %in% c("volume_m3","biomass_ton","AG_biomass_ton","carbon_stock_tC","co2_stock_tCO2"))
+
       bm_temp[condition] <- 
         lapply(bm_temp[condition], function(x) ifelse(bm_temp$largetree == 1, 
                                                       x/(bm_temp$largetree_area),
@@ -319,15 +340,13 @@ biomass_nfi <- function(data, byplot= FALSE, plotgrp=NULL, treegrp= NULL, strat=
                 carbon_stock_tC = sum(carbon_stock, na.rm=TRUE),
                 co2_stock_tCO2 = sum(co2_stock, na.rm=TRUE),.groups = 'drop')
 
-
-    condition <- (names(bm_temp) %in% c("volume_m3","biomass_ton","AG_biomass_ton","carbon_stock_tC","co2_stock_tCO2"))
-
     if(!largetreearea){ # 1.2.1 Biomass calculation by subplots excluding large tree survey plots  
 
       condition_ha <- c("volume_m3_ha","biomass_ton_ha","AG_biomass_ton_ha","carbon_stock_tC_ha","co2_stock_tCO2_ha")
       bm_temp[condition_ha] <-  NA
       bm_temp <- as.data.frame(bm_temp)
 
+      condition <- (names(bm_temp) %in% c("volume_m3","biomass_ton","AG_biomass_ton","carbon_stock_tC","co2_stock_tCO2"))
       condition_ha <- (names(bm_temp) %in% c("volume_m3_ha","biomass_ton_ha","AG_biomass_ton_ha","carbon_stock_tC_ha","co2_stock_tCO2_ha"))
 
       bm_temp[condition_ha] <- 
@@ -338,12 +357,14 @@ biomass_nfi <- function(data, byplot= FALSE, plotgrp=NULL, treegrp= NULL, strat=
 
       bm_temp[condition] <- NULL
       bm_temp$tree_area <- NULL
-      bm_temp$largetreearea <- NULL
+      bm_temp$largetree_area <- NULL
 
 
 
     }else{ # 1.2.2 Biomass calculation by subplots including large tree survey plots  
 
+      condition <- (names(bm_temp) %in% c("volume_m3","biomass_ton","AG_biomass_ton","carbon_stock_tC","co2_stock_tCO2"))
+
       bm_temp[condition] <- 
         lapply(bm_temp[condition], function(x) ifelse(bm_temp$largetree == 1, 
                                                       x/(bm_temp$largetree_area),
@@ -559,10 +580,12 @@ biomass_tsvis <- function(data, plotgrp=NULL, treegrp=NULL, strat="FORTYP_SUB",
   }
 
   if (clusterplot){
-    if(strat=="FORTYP_SUB"){
-      warning("When the param 'clusterplot' is set to TRUE, param 'strat' uses FORTYP_CLST (the forest type for the cluster plot) instead of FORTYP_SUB (the forest type for each subplot).")
-
-      strat <- c("FORTYP_CLST")
+    if(!is.null(strat) && strat=="FORTYP_SUB"){
+      stop("When the param 'clusterplot' is set to TRUE, param 'strat' uses FORTYP_CLST (the forest type for the cluster plot) instead of FORTYP_SUB (the forest type for each subplot).")
+    }
+
+    if(!is.null(plotgrp) && plotgrp=="FORTYP_SUB"){
+      stop("When the param 'clusterplot' is set to TRUE, param 'plotgrp' uses FORTYP_CLST (the forest type for the cluster plot) instead of FORTYP_SUB (the forest type for each subplot).")
     }
   }
 
@@ -598,6 +621,10 @@ biomass_tsvis <- function(data, plotgrp=NULL, treegrp=NULL, strat="FORTYP_SUB",
     data$tree <- data$tree %>% filter(WDY_PLNTS_TYP_CD == "1")
   }
 
+  if ("FORTYP_SUB" %in% names(data$plot)) {
+    data$plot <- data$plot %>% filter(!is.na(FORTYP_SUB))
+  }
+
   df <- left_join(data$tree[,c('CLST_PLOT', 'SUB_PLOT',"CYCLE", 'WDY_PLNTS_TYP_CD','SP', 'SPCD',
                                'CONDEC_CLASS_CD', 'DECEVER_CD', 'DBH', 'VOL_EST',  'LARGEP_TREE', treegrp )], 
                   data$plot[,c('CLST_PLOT', 'SUB_PLOT', "CYCLE", 'INVYR', "LAND_USE", "LAND_USECD",
@@ -611,12 +638,12 @@ biomass_tsvis <- function(data, plotgrp=NULL, treegrp=NULL, strat="FORTYP_SUB",
 
   if(!largetreearea){ 
     df <- df %>% filter(df$LARGEP_TREE == "0")
+    df$largetree <- 0
   }else{
     df$largetree <- ifelse(df$DBH>=30, 1, 0)
-    df$largetree_area <- 0.08 - ((df$NONFR_INCL_AREA_LARGEP*10)/10000) # unit m2/10
   }
 
-
+  df$largetree_area <- 0.08 - ((df$NONFR_INCL_AREA_LARGEP*10)/10000) # unit m2/10
   df$tree_area <- 0.04 - ((df$NONFR_INCL_AREA_SUBP*10)/10000)
 
   df <- bm_df(df)
@@ -660,15 +687,14 @@ biomass_tsvis <- function(data, plotgrp=NULL, treegrp=NULL, strat="FORTYP_SUB",
 
     bm_temp <- full_join(bm_temp, plot_area, by=c('CYCLE', 'INVYR', quo_name(plot_id)))
 
-    condition <- (names(bm_temp) %in% c("volume_m3","biomass_ton","AG_biomass_ton","carbon_stock_tC","co2_stock_tCO2"))
-
 
     if(!largetreearea){ # 1.1.1 Biomass calculation by cluster plots excluding large tree survey plots
 
       condition_ha <- c("volume_m3_ha","biomass_ton_ha","AG_biomass_ton_ha","carbon_stock_tC_ha","co2_stock_tCO2_ha")
       bm_temp[condition_ha] <-  NA
       bm_temp <- as.data.frame(bm_temp)
 
+      condition <- (names(bm_temp) %in% c("volume_m3","biomass_ton","AG_biomass_ton","carbon_stock_tC","co2_stock_tCO2"))
       condition_ha <- (names(bm_temp) %in% c("volume_m3_ha","biomass_ton_ha","AG_biomass_ton_ha","carbon_stock_tC_ha","co2_stock_tCO2_ha"))
 
       bm_temp[condition_ha] <- 
@@ -679,11 +705,12 @@ biomass_tsvis <- function(data, plotgrp=NULL, treegrp=NULL, strat="FORTYP_SUB",
 
       bm_temp[condition] <- NULL
       bm_temp$tree_area <- NULL
-      bm_temp$largetreearea <- NULL
+      bm_temp$largetree_area <- NULL
 
 
     }else{ # 1.1.2 Biomass calculation by cluster plots including large tree survey plots
 
+      condition <- (names(bm_temp) %in% c("volume_m3","biomass_ton","AG_biomass_ton","carbon_stock_tC","co2_stock_tCO2"))
       bm_temp[condition] <- 
         lapply(bm_temp[condition], function(x) ifelse(bm_temp$largetree == 1, 
                                                       x/(bm_temp$largetree_area),
@@ -713,15 +740,13 @@ biomass_tsvis <- function(data, plotgrp=NULL, treegrp=NULL, strat="FORTYP_SUB",
                 carbon_stock_tC = sum(carbon_stock, na.rm=TRUE),
                 co2_stock_tCO2 = sum(co2_stock, na.rm=TRUE),.groups = 'drop')
 
-
-    condition <- (names(bm_temp) %in% c("volume_m3","biomass_ton","AG_biomass_ton","carbon_stock_tC","co2_stock_tCO2"))
-
     if(!largetreearea){ # 1.2.1 Biomass calculation by subplots excluding large tree survey plots
 
       condition_ha <- c("volume_m3_ha","biomass_ton_ha","AG_biomass_ton_ha","carbon_stock_tC_ha","co2_stock_tCO2_ha")
       bm_temp[condition_ha] <-  NA
       bm_temp <- as.data.frame(bm_temp)
 
+      condition <- (names(bm_temp) %in% c("volume_m3","biomass_ton","AG_biomass_ton","carbon_stock_tC","co2_stock_tCO2"))
       condition_ha <- (names(bm_temp) %in% c("volume_m3_ha","biomass_ton_ha","AG_biomass_ton_ha","carbon_stock_tC_ha","co2_stock_tCO2_ha"))
 
       bm_temp[condition_ha] <- 
@@ -733,11 +758,12 @@ biomass_tsvis <- function(data, plotgrp=NULL, treegrp=NULL, strat="FORTYP_SUB",
 
       bm_temp[condition] <- NULL
       bm_temp$tree_area <- NULL
-      bm_temp$largetreearea <- NULL
+      bm_temp$largetree_area <- NULL
 
 
     }else{ # 1.2.2 Biomass calculation by subplots including large tree survey plots
 
+      condition <- (names(bm_temp) %in% c("volume_m3","biomass_ton","AG_biomass_ton","carbon_stock_tC","co2_stock_tCO2"))
       bm_temp[condition] <- 
         lapply(bm_temp[condition], function(x) ifelse(bm_temp$largetree == 1, 
                                                       x/(bm_temp$largetree_area),