From 2de451ca1b93d360f396d038a652099d9aaacaff Mon Sep 17 00:00:00 2001 From: Mahnken Date: Mon, 9 Mar 2020 16:10:35 +0100 Subject: [PATCH 01/17] correct biomass in DB corrects biomass compartment values for Bily-Kriz since the raw data is given in t/ha but labeled as kg/ha --- PROFOUND database/Processing/Create_Stand_Data.R | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/PROFOUND database/Processing/Create_Stand_Data.R b/PROFOUND database/Processing/Create_Stand_Data.R index d3e1402..1484c86 100644 --- a/PROFOUND database/Processing/Create_Stand_Data.R +++ b/PROFOUND database/Processing/Create_Stand_Data.R @@ -42,6 +42,12 @@ names(df) <- c("year", "species_id", "site_id", "dbhArith_cm", "ba_m2ha", "age" "stemBiomass_kgha", "rootBiomass_kgha") df$stem <- NULL +# biomass stock variables from t/ha into kg/ha because raw data values are in t/ha +df$foliageBiomass_kgha <- df$foliageBiomass_kgha * 1000 +df$branchesBiomass_kgha <- df$branchesBiomass_kgha * 1000 +df$stemBiomass_kgha <- df$stemBiomass_kgha * 1000 +df$rootBiomass_kgha <- df$rootBiomass_kgha * 1000 + #df <- dropDuplicates(df, Tree_Data$BilyKriz) #df <- df[ df$year %in% unique(Tree_Data$BilyKriz$year), ] Stand_Data$BilyKriz <- df From 3dfa079142654780a9bb74da8cca3754bf0c4f26 Mon Sep 17 00:00:00 2001 From: Mats Mahnken <16384076+matsmahnken@users.noreply.github.com> Date: Wed, 18 Mar 2020 11:05:37 +0100 Subject: [PATCH 02/17] correct flux unit conversion correct the conversion from gC m-2 to tC ha-1 --- ProfoundData/R/summarizePROFOUND.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ProfoundData/R/summarizePROFOUND.R b/ProfoundData/R/summarizePROFOUND.R index 970b12b..0b48bcb 100644 --- a/ProfoundData/R/summarizePROFOUND.R +++ b/ProfoundData/R/summarizePROFOUND.R @@ -183,7 +183,7 @@ summarizePROFOUND.FLUX <- function(data, by = "total"){ if (by == "year" || by == "total"){ # Convert to tC/ha colnames(subSummary) <- gsub("_gCm2", "_tCha1", colnames(subSummary)) - subSummary <-apply(subSummary, c(1,2), function(x) x*(1/1000000)*(100000/1)) + subSummary <-apply(subSummary, c(1,2), function(x) x*(1/1000000)*(10000/1)) subSummary <- as.data.frame(cbind(site, site_id, year,subSummary)) }else if (by == "day"){ mo <- unique(subData$mo) From fa85a708d7821c288acde7a48433e97a396020e8 Mon Sep 17 00:00:00 2001 From: Mats Mahnken Date: Tue, 21 Apr 2020 13:03:16 +0200 Subject: [PATCH 03/17] Revert "Revert "change variable Jcm2day to Jcm2 in Package"" This reverts commit 3854f3b06bfaf2808b363860e8ce3df0bbce9d1e. --- ProfoundData/R/summarizeData.R | 2 +- ProfoundData/R/summarizePROFOUND.R | 6 +++--- ProfoundData/data-raw/ChildDatasetSummary.Rmd | 2 +- ProfoundData/inst/rmd/ChildBoth.Rmd | 2 +- ProfoundData/inst/rmd/ChildSummary.Rmd | 2 +- 5 files changed, 7 insertions(+), 7 deletions(-) diff --git a/ProfoundData/R/summarizeData.R b/ProfoundData/R/summarizeData.R index dbc5055..251c03c 100644 --- a/ProfoundData/R/summarizeData.R +++ b/ProfoundData/R/summarizeData.R @@ -25,7 +25,7 @@ #' \itemize{ #' \item Climatic datasets #' \itemize{ -#' \item p_mm and rad_Jcm2day are total yearly values +#' \item p_mm and rad_Jcm2 are total yearly values #' \item tmax_degC, tmean_degC, tmin_degC, relhum_percent, airpress_hPa and wind_ms are mean yearly values #' } #' \item TREE dataset diff --git a/ProfoundData/R/summarizePROFOUND.R b/ProfoundData/R/summarizePROFOUND.R index 749430a..0b48bcb 100644 --- a/ProfoundData/R/summarizePROFOUND.R +++ b/ProfoundData/R/summarizePROFOUND.R @@ -11,10 +11,10 @@ summarizePROFOUND.CLIMATE <- function(data, by = "total"){ p_mm <- ifelse("p_mm" %in% colnames(subData),sum(subData$p_mm, na.rm = T),NA) relhum_percent <- ifelse("relhum_percent" %in% colnames(subData), mean(subData$relhum_percent, na.rm = T),NA) airpress_hPa <- ifelse("airpress_hPa" %in% colnames(subData), mean(subData$airpress_hPa, na.rm = T),NA) - rad_Jcm2day <- ifelse("rad_Jcm2day" %in% colnames(subData), sum(subData$rad_Jcm2day, na.rm = T),NA) + rad_Jcm2 <- ifelse("rad_Jcm2" %in% colnames(subData), sum(subData$rad_Jcm2, na.rm = T),NA) wind_ms <- ifelse("wind_ms" %in% colnames(subData), mean(subData$wind_ms, na.rm = T),NA) subSummary <- cbind(site, site_id, year, tmax_degC, tmean_degC, tmin_degC, p_mm, - relhum_percent, airpress_hPa, rad_Jcm2day, wind_ms) + relhum_percent, airpress_hPa, rad_Jcm2, wind_ms) return(subSummary) } # Summarize @@ -42,7 +42,7 @@ summarizePROFOUND.CLIMATE <- function(data, by = "total"){ summarizePROFOUND.ISIMIP <- function(data, by ="total"){ #by <- "total" - variables <- c("year", "tmax_degC","tmean_degC","tmin_degC","p_mm","relhum_percent","airpress_hPa","rad_Jcm2day", + variables <- c("year", "tmax_degC","tmean_degC","tmin_degC","p_mm","relhum_percent","airpress_hPa","rad_Jcm2", "wind_ms") # or do a long table if ("forcingDataset" %in% names(data)){ diff --git a/ProfoundData/data-raw/ChildDatasetSummary.Rmd b/ProfoundData/data-raw/ChildDatasetSummary.Rmd index dea31fd..e583405 100644 --- a/ProfoundData/data-raw/ChildDatasetSummary.Rmd +++ b/ProfoundData/data-raw/ChildDatasetSummary.Rmd @@ -93,7 +93,7 @@ df <- df[df$source != "FLUXNET",] df <- df[, !colnames(df) %in% c("source", "comments")] rownames(df) <- NULL -maskVariables <- c( "site_id", "date","year", "mo","day","airpress_hPa","p_mm", "rad_Jcm2day", "record_id", "relhum_percent", "tmax_degC", "tmean_degC","tmin_degC", "wind_ms") +maskVariables <- c( "site_id", "date","year", "mo","day","airpress_hPa","p_mm", "rad_Jcm2", "record_id", "relhum_percent", "tmax_degC", "tmean_degC","tmin_degC", "wind_ms") ``` diff --git a/ProfoundData/inst/rmd/ChildBoth.Rmd b/ProfoundData/inst/rmd/ChildBoth.Rmd index fb333f7..bad82b7 100644 --- a/ProfoundData/inst/rmd/ChildBoth.Rmd +++ b/ProfoundData/inst/rmd/ChildBoth.Rmd @@ -11,5 +11,5 @@ df <- rbind(df, df2) ```{r, eval = T, echo=F, message= F, warning=F} -pander(df, adding = 0, missing = '**--**', digits = 3, use.hyphening = TRUE, split.cells = 3, split.tables = 200, caption = tableCaption(paste("Summary of ", currentDataset, " for ", currentSiteName,". Note: Average of the annual sum of the variables p_mm and rad_Jcm2day. Rest of variables, average of the annual mean values.", sep=""))) +pander(df, adding = 0, missing = '**--**', digits = 3, use.hyphening = TRUE, split.cells = 3, split.tables = 200, caption = tableCaption(paste("Summary of ", currentDataset, " for ", currentSiteName,". Note: Average of the annual sum of the variables p_mm and rad_Jcm2. Rest of variables, average of the annual mean values.", sep=""))) ``` diff --git a/ProfoundData/inst/rmd/ChildSummary.Rmd b/ProfoundData/inst/rmd/ChildSummary.Rmd index 4e11fbb..8a61c42 100644 --- a/ProfoundData/inst/rmd/ChildSummary.Rmd +++ b/ProfoundData/inst/rmd/ChildSummary.Rmd @@ -8,5 +8,5 @@ df <- summarizeData(site = currentSiteName, dataset = currentDataset) ```{r, eval = T, echo=F, message= F, warning=F} -pander(df, adding = 0, missing = '**--**', round = 3, use.hyphening = TRUE, split.cells = 3, split.tables = 200, caption = tableCaption(paste("Summary of ", currentDataset, " for ", currentSiteName, ". Note: Average of the annual sum of the variables p_mm and rad_Jcm2day. Rest of variables, average of the annual mean values.", sep=""))) +pander(df, adding = 0, missing = '**--**', round = 3, use.hyphening = TRUE, split.cells = 3, split.tables = 200, caption = tableCaption(paste("Summary of ", currentDataset, " for ", currentSiteName, ". Note: Average of the annual sum of the variables p_mm and rad_Jcm2. Rest of variables, average of the annual mean values.", sep=""))) ``` From 975bbe5c651b84504eace49e1c91507b18d1afc4 Mon Sep 17 00:00:00 2001 From: Mahnken Date: Tue, 21 Apr 2020 16:12:54 +0200 Subject: [PATCH 04/17] minor changes DB creation corrects some minor issues that prevented compiling the database correctly --- PROFOUND database/Processing/summaryProfound.R | 2 +- PROFOUND database/createDB/Create_DB.R | 2 +- PROFOUND database/createDB/MetadataSITEDESCRIPTION_to_DB.R | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/PROFOUND database/Processing/summaryProfound.R b/PROFOUND database/Processing/summaryProfound.R index 34f0eb0..fa1fcc4 100644 --- a/PROFOUND database/Processing/summaryProfound.R +++ b/PROFOUND database/Processing/summaryProfound.R @@ -779,7 +779,7 @@ unique(unlist(plotAll)) return(unique(unlist(variablesAll)) ) for (i in 1:length(files)){ - table <-read.table(files[1], sep = ";", header = TRUE , colClasses = "character"), + table <-read.table(files[1], sep = ";", header = TRUE , colClasses = "character") unique(table$code_plot) unique(table$code_country) } diff --git a/PROFOUND database/createDB/Create_DB.R b/PROFOUND database/createDB/Create_DB.R index e1dfc70..4f2975b 100644 --- a/PROFOUND database/createDB/Create_DB.R +++ b/PROFOUND database/createDB/Create_DB.R @@ -24,7 +24,7 @@ source("Version_to_DB.R") source("Sites_to_DB.R") source("Create_SITES_Views.R") source("MetadataSITES_to_DB.R") -source("SITEDESCRIPTION_to_DB.R") +source("SITEDESCRIPTION_to_DB-2.R") source("MetadataSITEDESCRIPTION_to_DB.R") source("Create_SITEDESCRIPTION_Views.R") # create ecological description diff --git a/PROFOUND database/createDB/MetadataSITEDESCRIPTION_to_DB.R b/PROFOUND database/createDB/MetadataSITEDESCRIPTION_to_DB.R index 3f0437d..7c44435 100644 --- a/PROFOUND database/createDB/MetadataSITEDESCRIPTION_to_DB.R +++ b/PROFOUND database/createDB/MetadataSITEDESCRIPTION_to_DB.R @@ -11,8 +11,8 @@ columns <- c("record_id","variable", "site_id", "type", "units", "description") # Load libraries # open connection to DB db <- dbConnect(SQLite(), dbname= myDB) -if ( "METADATA_SITES_master" %in% dbListTables(db)){ - dbSendQuery(db, "DROP TABLE METADATA_SITES_master")} +if ( "METADATA_SITEDESCRIPTION_master" %in% dbListTables(db)){ + dbSendQuery(db, "DROP TABLE METADATA_SITEDESCRIPTION_master")} # create table in DB (cant type minus) dbSendQuery(conn = db, "CREATE TABLE METADATA_SITEDESCRIPTION_master From 6cabb0e81c117687bc6c8fecb7a62d64685f4b6a Mon Sep 17 00:00:00 2001 From: Mahnken Date: Tue, 21 Apr 2020 16:17:39 +0200 Subject: [PATCH 05/17] remove repeated lai measurements per year in Soro subsets Soro LAI measurement data to include only one measurement of LAI per year - two measurements are removed, one from August 2009 and one from August 2013 --- PROFOUND database/Processing/Create_Stand_Data.R | 3 +++ 1 file changed, 3 insertions(+) diff --git a/PROFOUND database/Processing/Create_Stand_Data.R b/PROFOUND database/Processing/Create_Stand_Data.R index 1484c86..876404f 100644 --- a/PROFOUND database/Processing/Create_Stand_Data.R +++ b/PROFOUND database/Processing/Create_Stand_Data.R @@ -180,6 +180,9 @@ cat(Soroe_LAI_2000_2013.df.des) # Description is all there df <- Soroe_LAI_2000_2013.df df$species_id <- "fasy" +# reduce to single lai measurement per year: +# use only July measurements since most often lai is measured in July in Soro +df <- df[which(!duplicated(df$year)),] head(df) names(df) <- gsub("LAI", "lai", names(df)) Stand_Data$Soro<- df From 417044bb8496e819f8b8db3351e3140953d41bd4 Mon Sep 17 00:00:00 2001 From: Mahnken Date: Tue, 21 Apr 2020 16:18:32 +0200 Subject: [PATCH 06/17] update Soro tree data select new file with updated Soro tree data --- PROFOUND database/Processing/Create_Tree_Data.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PROFOUND database/Processing/Create_Tree_Data.R b/PROFOUND database/Processing/Create_Tree_Data.R index 64349e1..4a5c0ef 100644 --- a/PROFOUND database/Processing/Create_Tree_Data.R +++ b/PROFOUND database/Processing/Create_Tree_Data.R @@ -206,7 +206,7 @@ Tree_Data$Solling_305 <- df #------------------------------------------------------------------------------# # Soro #------------------------------------------------------------------------------# -tree_file <- "./Soro/treedata_for_database_soroe_20-03-2017.txt" +tree_file <- "./Soro/treedata_for_database_soroe_16-04-2020.txt" df <- read.table(tree_file, header=T, sep="\t") # description says height and dbh in m. Dbh it is in cm!!! names(df) From 9bb92d95a6cc47bc4f056d6e4b35bf4195811aa3 Mon Sep 17 00:00:00 2001 From: Mats Mahnken Date: Tue, 28 Apr 2020 13:49:53 +0200 Subject: [PATCH 07/17] update plotPROFOUND.TREE include possibility of only showing DBH plot instead of DBH, height, DBH~height --- ProfoundData/R/plotPROFOUND.R | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/ProfoundData/R/plotPROFOUND.R b/ProfoundData/R/plotPROFOUND.R index d6fe7a4..2b456c8 100644 --- a/ProfoundData/R/plotPROFOUND.R +++ b/ProfoundData/R/plotPROFOUND.R @@ -15,18 +15,16 @@ plotPROFOUND.TREE <-function(tmp){ }else{ plotDBH <- FALSE plotHeight <- FALSE - plotCombined <- TRUE + plotCombined <- FALSE overviewPlots <- 0 if ("dbh1_cm" %in% names(dataSpp)) plotDBH <- TRUE if ("height1_m" %in% names(dataSpp)) plotHeight <- TRUE - if(!is.null(tmp[["variables"]]) & length(tmp[["variablesChecked"]]) <= 2) plotCombined <- F + if(plotDBH & plotHeight) plotCombined <- TRUE # Check if only variable is requested if (plotHeight & plotDBH & plotCombined){ overviewPlots <- 4 - }else if (plotHeight & plotDBH & !plotCombined){ - overviewPlots <- 2 } else if (plotHeight || plotDBH & !plotCombined){ - overviewPlots <- 1 + overviewPlots <- 2 } # This a values for segment(s) epsilon <- 0.1 @@ -40,7 +38,7 @@ plotPROFOUND.TREE <-function(tmp){ oldpar <- par(mfrow = c(1,1), mar=c(4,4,4,2)) on.exit(par(oldpar)) } - if (plotCombined){ + # Histrogram based on year # create positions for tick marks, one more than number of bars atYear <- 1:(length(unique(dataSpp$year)) + 1) @@ -51,7 +49,7 @@ plotPROFOUND.TREE <-function(tmp){ # add x-axis with centered position, with labels, but without ticks. axis(side = 1, at = mp[seq(1, length(unique(dataSpp$year)), 2)], tick = FALSE, labels = unique(dataSpp$year)[seq(1, length(unique(dataSpp$year)), 2)]) - } + # Plot averaged DBH if(plotDBH){ meanSppDBH <- aggregate(dataSpp$dbh1_cm ~ dataSpp$year, dataSpp, mean, na.action = na.omit, simplify = T) From 0451ca99753e19a616bb06cfaacf751e62a845f0 Mon Sep 17 00:00:00 2001 From: Mahnken Date: Mon, 4 May 2020 11:12:03 +0200 Subject: [PATCH 08/17] include Soro biomass data read data on biomass compartments for Soro and include it in the STAND information --- PROFOUND database/Processing/Create_Stand_Data.R | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/PROFOUND database/Processing/Create_Stand_Data.R b/PROFOUND database/Processing/Create_Stand_Data.R index 876404f..2f61921 100644 --- a/PROFOUND database/Processing/Create_Stand_Data.R +++ b/PROFOUND database/Processing/Create_Stand_Data.R @@ -185,13 +185,19 @@ df$species_id <- "fasy" df <- df[which(!duplicated(df$year)),] head(df) names(df) <- gsub("LAI", "lai", names(df)) -Stand_Data$Soro<- df + #inFile <- "/home/trashtos/ownCloud/PROFOUND_Data/Processed/Soro/Standdata_for_DB.txt" #df <- read.table(inFile, header = T, sep = "\t") #df <- df[,colSums(is.na(df)) Date: Mon, 4 May 2020 11:12:40 +0200 Subject: [PATCH 09/17] update Soro tree data update tree data for Soro --- PROFOUND database/Processing/Create_Tree_Data.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/PROFOUND database/Processing/Create_Tree_Data.R b/PROFOUND database/Processing/Create_Tree_Data.R index 4a5c0ef..19a5c45 100644 --- a/PROFOUND database/Processing/Create_Tree_Data.R +++ b/PROFOUND database/Processing/Create_Tree_Data.R @@ -206,7 +206,7 @@ Tree_Data$Solling_305 <- df #------------------------------------------------------------------------------# # Soro #------------------------------------------------------------------------------# -tree_file <- "./Soro/treedata_for_database_soroe_16-04-2020.txt" +tree_file <- "./Soro/treedata_for_database_soroe_28-04-2020.txt" df <- read.table(tree_file, header=T, sep="\t") # description says height and dbh in m. Dbh it is in cm!!! names(df) From 1fdd02f90d0e793d8008f9428ec57f819f87b017 Mon Sep 17 00:00:00 2001 From: Mats Mahnken Date: Mon, 4 May 2020 15:49:37 +0200 Subject: [PATCH 10/17] update citation info included new authors and new DOI link of the updated Profound DB version --- ProfoundData/inst/CITATION | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/ProfoundData/inst/CITATION b/ProfoundData/inst/CITATION index f4db055..b28c0a4 100644 --- a/ProfoundData/inst/CITATION +++ b/ProfoundData/inst/CITATION @@ -16,10 +16,10 @@ citEntry( entry = "Misc", title = "The PROFOUND database for evaluating vegetation models and simulating climate impacts on forests", copyright = "Data Licence: CC Attribution 4.0 (CC BY-NC 4.0)", - url = "http://dataservices.gfz-potsdam.de/pik/showshort.php?id=escidoc:2549901", + url = "http://doi.org/10.5880/PIK.2020.006", publisher = "GFZ Data Services", - author = "Reyer, Christopher and Silveyra Gonzalez, Ramiro and Dolos, Klara and Hartig, Florian and Hauf, Ylva and Noack, Matthias and Lasch-Born, Petra and Rötzer, Thomas and Pretzsch, Hans and Meesenburg, Henning and Fleck, Stefan and Wagner, Markus and Bolte, Andreas and Sanders, Tanja and Kolari, Pasi and Mäkelä, Annikki and Vesala, Timo and Mammarella, Ivan and Pumpanen, Jukka and Matteucci, Giorgio and Collalti, Alessio and D’Andrea, Ettore and Foltýnová, Lenka and Krejza, Jan and Ibrom, Andreas and Pilegaard, Kim and Loustau, Denis and Bonnefond, Jean-Marc and Berbigier, Paul and Picart, Delphine and Lafont, Sébastien and Dietze, Michael and Cameron, David and Vieno, Massimo and Tian, Hanqin and Palacios, Alicia and Cicuendez, Victor and Recuero, Laura and Wieze, Klaus and Büchner, Matthias and Lange, Stefan and Volkholz, Jan and Kim, Hyungjun and Weedon, Graham and Sheffield, Justin and Vega del Valle, Iliusi and Suckow, Felicitas and Horemans, Joanna and Martel, Simon and Bohn, Friedrich and Steinkamp, Jörg and Chikalanov, Alexandre and Frieler, Katja", - year = "2019", - doi = "10.5880/pik.2019.008", + author = "Reyer, Christopher and Silveyra Gonzalez, Ramiro and Dolos, Klara and Hartig, Florian and Hauf, Ylva and Noack, Matthias and Lasch-Born, Petra and Rötzer, Thomas and Pretzsch, Hans and Meesenburg, Henning and Fleck, Stefan and Wagner, Markus and Bolte, Andreas and Sanders, Tanja and Kolari, Pasi and Mäkelä, Annikki and Vesala, Timo and Mammarella, Ivan and Pumpanen, Jukka and Matteucci, Giorgio and Collalti, Alessio and D’Andrea, Ettore and Foltýnová, Lenka and Krejza, Jan and Ibrom, Andreas and Pilegaard, Kim and Loustau, Denis and Bonnefond, Jean-Marc and Berbigier, Paul and Picart, Delphine and Lafont, Sébastien and Dietze, Michael and Cameron, David and Vieno, Massimo and Tian, Hanqin and Palacios, Alicia and Cicuendez, Victor and Recuero, Laura and Wieze, Klaus and Büchner, Matthias and Lange, Stefan and Volkholz, Jan and Kim, Hyungjun and Weedon, Graham and Sheffield, Justin and Vega del Valle, Iliusi and Suckow, Felicitas and Horemans, Joanna and Martel, Simon and Bohn, Friedrich and Steinkamp, Jörg and Chikalanov, Alexandre and Mahnken, Mats and Gutsch, Martin and Trotta, Carlo and Babst, Flurin and Frieler, Katja", + year = "2020", + doi = "10.5880/PIK.2020.006", textVersion = "Reyer, C., Silveyra Gonzalez, R., Dolos, K., Hartig, F., Hauf, Y., Noack, M., … Frieler, K. (2019). The PROFOUND database for evaluating vegetation models and simulating climate impacts on forests [Data set]. https://doi.org/10.5880/pik.2019.008" ) \ No newline at end of file From 95b3ae72e39aabe02f25217bc4312bbfda211e14 Mon Sep 17 00:00:00 2001 From: Mats Mahnken Date: Mon, 4 May 2020 16:23:35 +0200 Subject: [PATCH 11/17] update release notes of DB version 0.3 --- PROFOUND database/readme.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/PROFOUND database/readme.md b/PROFOUND database/readme.md index ed9821d..79008dd 100644 --- a/PROFOUND database/readme.md +++ b/PROFOUND database/readme.md @@ -11,6 +11,22 @@ # News +## v0.3 - Release Notes + +### Changes in existing datasets + +* TREE: removed duplicates in TREE views coming from TREE_master and PLOTSIZE_master JOIN for Soro, KROOF and Hyytiala. Replaced entire Soro data with new updated data now available from 1994-2017. +* STAND: corrected values for foliageBiomass_kgha, branchesBiomass_kgha, stemBiomass_kgha and rootBiomass_kgha for Bily Kriz to match unit. Replaced Soro data with new updated including biomass data available from 1994-2017. +* CLIMATE_ISMIPFT: renamed rad_Jcm2day to rad_Jcm2. +* METADATA_CLIMATE_ISIMIPFT: renamed unit of variable rad_Jcm2day from J cm-2 day-1 to J cm-2. CLIMATE_ISIMIP2A: renamed rad_Jcm2day to rad_Jcm2. +* METADATA_CLIMATE_ISIMIP2A: renamed unit of variable rad_Jcm2day from J cm-2 day-1 to J cm-2. CLIMATE_ISIMIP2B: renamed rad_Jcm2day to rad_Jcm2. +* METADATA_CLIMATE_ISIMIP2B: renamed unit of variable rad_Jcm2day from J cm-2 day-1 to J cm-2. CLIMATE_ISIMIP2BLBC: renamed rad_Jcm2day to rad_Jcm2. +* METADATA_CLIMATE_ISIMIP2BLBC: renamed unit of variable rad_Jcm2day from J cm-2 day-1 to J cm-2. CLIMATE_LOCAL: renamed rad_Jcm2day to rad_Jcm2. +* METADATA_CLIMATE_LOCAL: renamed unit of variable rad_Jcm2day from J cm-2 day-1 to J cm-2. +* METADATA_MODIS_MOD17A2: renamed unit of variables gpp_gCm2d and psNet_gm2d from gC m-2 d to gC m-2 d-1. +* SITEDESCRIPTION: minor changes in Soro site description. SOURCE: corrected reference DOI link. + + ## v0.2.0 - Release Notes ### New datasets From e540b87c43270ada3c784aacc78a7a64c52c685e Mon Sep 17 00:00:00 2001 From: Mats Mahnken Date: Mon, 4 May 2020 16:26:34 +0200 Subject: [PATCH 12/17] update vignettes small typo corrections and DOI link changes produced with DB version 0.3 --- ProfoundData/data-raw/ChildDatasetSummary.Rmd | 8 +- ProfoundData/data-raw/PROFOUNDdatabase.Rmd | 6 +- ProfoundData/data-raw/ProfoundData.Rmd | 24 +- ProfoundData/vignettes/PROFOUNDdatabase.html | 19 +- ProfoundData/vignettes/ProfoundData.html | 497 +++++++++--------- 5 files changed, 278 insertions(+), 276 deletions(-) diff --git a/ProfoundData/data-raw/ChildDatasetSummary.Rmd b/ProfoundData/data-raw/ChildDatasetSummary.Rmd index e583405..f1732c7 100644 --- a/ProfoundData/data-raw/ChildDatasetSummary.Rmd +++ b/ProfoundData/data-raw/ChildDatasetSummary.Rmd @@ -11,7 +11,7 @@ df <- df[, !colnames(df) %in% c("source")] rownames(df) <- NULL ``` -The sites parameters were provided by the local site data responsibles. The sites variables that we included in the database are listed in the table below. +The site parameters were provided by the local site data responsibles. The site variables that we included in the database are listed in the table below. ```{r, echo=F, warning = F, message=F} @@ -27,7 +27,7 @@ df <- df[, !colnames(df) %in% c("source")] rownames(df) <- NULL ``` -The sites description were provided by the local site data responsibles. The site description variables that we included in the database are listed in the table below. +The site description was provided by the local site data responsibles. The site description variables that we included in the database are listed in the table below. ```{r, echo=F, warning = F, message=F} @@ -75,7 +75,7 @@ df <- df[, !colnames(df) %in% c("source")] rownames(df) <- NULL ``` -The soil data were provided by the local site data responsibles. The variables that we included in the database are listed in the table below. The data is very heteregenous, therefore not all variables are available for each site. +The soil data were provided by the local site data responsibles. The variables that we included in the database are listed in the table below. The data is very heterogeneous, therefore not all variables are available for each site. ```{r, echo=F, warning = F, message=F} pander(df, adding = 0, missing = '**--**', round = 3, use.hyphening = TRUE, split.cells = 3, split.tables = 200, caption = tableCaption("Description of SOIL variables included in the database.")) @@ -103,7 +103,7 @@ pander(df, adding = 0, missing = '**--**', round = 3, use.hyphening = TRUE, s ## Dataset CLIMATE_LOCAL -The CLIMATE LOCAL data refers to climate data measured at each forest site or meteorological stations close to the site of the forest site. For those forest sites for which the data has been derived from half-hourly [FLUXNET2015](http://fluxnet.fluxdata.org/) data, we also provide the original half-hourly data in the table METEOROLOGICAL. +The CLIMATE LOCAL data refers to climate data measured at each forest site or meteorological stations close to the site of the forest site. For those forest sites for which the data has been derived from half-hourly [FLUXNET2015](http://fluxnet.fluxdata.org/) data, we also provide the original half-hourly data in the table METEOROLOGICAL. When relative humidity was not part of the original data, we calculated it from the vapour pressure deficit and the daily temperatures as diff --git a/ProfoundData/data-raw/PROFOUNDdatabase.Rmd b/ProfoundData/data-raw/PROFOUNDdatabase.Rmd index bf2e0d3..680a2ab 100644 --- a/ProfoundData/data-raw/PROFOUNDdatabase.Rmd +++ b/ProfoundData/data-raw/PROFOUNDdatabase.Rmd @@ -2,7 +2,7 @@ title: "The PROFOUND database" author: "Ramiro Silveyra Gonzalez, Christopher Reyer, Mats Mahnken, Florian Hartig" date: "`r Sys.Date()`" -abstract: "This vignette provides an overview of the Profound databse for benchmarking forest vegetation models, in particular database structure, content, data policy and an overview of each forest site contained in the database. \n \n \n" +abstract: "This vignette provides an overview of the Profound database for benchmarking forest vegetation models, in particular database structure, content, data policy and an overview of each forest site contained in the database. \n \n \n" output: rmarkdown::html_vignette: toc: true @@ -67,9 +67,9 @@ set.seed(1) # Overview -The PROFOUND database (PROFOUND DB) brings together data from a wide range of data sources to evaluate vegetation models and simulate climate impacts at the forest stand scale. It includes 9 forest sites across Europe, and provides for them a site description as well as soil, climate, CO2, Nitrogen deposition, tree-level, forest stand-level and remote sensing data. Moreover, for a subset of 5 sites, also time series of carbon fluxes, energy balances and soil water are available. +The PROFOUND database (PROFOUND DB) brings together data from a wide range of data sources to evaluate vegetation models and simulate climate impacts at the forest stand scale. It includes 9 forest sites across Europe, and provides for them a site description as well as soil, climate, CO2, Nitrogen deposition, tree-level, forest stand-level and remote sensing data. Moreover, for a subset of 5 sites, also time series of carbon fluxes, energy balances and soil water are available. -For more details, see the [ProfoundData website](http://doi.org/10.5880/PIK.2019.008), as well as Reyer et al, The PROFOUND database for evaluating vegetation models and simulating climate impacts on forests, Earth Syst. Sci. Data Discuss., [https://doi.org/10.5194/essd-2019-220](https://doi.org/10.5194/essd-2019-220), in review, 2019. +For more details, see the [ProfoundData website](http://doi.org/10.5880/PIK.2020.006), as well as Reyer et al, The PROFOUND database for evaluating vegetation models and simulating climate impacts on forests, Earth Syst. Sci. Data Discuss., [https://doi.org/10.5194/essd-2019-220](https://doi.org/10.5194/essd-2019-220), in review, 2019. # Data Policy diff --git a/ProfoundData/data-raw/ProfoundData.Rmd b/ProfoundData/data-raw/ProfoundData.Rmd index 10a52c1..d669b5a 100644 --- a/ProfoundData/data-raw/ProfoundData.Rmd +++ b/ProfoundData/data-raw/ProfoundData.Rmd @@ -38,11 +38,11 @@ set.seed(1) # ProfoundData R-package: using the PROFOUND database from R -The ProfoundData package serves as interface to access the [PROFOUND database](PROFOUNDdatabase.html). Three main functions are included to achieve this goal: a browseData function for exploring the database, a getData function for downloading data fromm the database and a plotData function to quickly inspect any variable of the datasets. +The ProfoundData package serves as interface to access the [PROFOUND database](PROFOUNDdatabase.html). Three main functions are included to achieve this goal: a browseData function for exploring the database, a getData function for downloading data from the database and a plotData function to quickly inspect any variable of the datasets. The functions allow to retrieve only data from one site and one dataset at a time. For downloading data of more than one dataset or of more than one site, the function should be called as many times as the number of desired sites or datasets. Additionally, flags and other parameters can be passed to the functions. The package also includes utilities functions to do tasks such as inspecting the data or writing NetCDF files. -To see the suggested ciation for the package, run +To see the suggested citation for the package, run ```{r} library(ProfoundData) @@ -53,24 +53,24 @@ citation("ProfoundData") ## Database download -Profound database is provided in SQLite and can be downloaded either by hand at [http://doi.org/10.5880/PIK.2019.008](http://doi.org/10.5880/PIK.2019.008) or via the +The Profound database is provided in SQLite and can be downloaded either by hand at [http://doi.org/10.5880/PIK.2020.006](http://doi.org/10.5880/PIK.2020.006) or via ```{r, eval = F} sqlfile = downloadDatabase() ``` -Per default, the database is downloaded into the currrent working directory, but you can specify another location in the function. The function returns the current databse location, which can be passed on the the setDB function (see below). +Per default, the database is downloaded into the current working directory, but you can specify another location in the function. The function returns the current database location, which can be passed on to the setDB function (see below). ## Database connection -For using a locally stored database with the ProfoundData package, the first step is to call the *setDB*. The function requires a **valid absolute path to the PROFOUND database**. +For using a locally stored database with the ProfoundData package, the first step is to call *setDB*. The function requires a **valid absolute path to the PROFOUND database**. ```{r, eval = T} myDB <- path.expand("/Users/florian/temp/ProfoundData.sqlite") setDB(myDB) ``` -To check the database connection you can use the use *getDB*, which returns the database path and also informs about the database version. +To check the database connection you can use *getDB*, which returns the database path and also informs about the database version. ```{r, eval = T} getDB() @@ -171,7 +171,7 @@ policy <- browseData(dataset = "POLICY", site = "solling_spruce") ### Data overviews of the available data -The *summarizeData* function allows to obtain data summaries and overviews of the data depending on **mode**. If you choose the mode overview, *summarizeData* will return a data frame with the years and number of observations, the first and last value, and the min and max value, as in the example below. +The *summarizeData* function allows to obtain data summaries and overviews of the data depending on **mode**. If you choose the mode overview, *summarizeData* will return a data frame with the years and number of observations, the first and last value, and the min and max value, as in the example below. ```{r, fig.show='hold', echo=T, message= F, warning=F} data <-summarizeData(dataset = "CLIMATE_LOCAL", site = "bily_kriz", mode = "overview") @@ -412,7 +412,7 @@ data <- getData(dataset = "FLUX", site = "soro", ``` # The plotData function -The plotData function performs a query to the database, downloads the data, applies the desired options (time period, quality flag, etc.) and shapes the final data into a time series for plotting. It requires a dataset name and a site. Check the help files to see what datasets are supported. +The plotData function performs a query to the database, downloads the data, applies the desired options (time period, quality flag, etc.) and shapes the final data into a time series for plotting. It requires a dataset name and a site. Check the help files to see what datasets are supported. ## Normal plotting @@ -426,7 +426,7 @@ Or for TREE data ```{r, fig.show='hold',echo=T, results="hide", message= F, warning=F} plotData(dataset = "TREE", site = "solling_beech", automaticPanels = TRUE) ``` -Note that the argument *automaticPanels* defines whether the plot in a panel. +Note that the argument *automaticPanels* defines whether to plot in a panel. ## Additional options @@ -527,7 +527,7 @@ Hint: Check the last section for further information about SQL syntax's. # The reportDB function -This function makes possible to create reates a site-by-site report of all avalaible data in the PROFOUND database. The summary is created with a rmarkdown document, which is rendered and saved as a html document. The report provdes an exhaustive description and visualization of the PROFOUND database. +This function permits creating a site-by-site report of all avalaible data in the PROFOUND database. The summary is created with a rmarkdown document, which is rendered and saved as a html document. The report provides an exhaustive description and visualization of the PROFOUND database. The function requires a path where to save the html document. If no path is specified, the working directory will be used as output directory. @@ -535,9 +535,9 @@ The function requires a path where to save the html document. If no path is spec reportDB(outDir = tempdir()) ``` -Please note that creating the report it might take several minutes. +Please note that creating the report might take several minutes. -# Using the databse via sql +# Using the database via sql To access the database you can use an SQLite database explorer such as [SQLiteStudio](http://sqlitestudio.pl/). Such software allows to visualize and download data through an interface, as well as writing SQL statements. Further information on SQLite characteristics can be found on the [SQLite website](https://www.sqlite.org/lang.html). Besides, there are plenty of resources about using SQL like [this one](http://www.w3schools.com/sql/default.asp) diff --git a/ProfoundData/vignettes/PROFOUNDdatabase.html b/ProfoundData/vignettes/PROFOUNDdatabase.html index 10d2252..c9410d6 100644 --- a/ProfoundData/vignettes/PROFOUNDdatabase.html +++ b/ProfoundData/vignettes/PROFOUNDdatabase.html @@ -13,7 +13,7 @@ - + The PROFOUND database @@ -213,7 +213,8 @@ code > span.co { color: #888888; font-style: italic; } code > span.ot { color: #007020; } code > span.al { color: #ff0000; font-weight: bold; } -code > span.fu { color: #900; font-weight: bold; } code > span.er { color: #a61717; background-color: #e3d2d2; } +code > span.fu { color: #900; font-weight: bold; } +code > span.er { color: #a61717; background-color: #e3d2d2; } @@ -228,10 +229,10 @@

The PROFOUND database

Ramiro Silveyra Gonzalez, Christopher Reyer, Mats Mahnken, Florian Hartig

-

2020-03-29

+

2020-05-04

Abstract

-

This vignette provides an overview of the Profound databse for benchmarking forest vegetation models, in particular database structure, content, data policy and an overview of each forest site contained in the database.

+

This vignette provides an overview of the Profound database for benchmarking forest vegetation models, in particular database structure, content, data policy and an overview of each forest site contained in the database.

@@ -266,7 +267,7 @@

2020-03-29

Overview

The PROFOUND database (PROFOUND DB) brings together data from a wide range of data sources to evaluate vegetation models and simulate climate impacts at the forest stand scale. It includes 9 forest sites across Europe, and provides for them a site description as well as soil, climate, CO2, Nitrogen deposition, tree-level, forest stand-level and remote sensing data. Moreover, for a subset of 5 sites, also time series of carbon fluxes, energy balances and soil water are available.

-

For more details, see the ProfoundData website, as well as Reyer et al, The PROFOUND database for evaluating vegetation models and simulating climate impacts on forests, Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2019-220, in review, 2019.

+

For more details, see the ProfoundData website, as well as Reyer et al, The PROFOUND database for evaluating vegetation models and simulating climate impacts on forests, Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2019-220, in review, 2019.

Data Policy

@@ -1665,9 +1666,9 @@

Dataset CLIMATE

Total daily precipitation -rad_Jcm2day +rad_Jcm2 REAL -J cm-2 day-1 +J cm-2 Total daily global radiation @@ -3209,7 +3210,7 @@

Dataset MODIS

gpp_gCm2d REAL -gC m-2 d +gC m-2 d-1 Gross Primary Production. Valid range: -375 – 375. Fill value: NA. Spatial resolution 1 km. Temporal resolution: 8-day accumulation. MOD17A2 @@ -3223,7 +3224,7 @@

Dataset MODIS

psNet_gCm2d REAL -gC m-2 d +gC m-2 d-1 Net Photosynthesis (GPP – maintenance respiration). Valid range: -375 – 375. Fill value: NA. Spatial resolution 1 km. Temporal resolution: 8-day accumulation. MOD17A2 diff --git a/ProfoundData/vignettes/ProfoundData.html b/ProfoundData/vignettes/ProfoundData.html index 3a86619..8fc5e76 100644 --- a/ProfoundData/vignettes/ProfoundData.html +++ b/ProfoundData/vignettes/ProfoundData.html @@ -13,7 +13,7 @@ - + The ProfoundData R-package @@ -299,7 +299,8 @@ code > span.co { color: #888888; font-style: italic; } code > span.ot { color: #007020; } code > span.al { color: #ff0000; font-weight: bold; } -code > span.fu { color: #900; font-weight: bold; } code > span.er { color: #a61717; background-color: #e3d2d2; } +code > span.fu { color: #900; font-weight: bold; } +code > span.er { color: #a61717; background-color: #e3d2d2; } @@ -314,7 +315,7 @@

The ProfoundData R-package

Ramiro Silveyra Gonzalez, Christopher Reyer, Mats Mahnken, Florian Hartig

-

2020-03-29

+

2020-05-04

Abstract

This vignette provides an overview of the Profound data R package. For an overview about the database, see the separate vignette PROFOUNDdatabase.

@@ -359,13 +360,13 @@

2020-03-29

  • The queryDB function: parsing your own queries
  • The reportDB function
    • -
  • Using the databse via sql
    • +
  • Using the database via sql

    • ProfoundData R-package: using the PROFOUND database from R

    -

    The ProfoundData package serves as interface to access the PROFOUND database. Three main functions are included to achieve this goal: a browseData function for exploring the database, a getData function for downloading data fromm the database and a plotData function to quickly inspect any variable of the datasets.

    +

    The ProfoundData package serves as interface to access the PROFOUND database. Three main functions are included to achieve this goal: a browseData function for exploring the database, a getData function for downloading data from the database and a plotData function to quickly inspect any variable of the datasets.

    The functions allow to retrieve only data from one site and one dataset at a time. For downloading data of more than one dataset or of more than one site, the function should be called as many times as the number of desired sites or datasets. Additionally, flags and other parameters can be passed to the functions. The package also includes utilities functions to do tasks such as inspecting the data or writing NetCDF files.

    To see the suggested ciation for the package, run

    library(ProfoundData)
@@ -373,14 +374,14 @@ 
    ProfoundData R-package: using the PROFOUND database from R
    
 
    ## 
 ## To cite the 'ProfoundData' package in publications use:
 ## 
-##   Reyer, C. (2019). The PROFOUND Database for evaluating
-##   vegetation models and simulating climate impacts on forest
-##   stands. Submitted to Earth System Science Data.
+##   Reyer, C. (2019). The PROFOUND Database for evaluating vegetation
+##   models and simulating climate impacts on forest stands. Submitted to
+##   Earth System Science Data.
 ## 
-##   Reyer, C., Silveyra Gonzalez, R., Dolos, K., Hartig, F., Hauf,
-##   Y., Noack, M., … Frieler, K. (2019). The PROFOUND database for
-##   evaluating vegetation models and simulating climate impacts on
-##   forests [Data set]. https://doi.org/10.5880/pik.2019.008
+##   Reyer, C., Silveyra Gonzalez, R., Dolos, K., Hartig, F., Hauf, Y.,
+##   Noack, M., … Frieler, K. (2020). The PROFOUND database for evaluating
+##   vegetation models and simulating climate impacts on forests [Data
+##   set]. https://doi.org/10.5880/PIK.2020.006
 ## 
 ## To see these entries in BibTeX format, use 'print(<citation>,
 ## bibtex=TRUE)', 'toBibtex(.)', or set
@@ -390,18 +391,18 @@ 
    ProfoundData R-package: using the PROFOUND database from R
    
 
    First Steps
    
 
    
 
    Database download
    
-
    Profound database is provided in SQLite and can be downloaded either by hand at http://doi.org/10.5880/PIK.2019.008 or via the
    
+
    The Profound database is provided in SQLite and can be downloaded either by hand at http://doi.org/10.5880/PIK.2020.006 or via
    
 
-
    Per default, the database is downloaded into the currrent working directory, but you can specify another location in the function. The function returns the current databse location, which can be passed on the the setDB function (see below).
    
+
    Per default, the database is downloaded into the current working directory, but you can specify another location in the function. The function returns the current database location, which can be passed on to the setDB function (see below).
    
 
    
 
    
 
    Database connection
    
-
    For using a locally stored database with the ProfoundData package, the first step is to call the setDB. The function requires a valid absolute path to the PROFOUND database.
    
-
    myDB <- path.expand("/Users/florian/temp/ProfoundData.sqlite")
+
    For using a locally stored database with the ProfoundData package, the first step is to call setDB. The function requires a valid absolute path to the PROFOUND database.
    
+
-
    To check the database connection you can use the use getDB, which returns the database path and also informs about the database version.
    
+
    To check the database connection you can use getDB, which returns the database path and also informs about the database version.
    
 
-
    ## Database version is 0.2.0
    
+
    ## Database version is 0.3
    
 
    ## [1] "/Users/florian/temp/ProfoundData.sqlite"
    
 
    
 
    
@@ -829,7 +830,7 @@ 
    Data overviews of the available data
    
 
 bily_kriz
 3
-rad_Jcm2day
+rad_Jcm2
 3.706045e+05
 3.871684e+05
 3.418508e+05
@@ -971,7 +972,7 @@ 
    Data overviews of the available data
    
 3
 GFDLESM2M
 historical
-rad_Jcm2day
+rad_Jcm2
 3.780155e+05
 3.823430e+05
 3.557333e+05
@@ -1091,7 +1092,7 @@ 
    Data overviews of the available data
    
 3
 GFDLESM2M
 piControl
-rad_Jcm2day
+rad_Jcm2
 4.141776e+05
 3.772647e+05
 3.423868e+05
@@ -1211,7 +1212,7 @@ 
    Data overviews of the available data
    
 3
 GFDLESM2M
 rcp2p6
-rad_Jcm2day
+rad_Jcm2
 3.780991e+05
 3.964951e+05
 3.529131e+05
@@ -1331,7 +1332,7 @@ 
    Data overviews of the available data
    
 3
 GFDLESM2M
 rcp4p5
-rad_Jcm2day
+rad_Jcm2
 4.187450e+05
 3.932176e+05
 3.658412e+05
@@ -1451,7 +1452,7 @@ 
    Data overviews of the available data
    
 3
 GFDLESM2M
 rcp6p0
-rad_Jcm2day
+rad_Jcm2
 3.782895e+05
 3.776877e+05
 3.467031e+05
@@ -1571,7 +1572,7 @@ 
    Data overviews of the available data
    
 3
 GFDLESM2M
 rcp8p5
-rad_Jcm2day
+rad_Jcm2
 3.672316e+05
 3.959328e+05
 3.550359e+05
@@ -1691,7 +1692,7 @@ 
    Data overviews of the available data
    
 3
 HadGEM2ES
 historical
-rad_Jcm2day
+rad_Jcm2
 4.270536e+05
 3.921624e+05
 3.381196e+05
@@ -1811,7 +1812,7 @@ 
    Data overviews of the available data
    
 3
 HadGEM2ES
 piControl
-rad_Jcm2day
+rad_Jcm2
 4.408675e+05
 3.919564e+05
 3.673516e+05
@@ -1931,7 +1932,7 @@ 
    Data overviews of the available data
    
 3
 HadGEM2ES
 rcp2p6
-rad_Jcm2day
+rad_Jcm2
 3.877499e+05
 4.497789e+05
 3.776577e+05
@@ -2051,7 +2052,7 @@ 
    Data overviews of the available data
    
 3
 HadGEM2ES
 rcp4p5
-rad_Jcm2day
+rad_Jcm2
 4.036507e+05
 4.304601e+05
 3.571120e+05
@@ -2171,7 +2172,7 @@ 
    Data overviews of the available data
    
 3
 HadGEM2ES
 rcp6p0
-rad_Jcm2day
+rad_Jcm2
 4.420520e+05
 4.397051e+05
 3.743635e+05
@@ -2291,7 +2292,7 @@ 
    Data overviews of the available data
    
 3
 HadGEM2ES
 rcp8p5
-rad_Jcm2day
+rad_Jcm2
 4.058588e+05
 4.509622e+05
 3.958738e+05
@@ -2411,7 +2412,7 @@ 
    Data overviews of the available data
    
 3
 IPSLCM5ALR
 historical
-rad_Jcm2day
+rad_Jcm2
 4.301708e+05
 3.964781e+05
 3.530505e+05
@@ -2531,7 +2532,7 @@ 
    Data overviews of the available data
    
 3
 IPSLCM5ALR
 piControl
-rad_Jcm2day
+rad_Jcm2
 4.056774e+05
 4.117241e+05
 3.646121e+05
@@ -2651,7 +2652,7 @@ 
    Data overviews of the available data
    
 3
 IPSLCM5ALR
 rcp2p6
-rad_Jcm2day
+rad_Jcm2
 4.192525e+05
 4.093297e+05
 3.755701e+05
@@ -2771,7 +2772,7 @@ 
    Data overviews of the available data
    
 3
 IPSLCM5ALR
 rcp4p5
-rad_Jcm2day
+rad_Jcm2
 4.138551e+05
 4.213282e+05
 3.825715e+05
@@ -2891,7 +2892,7 @@ 
    Data overviews of the available data
    
 3
 IPSLCM5ALR
 rcp6p0
-rad_Jcm2day
+rad_Jcm2
 4.427263e+05
 4.408261e+05
 3.666051e+05
@@ -3011,7 +3012,7 @@ 
    Data overviews of the available data
    
 3
 IPSLCM5ALR
 rcp8p5
-rad_Jcm2day
+rad_Jcm2
 3.585790e+05
 4.184550e+05
 3.585790e+05
@@ -3131,7 +3132,7 @@ 
    Data overviews of the available data
    
 3
 MIROC5
 historical
-rad_Jcm2day
+rad_Jcm2
 4.319353e+05
 4.356081e+05
 3.327256e+05
@@ -3251,7 +3252,7 @@ 
    Data overviews of the available data
    
 3
 MIROC5
 piControl
-rad_Jcm2day
+rad_Jcm2
 4.340896e+05
 4.622626e+05
 4.122271e+05
@@ -3371,7 +3372,7 @@ 
    Data overviews of the available data
    
 3
 MIROC5
 rcp2p6
-rad_Jcm2day
+rad_Jcm2
 4.015045e+05
 4.496680e+05
 3.932749e+05
@@ -3491,7 +3492,7 @@ 
    Data overviews of the available data
    
 3
 MIROC5
 rcp4p5
-rad_Jcm2day
+rad_Jcm2
 3.864426e+05
 4.578805e+05
 3.864426e+05
@@ -3611,7 +3612,7 @@ 
    Data overviews of the available data
    
 3
 MIROC5
 rcp6p0
-rad_Jcm2day
+rad_Jcm2
 4.104626e+05
 4.678674e+05
 4.053620e+05
@@ -3731,7 +3732,7 @@ 
    Data overviews of the available data
    
 3
 MIROC5
 rcp8p5
-rad_Jcm2day
+rad_Jcm2
 4.216762e+05
 4.793708e+05
 3.965346e+05
@@ -4394,7 +4395,7 @@ 
    CLIMATE_LOCAL
    
 p_mm
 relhum_percent
 airpress_hPa
-rad_Jcm2day
+rad_Jcm2
 wind_ms
 
 
@@ -4536,7 +4537,7 @@ 
    CLIMATE_ISIMIP
    
 p_mm
 relhum_percent
 airpress_hPa
-rad_Jcm2day
+rad_Jcm2
 wind_ms
 
 
@@ -4870,7 +4871,7 @@ 
    CLIMATE_ISIMIP
    
 p_mm
 relhum_percent
 airpress_hPa
-rad_Jcm2day
+rad_Jcm2
 wind_ms
 
 
@@ -4994,226 +4995,226 @@ 
    FLUX
    
 bily_kriz
 3
 2000
--38.78573
--39.59809
-15.209695
-15.86517
-97.83216
-2.408624
-102.09309
-2.440183
-138.66666
-3.967526
-145.19560
-4.126893
-58.23775
-7.234624
-67.81385
-7.632900
-107.9271
-4.083021
-110.7110
-4.281572
+-3.878573
+-3.959809
+1.5209695
+1.586517
+9.783216
+0.2408624
+10.209309
+0.2440183
+13.866666
+0.3967526
+14.519560
+0.4126893
+5.823775
+0.7234624
+6.781385
+0.7632900
+10.79271
+0.4083021
+11.07110
+0.4281572
 
 
 bily_kriz
 3
 2001
--32.77164
--36.29736
-11.523480
-11.77295
-51.97413
-2.064628
-54.90414
-2.072944
-86.48057
-3.049352
-99.01904
-3.346192
-77.40778
-3.178191
-78.30948
-4.676769
-116.1664
-2.044694
-112.0838
-2.611838
+-3.277164
+-3.629736
+1.1523480
+1.177295
+5.197413
+0.2064628
+5.490414
+0.2072944
+8.648057
+0.3049351
+9.901904
+0.3346192
+7.740778
+0.3178191
+7.830948
+0.4676770
+11.61664
+0.2044694
+11.20838
+0.2611837
 
 
 bily_kriz
 3
 2002
--36.58319
--37.97092
-9.151159
-11.09704
-63.96572
-1.678422
-59.06654
-2.507639
-103.28778
-2.665789
-98.69803
-3.657584
-73.20840
-3.276043
-54.78220
-3.948784
-114.9007
-2.011733
-121.0953
-2.635683
+-3.658319
+-3.797092
+0.9151159
+1.109704
+6.396572
+0.1678421
+5.906655
+0.2507639
+10.328778
+0.2665789
+9.869803
+0.3657584
+7.320840
+0.3276043
+5.478220
+0.3948784
+11.49007
+0.2011733
+12.10953
+0.2635683
 
 
 bily_kriz
 3
 2003
--91.17122
--90.71734
-11.427876
-12.15067
-113.99077
-2.434624
-113.01510
-2.925302
-205.16419
-4.039363
-203.70148
-5.157969
-85.56300
-3.735950
-93.86853
-5.552283
-177.0804
-2.699202
-186.4835
-4.224106
+-9.117121
+-9.071734
+1.1427876
+1.215067
+11.399078
+0.2434624
+11.301510
+0.2925302
+20.516419
+0.4039363
+20.370148
+0.5157969
+8.556300
+0.3735950
+9.386853
+0.5552283
+17.70804
+0.2699202
+18.64835
+0.4224106
 
 
 bily_kriz
 3
 2004
--84.57856
--83.56907
-27.092536
-39.38024
-63.33830
-1.440231
-63.31870
-1.718276
-146.77583
-3.967510
-150.77614
-5.129495
-103.02871
-4.847279
-93.67065
-5.601932
-174.2867
-4.021578
-182.9802
-4.963656
+-8.457856
+-8.356907
+2.7092536
+3.938024
+6.333830
+0.1440231
+6.331870
+0.1718276
+14.677583
+0.3967510
+15.077614
+0.5129495
+10.302871
+0.4847279
+9.367065
+0.5601932
+17.42867
+0.4021577
+18.29802
+0.4963656
 
 
 bily_kriz
 3
 2005
--79.08237
--82.49708
-8.661794
-12.04517
-52.72831
-2.710158
-59.54222
-2.576154
-134.15438
-5.274783
-142.76343
-5.185471
-60.53836
-6.489167
-68.58801
-8.837533
-182.7498
-5.116223
-198.8996
-5.399609
-
-
-bily_kriz
-3
-2006
--64.37540
--65.07293
-24.926481
-27.89668
-78.65130
-2.017064
-79.05678
-1.689278
-144.79195
-4.331742
-146.42456
-3.842385
-80.37568
-5.130079
-83.52022
-4.773277
-191.4361
-3.560452
-187.8914
-3.345761
+-7.908237
+-8.249708
+0.8661794
+1.204516
+5.272831
+0.2710158
+5.954222
+0.2576154
+13.415438
+0.5274783
+14.276343
+0.5185471
+6.053836
+0.6489167
+6.858801
+0.8837533
+18.27498
+0.5116223
+19.88996
+0.5399609
+
+
+bily_kriz
+3
+2006
+-6.437540
+-6.507293
+2.4926481
+2.789668
+7.865130
+0.2017064
+7.905678
+0.1689278
+14.479195
+0.4331742
+14.642456
+0.3842385
+8.037567
+0.5130079
+8.352022
+0.4773277
+19.14361
+0.3560452
+18.78914
+0.3345761
 
 
 bily_kriz
 3
 2007
--75.93613
--74.22389
-31.515550
-27.52587
-110.94775
-3.409521
-95.03352
-3.798527
-184.80026
-4.826859
-181.54589
-5.190658
-94.69553
-7.085845
-69.07559
-7.696311
-193.1778
-3.219596
-186.9977
-4.493286
+-7.593613
+-7.422389
+3.1515550
+2.752587
+11.094775
+0.3409521
+9.503352
+0.3798527
+18.480026
+0.4826859
+18.154589
+0.5190658
+9.469553
+0.7085845
+6.907559
+0.7696311
+19.31778
+0.3219596
+18.69977
+0.4493286
 
 
 bily_kriz
 3
 2008
--83.49085
--82.75882
-36.022763
-29.02647
-100.60264
-1.775322
-93.38333
-1.995026
-181.80827
-3.722435
-181.59439
-3.912224
-104.22396
-8.265871
-102.95398
-6.246577
-202.5231
-4.299510
-204.7656
-3.643597
+-8.349085
+-8.275882
+3.6022763
+2.902647
+10.060264
+0.1775322
+9.338333
+0.1995026
+18.180827
+0.3722435
+18.159439
+0.3912224
+10.422396
+0.8265871
+10.295398
+0.6246577
+20.25231
+0.4299510
+20.47656
+0.3643597
 
 
 
@@ -5275,7 +5276,7 @@ 
    SITES
    
 
    A text description can be obtained from SITEDESCRIPTION
    
 
 
-
    ## [1] "The ICOS site Sorø (DK-Sor in the FLUXNET and ICOS data bases) is located in Denmark at an elevation of 40 m.a.s.l.. The climate is warm temperate and fully humid with a mean annual temperature of 9°C and annual precipitation sum of 774 mm during the period 1996-2010. The soil has been classified as an Alfisols/Molisols. Potential natural vegetation is deciduous broad-leaved forest dominated by Fagus sylvatica. Other species occurring in the area are Fraxinus excelsior, Larix decidua, Picea abies, Quercus spp., Acer spp. However, the region is mostly used as cropland. Data on tree DBH are reconstructed from tree ring measurement (Babst et al. 2014) and historical management information for the time period from 1944 to 2010. The mean DBH of this Fagus sylvatica stand was 29 cm in the year 2010. More information about the site can be found in Ladekarl (2001), Pilegaard et al. (2003, 2011), and Wu et al. (2013)."
    
+
    ## [1] "The ICOS site Sorø (DK-Sor in the FLUXNET and ICOS data bases) is located in Denmark at an elevation of 40 m.a.s.l.. The climate is warm temperate and fully humid with a mean annual temperature of 9°C and annual precipitation sum of 774 mm during the period 1996-2010. The soil has been classified as an Alfisols/Molisols. Potential natural vegetation is deciduous broad-leaved forest dominated by Fagus sylvatica. Other species occurring in the area are Fraxinus excelsior, Larix decidua, Picea abies, Quercus spp., Acer spp. However, the region is mostly used as cropland. Data on tree DBH are reconstructed from tree ring measurement (Babst et al. 2014) and historical management information for the time period from 1994 to 2017. The mean DBH of this Fagus sylvatica stand was 41 cm in the year 2017. More information about the site can be found in Ladekarl (2001), Pilegaard et al. (2003, 2011), and Wu et al. (2013)."

    DATASETS

    @@ -5292,7 +5293,7 @@

    collapse

    ##  [1] "record_id"      "site"           "site_id"        "date"          
 ##  [5] "forcingDataset" "day"            "mo"             "year"          
 ##  [9] "tmax_degC"      "tmean_degC"     "tmin_degC"      "p_mm"          
-## [13] "relhum_percent" "airpress_hPa"   "rad_Jcm2day"    "wind_ms"
    +## [13] "relhum_percent" "airpress_hPa" "rad_Jcm2" "wind_ms"

    We recommend to unset collapse when downloading SOIL data because in many cases SOIL is a collection of tables.

    @@ -5329,7 +5330,7 @@

    forcingDataset, forcingCondition

    p_mm relhum_percent airpress_hPa -rad_Jcm2day +rad_Jcm2 wind_ms @@ -5471,7 +5472,7 @@

    forcingDataset, forcingCondition

    p_mm relhum_percent airpress_hPa -rad_Jcm2day +rad_Jcm2 wind_ms @@ -5728,10 +5729,10 @@

    The plotData function

    Normal plotting

    A simple plot call looks like

    -

    +

    Or for TREE data

    -

    Note that the argument automaticPanels defines whether the plot in a panel.

    +

    Note that the argument automaticPanels defines whether to plot in a panel.

     -

    +

    @@ -5802,13 +5803,13 @@

    The queryDB function: parsing your own queries

    The reportDB function

    -

    This function makes possible to create reates a site-by-site report of all avalaible data in the PROFOUND database. The summary is created with a rmarkdown document, which is rendered and saved as a html document. The report provdes an exhaustive description and visualization of the PROFOUND database.

    +

    This function permits creating a site-by-site report of all avalaible data in the PROFOUND database. The summary is created with a rmarkdown document, which is rendered and saved as a html document. The report provides an exhaustive description and visualization of the PROFOUND database.

    The function requires a path where to save the html document. If no path is specified, the working directory will be used as output directory.

    -

    Please note that creating the report it might take several minutes.

    +

    Please note that creating the report might take several minutes.

    -
    -

    Using the databse via sql

    +
    +

    Using the database via sql

    To access the database you can use an SQLite database explorer such as SQLiteStudio. Such software allows to visualize and download data through an interface, as well as writing SQL statements. Further information on SQLite characteristics can be found on the SQLite website. Besides, there are plenty of resources about using SQL like this one

    From 3b0a299c21bc07ddf09e180180176aef606c28b2 Mon Sep 17 00:00:00 2001 From: Mats Mahnken Date: Mon, 4 May 2020 16:27:33 +0200 Subject: [PATCH 13/17] minor changes of typo and DOI link changed DOI link for new DB version 0.3 --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index aee3b75..6a7423d 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # The Profound dataset for checking and benchmarking of dynamic vegetation models -The PROFOUND database is a collection of data for calibrating, validating and benchmarking dynamic vegetation models, created by [Cost Action FP1304 PROFOUND](https://twitter.com/FP1304Profound). The database itself, including document and description of the dasta, is hosted by the Potsdam Institute for Climate Research [http://doi.org/10.5880/PIK.2019.008](http://doi.org/10.5880/PIK.2019.008). You can dowload the database either there, or, via the R pacakge (see below). The source code that was used to create the database is available [here](https://github.com/COST-FP1304-PROFOUND/ProfoundData/tree/master/PROFOUND%20database). +The PROFOUND database is a collection of data for calibrating, validating and benchmarking dynamic vegetation models, created by [Cost Action FP1304 PROFOUND](https://twitter.com/FP1304Profound). The database itself, including documentation and description of the data, is hosted by the Potsdam Institute for Climate Research [http://doi.org/10.5880/PIK.2020.006](http://doi.org/10.5880/PIK.2020.006). You can download the database either there, or, via the R package (see below). The source code that was used to create the database is available [here](https://github.com/COST-FP1304-PROFOUND/ProfoundData/tree/master/PROFOUND%20database). ## Installing the ProfoundData R package @@ -17,7 +17,7 @@ devtools::install_github(repo = "COST-FP1304-PROFOUND/ProfoundData", subdir = "ProfoundData", dependencies = T, build_vignettes = T) ``` -Below the status of the automatic Travis CI tests on the master branch (if this doesn load see [here](https://travis-ci.org/COST-FP1304-PROFOUND/ProfoundData)) +Below the status of the automatic Travis CI tests on the master branch (if this doesn't load see [here](https://travis-ci.org/COST-FP1304-PROFOUND/ProfoundData)) [![Build Status](https://travis-ci.org/COST-FP1304-PROFOUND/ProfoundData.svg?branch=master)](https://travis-ci.org/COST-FP1304-PROFOUND/ProfoundData) From 20cab2be17e5c5d8fc4f654083f734f50e16b98b Mon Sep 17 00:00:00 2001 From: Mats Mahnken Date: Mon, 4 May 2020 16:28:37 +0200 Subject: [PATCH 14/17] update download link for sqlite DB include new download link for DB version 0.3 --- ProfoundData/R/registerDatabaseFunctions.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ProfoundData/R/registerDatabaseFunctions.R b/ProfoundData/R/registerDatabaseFunctions.R index 45efc4c..a997677 100644 --- a/ProfoundData/R/registerDatabaseFunctions.R +++ b/ProfoundData/R/registerDatabaseFunctions.R @@ -66,7 +66,7 @@ downloadDatabase<- function(location=NULL){ #if(is.null(location)) location = choose_directory() if(is.null(location)) location = getwd() file = paste(location, "/ProfoundData.zip", sep = "") - download.file("http://www.pik-potsdam.de/data/doi/10.5880/PIK.2019.008/ProfoundData.zip" + download.file("http://www.pik-potsdam.de/data/doi/10.5880/PIK.2020.006/ProfoundData.zip" , file) if(file.exists(file)) message("download successfull, trying to unzip. This may not work on some operating systems. In this case, locate the downloaded file and unzip by hand.") From bccba0e2d8b2751122e2b559d2185e98ffc356ff Mon Sep 17 00:00:00 2001 From: Mats Mahnken Date: Mon, 4 May 2020 16:35:28 +0200 Subject: [PATCH 15/17] update release notes for v 0.3.0 --- ProfoundData/NEWS.md | 18 ++++++------------ 1 file changed, 6 insertions(+), 12 deletions(-) diff --git a/ProfoundData/NEWS.md b/ProfoundData/NEWS.md index cd187bb..0eb8475 100644 --- a/ProfoundData/NEWS.md +++ b/ProfoundData/NEWS.md @@ -1,24 +1,18 @@ -# ProfoundData 0.2.2 - -New features - -- - -Major changes - -- None +# ProfoundData 0.3.0 Minor changes -- Add +- renamed variable "Jcm2day" to "Jcm2" +- updated DOI and download links to reference to DB version 0.3 +- minor change to plotting TREE variables Bugfixes -- Add, ideally with issue / commit +- corrected flux unit conversion error in summarizeData() (see commit 3dfa079142654780a9bb74da8cca3754bf0c4f26) # ProfoundData 0.2.1 -small updates and improcement of user-experience +small updates and improvement of user-experience # ProfoundData 0.2.0 From c5a6107bfca5190de37ccc05a641e5d735a3da95 Mon Sep 17 00:00:00 2001 From: Mats Mahnken Date: Mon, 4 May 2020 16:36:55 +0200 Subject: [PATCH 16/17] update version number and date --- ProfoundData/DESCRIPTION | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ProfoundData/DESCRIPTION b/ProfoundData/DESCRIPTION index 8e4e432..88cc50f 100644 --- a/ProfoundData/DESCRIPTION +++ b/ProfoundData/DESCRIPTION @@ -1,7 +1,7 @@ Package: ProfoundData Title: Downloading and Exploring Data from the PROFOUND Database -Version: 0.2.1 -Date: 2020-03-13 +Version: 0.3.0 +Date: 2020-05-04 Authors@R: c(person("Ramiro", "Silveyra Gonzalez", email = "rasilgon@gmail.com", role = c("aut")), person("Christopher", "Reyer", email = "reyer@pik-potsdam.de", role = c("aut")), person("Mahnken", "Mats", email = "mahnken@pik-potsdam.de", role = c("aut")), From 6d1c3a371664a650eb3b837b2c9e0b9d967e6a36 Mon Sep 17 00:00:00 2001 From: Mats Mahnken Date: Wed, 27 May 2020 15:39:46 +0200 Subject: [PATCH 17/17] update citation update year and DOI link of DB citation --- ProfoundData/inst/CITATION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ProfoundData/inst/CITATION b/ProfoundData/inst/CITATION index b28c0a4..88470f4 100644 --- a/ProfoundData/inst/CITATION +++ b/ProfoundData/inst/CITATION @@ -21,5 +21,5 @@ citEntry( author = "Reyer, Christopher and Silveyra Gonzalez, Ramiro and Dolos, Klara and Hartig, Florian and Hauf, Ylva and Noack, Matthias and Lasch-Born, Petra and Rötzer, Thomas and Pretzsch, Hans and Meesenburg, Henning and Fleck, Stefan and Wagner, Markus and Bolte, Andreas and Sanders, Tanja and Kolari, Pasi and Mäkelä, Annikki and Vesala, Timo and Mammarella, Ivan and Pumpanen, Jukka and Matteucci, Giorgio and Collalti, Alessio and D’Andrea, Ettore and Foltýnová, Lenka and Krejza, Jan and Ibrom, Andreas and Pilegaard, Kim and Loustau, Denis and Bonnefond, Jean-Marc and Berbigier, Paul and Picart, Delphine and Lafont, Sébastien and Dietze, Michael and Cameron, David and Vieno, Massimo and Tian, Hanqin and Palacios, Alicia and Cicuendez, Victor and Recuero, Laura and Wieze, Klaus and Büchner, Matthias and Lange, Stefan and Volkholz, Jan and Kim, Hyungjun and Weedon, Graham and Sheffield, Justin and Vega del Valle, Iliusi and Suckow, Felicitas and Horemans, Joanna and Martel, Simon and Bohn, Friedrich and Steinkamp, Jörg and Chikalanov, Alexandre and Mahnken, Mats and Gutsch, Martin and Trotta, Carlo and Babst, Flurin and Frieler, Katja", year = "2020", doi = "10.5880/PIK.2020.006", - textVersion = "Reyer, C., Silveyra Gonzalez, R., Dolos, K., Hartig, F., Hauf, Y., Noack, M., … Frieler, K. (2019). The PROFOUND database for evaluating vegetation models and simulating climate impacts on forests [Data set]. https://doi.org/10.5880/pik.2019.008" + textVersion = "Reyer, C., Silveyra Gonzalez, R., Dolos, K., Hartig, F., Hauf, Y., Noack, M., … Frieler, K. (2020). The PROFOUND database for evaluating vegetation models and simulating climate impacts on forests [Data set]. http://doi.org/10.5880/PIK.2020.006" ) \ No newline at end of file