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Haffenden Austin
landclimSetup
Commits
68233032
Commit
68233032
authored
Oct 30, 2017
by
Haffenden Austin
Browse files
Initial commit to gitlab
parents
Changes
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"contents" : "#' @title Script to create and check the Landclim SED climate files from a\n#' climate list\n#' @description This script takes a list of climate data frames with\n#' each element in the form:\n#' x (lon), y (lat), year, temperature (jan - dec),\n#' precipitiation (jan - dec) and creates the necessary spatially\n#' explicit data files (SED) for landclim\n#' @param\n#' @param\n#' @return NULL\n#' @keywords CoFoLaMo, Dischma, spin-up, climate\n#' @author Austin Haffenden\n#' @example /don't run {}\n#'\nSED_climate_from_list <- function(clim_list, \n latitude, \n ref_elev, \n file_prefix, \n clim_dir, \n start_file_number = 0) { # number you want the years to start at\n \n save_clim <- function(list_no, start_file_number){\n \n curr_clim <- clim_list[[list_no]]\n #print(curr_clim[1,])\n \n #curr_year <- unique(curr_clim$year)\n #lc_year <- curr_year - min_year + year_offset\n lc_year <- (list_no-1) + start_file_number\n # cat(\"list_no is: \", list_no, \"\\n\")\n # cat(\"start_file_number is: \", start_file_number, \"\\n\")\n # cat(\"lc_year is: \", lc_year, \"\\n\")\n # stop()\n\n curr_file <- file.path(clim_dir, paste0(paste(file_prefix, lc_year, sep = \"_\"), \".txt\"))\n cat(curr_file, \"\\n\")\n con <- file(curr_file, open = \"wt\")\n\n writeLines(\"#header\tinfo#\", con)\n writeLines(paste(latitude, \"#average latitude of the sites -\tused\tfor\tcacluating\tdrought\tindex\tin\tmodel\tbugmann#\"), con)\n writeLines(paste(ref_elev, \"#reference elevation#\"), con)\n writeLines(\"#\tmean\tmonthly\ttemperature\t?C\ttotal\tmonthly\tprecipitation\tmm\t#\", con)\n writeLines(\"#\tx y year jan\tfeb\tmarz\tapril\tmai\tjune\tjuly\taug\tsept\toct\tnov\tdec\tjan\tfeb\tmarz\tapril\tmai\tjune\tjuly\taug\tsept\toct\tnov\tdec\t#\", con)\n\n write.table(as.matrix(curr_clim),\n #file = file.path(clim_dir, paste0(paste(file_prefix, i-1, sep = \"_\"), \".txt\") ),\n file = con,\n row.names = FALSE, col.names = FALSE,\n append = TRUE)\n close(con)\n \n }\n \n # now just for test to call function\n # years <- unique(clim_list$year) \n # min_year <- min(years)\n \n #doParallel::registerDoParallel(cores = 3)\n #plyr::ddply(clim_list, ~ year, save_clim, min_year) \n #.parallel = TRUE)\n \n list_levels <- seq(1, length(clim_list), 1)\n \n # start_no <- start_file_number\n # return(start_no)\n lapply(list_levels, save_clim, start_file_number)\n \n return(1)\n}\n\n\n",
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"contents" : "#' @title Script to create and check the Landclim SED climate files from a\n#' climate data frame\n#' @description This script takes a climate data frame in the form:\n#' x (lon), y (lat), year, temperature (jan - dec),\n#' precipitiation (jan - dec) and creates the necessary spatially\n#' explicit data files (SED) for landclim\n#' @param\n#' @param\n#' @return NULL\n#' @keywords CoFoLaMo, Dischma, spin-up, climate\n#' @author Austin Haffenden\n#' @example /don't run {}\n#'\nSED_climate_from_dataframe <- function(clim_file, \n latitude, \n ref_elev, \n file_prefix, \n clim_dir, \n year_offset = 0) { # number you want the years to start at\n \n save_clim <- function(curr_clim, min_year){\n \n curr_year <- unique(curr_clim$year)\n lc_year <- curr_year - min_year + year_offset\n \n curr_file <- file.path(clim_dir, paste0(paste(file_prefix, lc_year, sep = \"_\"), \".txt\"))\n cat(curr_file, \"\\n\")\n con <- file(curr_file, open = \"wt\")\n\n writeLines(\"#header\tinfo#\", con)\n writeLines(paste(latitude, \"#average latitude of the sites -\tused\tfor\tcacluating\tdrought\tindex\tin\tmodel\tbugmann#\"), con)\n writeLines(paste(ref_elev, \"#reference elevation#\"), con)\n writeLines(\"#\tmean\tmonthly\ttemperature\t?C\ttotal\tmonthly\tprecipitation\tmm\t#\", con)\n writeLines(\"#\tx y year jan\tfeb\tmarz\tapril\tmai\tjune\tjuly\taug\tsept\toct\tnov\tdec\tjan\tfeb\tmarz\tapril\tmai\tjune\tjuly\taug\tsept\toct\tnov\tdec\t#\", con)\n\n write.table(as.matrix(curr_clim),\n #file = file.path(clim_dir, paste0(paste(file_prefix, i-1, sep = \"_\"), \".txt\") ),\n file = con,\n row.names = FALSE, col.names = FALSE,\n append = TRUE)\n close(con)\n \n }\n \n # now just for test to call function\n years <- unique(clim_file$year) \n #return(years)\n min_year <- min(years)\n \n #doParallel::registerDoParallel(cores = 3)\n plyr::ddply(clim_file, ~ year, save_clim, min_year) \n #.parallel = TRUE)\n return(1)\n}\n\n\n",
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"contents" : "#' @title Creates teh simulation file\n#' @description Requires a base_SED_ctl.xml file to be in the xml dir\n#' @param\n#' @param\n#' @return NULL\n#' @keywords CoFoLaMo, Dischma, spin-up, climate\n#' @author Austin Haffenden\n#' @example /don't run {}\n#'\ncreate_SED_sim_file <- function(sim_simulation_dir, \n sim_xml_dir,\n file_root) {\n \n dir.create(sim_simulation_dir)\n \n base_SED_ctl <- XML::xmlRoot(XML::xmlTreeParse(file.path(sim_xml_dir, \"base_SED_ctl.xml\")))\n \n XML::xmlValue(XML::xmlChildren(base_SED_ctl)[[\"climate\"]][[\"fileNameStructure\"]]) <- paste0(\"../climate/\", file_root, \"/\", file_root, \"_{year}.txt\")\n \n XML::xmlValue(XML::xmlChildren(base_SED_ctl)[[\"speciesAttributes\"]]) <- paste0(\"../xml_input/\", file_root, \"_species.xml\")\n XML::xmlValue(XML::xmlChildren(base_SED_ctl)[[\"treeInitState\"]]) <- paste0(\"../initialstate/\", file_root, \"_tree_init.csv\")\n \n XML::xmlValue(XML::xmlChildren(base_SED_ctl)[[\"landtypePars\"]]) <- paste0(\"../xml_input/landType_noregeneration.xml\")\n \n XML::xmlValue(XML::xmlChildren(base_SED_ctl)[[\"landMask\"]]) <- paste0(\"../landscape/\", file_root, \"/\",\"SED_landtype.asc\")\n XML::xmlValue(XML::xmlChildren(base_SED_ctl)[[\"soilDepth\"]]) <- paste0(\"../landscape/\", file_root, \"/\",\"SED_soildepth.asc\")\n XML::xmlValue(XML::xmlChildren(base_SED_ctl)[[\"slope\"]]) <- paste0(\"../landscape/\", file_root, \"/\",\"SED_slope.asc\")\n XML::xmlValue(XML::xmlChildren(base_SED_ctl)[[\"aspect\"]]) <- paste0(\"../landscape/\", file_root, \"/\",\"SED_aspect.asc\")\n XML::xmlValue(XML::xmlChildren(base_SED_ctl)[[\"elevation\"]]) <- paste0(\"../landscape/\", file_root, \"/\", \"SED_elevation.asc\")\n XML::xmlValue(XML::xmlChildren(base_SED_ctl)[[\"availableNitrogen\"]]) <- paste0(\"../landscape/\", file_root, \"/\",\"SED_nitrogen.asc\")\n XML::xmlValue(XML::xmlChildren(base_SED_ctl)[[\"landtype\"]]) <- paste0(\"../landscape/\", file_root, \"/\",\"SED_landtype.asc\")\n \n XML::xmlValue(XML::xmlChildren(base_SED_ctl)[[\"output\"]][[\"path\"]]) <- paste0(\"../output/\", file_root)\n XML::xmlValue(XML::xmlChildren(base_SED_ctl)[[\"iterations\"]]) <- 1\n XML::saveXML(base_SED_ctl, file = file.path(sim_simulation_dir, paste0(file_root, \"_ctl.xml\")))\n \n \n}",
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.Rproj.user/49F8FBDB/unsaved-notebooks/3AAC32CF/1/cqbrv71jjoyaj/000002.csv
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"0","#detach(""package:landclimGrowth"", unload = TRUE) # during package building"
"0","library(landclimGrowth)"
"0","library(landclimCalibration)"
"0","library(rhelpers)"
"0","set_paths()"
"0","root_dir <- c(""/home/austin/partage/austin.haffenden/Private/landclim/landclim_calibration/TG14_one_sp"")"
.Rproj.user/49F8FBDB/unsaved-notebooks/3AAC32CF/1/csetup_chunk/000002.csv
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"0","knitr::opts_chunk$set(echo = TRUE)"
.Rproj.user/shared/notebooks/paths
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/home/austin/Desktop/SED_climate_from_list.R="30D49998"
/media/austin/DATADRIVE1/git_repos/code_working/1. data_preparation/Claro/Claro_landscape_products.R="713372D"
/media/austin/DATADRIVE1/git_repos/code_working/1. data_preparation/IFN/ifn_download_processing.R="AF31BFBD"
/media/austin/DATADRIVE1/git_repos/code_working/1. data_preparation/LAI/fra_lai_nasa.R="B0522104"
/media/austin/DATADRIVE1/git_repos/code_working/1. data_preparation/LAI/initial_graphs.R="7CE87914"
/media/austin/DATADRIVE1/git_repos/code_working/1. data_preparation/LAI/sonohat_forrestser.R="45CEB67F"
/media/austin/DATADRIVE1/git_repos/code_working/2. Landclim_setup/IFN_input_data_preparation.R="DEABC03B"
/media/austin/DATADRIVE1/git_repos/code_working/2. Landclim_setup/TG14_plot_setup_for_LC_growth_calibration_one_sp.R="31D030E3"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/IFN_forrester_foliage_pars.R="5E56B539"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/SED_climate_from_dataframe.R="88830A42"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/SED_climate_from_list.R="AFCB20F3"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/add_to_init_file.R="1C6414CD"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/check_SED_files.R="D05132B"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/create_IFN_species_pars.R="30B99465"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/create_SED_XML_species.R="FAA88A7D"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/create_SED_climate_file.R="7602A2B8"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/create_SED_files.R="99D18415"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/create_SED_initialstate_file.R="A5788C35"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/create_SED_raster.R="3BE94EC9"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/create_SED_sim_file.R="7C055F16"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/create_harvest_pars.R="DA1A4702"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/create_tree_init_params.R="6D35DD5"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/get_climate_fm_ISIMIP_stk.R="F5D9B72F"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/get_ifn_climate.R="B548EF8E"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/get_lapse_rates.R="F8DD57BD"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/lapse_adjust_climate.R="A353D90C"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/make_SED_landscape.R="6557A8A4"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/make_single_raster.R="8062E5E"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/read_climate_file.R="72FE6BA8"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/setup_init_file.R="B29E3CF"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/write_SED_climate_data.R="EDDD9C97"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/write_climate_file_NON_SED.R="D3FE6318"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/write_latitude_to_climate_file.R="D882E799"
/media/austin/DATADRIVE1/git_repos/code_working/8. r_packages/landclimSetup/R/write_species_xml.R="5A4A084E"
DESCRIPTION
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Package: landclimSetup
Type: Package
Title: Takes prepared data files and formats them to meet landclim requirements
Version: 0.0.0.9000
Authors@R: c(
person("Austin", "Haffenden", email = "austin.haffenden@irstea.fr", role = "cre", "aut"))
Maintainer: <austin.haffenden@irstea.fr>
Description: More about what it does (maybe more than one line)
Use four spaces when indenting paragraphs within the Description.
License: GPL-3
Encoding: UTF-8
LazyData: true
Imports:
raster,
dplyr,
doParallel,
rts,
XML,
ifnHelpers
RoxygenNote: 5.0.1
Suggests: testthat
NAMESPACE
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exportPattern("^[[:alpha:]]+")
R/.Rhistory
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R/IFN_forrester_foliage_pars.R
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# creates init file parameters for the species not represented by randomly selecting
# values from a species of the same leaf type
IFN_forrester_foliage_pars
<-
function
(
spp_name
,
spp_leaf_type
,
in_component
=
"Leaf area"
)
{
curr_dat
<-
subset
(
for_pars
,
Component
==
in_component
)
# cat("spp_name: ", spp_name, "\n")
# cat("spp_leaf_type: ", spp_leaf_type, "\n")
#
# forr_spp
forr_spp
<-
curr_dat
$
spp_id
# if we have the params for our species
if
(
spp_name
%in%
forr_spp
)
{
out_dat
<-
subset
(
curr_dat
,
spp_id
==
spp_name
)[,
c
(
"B0"
,
"B1"
)]
return
(
out_dat
)
}
else
if
(
spp_leaf_type
==
"EVERGREEN"
)
{
out_dat
<-
subset
(
curr_dat
,
spp_id
==
"conifer"
)[,
c
(
"B0"
,
"B1"
)]
return
(
out_dat
)
}
else
if
(
spp_leaf_type
==
"DECIDUOUS"
)
{
out_dat
<-
subset
(
curr_dat
,
spp_id
==
"broad_leaf"
)[,
c
(
"B0"
,
"B1"
)]
return
(
out_dat
)
}
else
{
stop
(
paste0
(
"Spp_name: "
,
spp_name
,
" and spp_leaf_type : "
,
spp_leaf_type
,
" unknown in landclimSetup::IFN_forrester_foliage_pars"
))
}
}
\ No newline at end of file
R/SED_climate_from_dataframe.R
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#' @title Script to create and check the Landclim SED climate files from a
#' climate data frame
#' @description This script takes a climate data frame in the form:
#' x (lon), y (lat), year, temperature (jan - dec),
#' precipitiation (jan - dec) and creates the necessary spatially
#' explicit data files (SED) for landclim
#' @param
#' @param
#' @return NULL
#' @keywords CoFoLaMo, Dischma, spin-up, climate
#' @author Austin Haffenden
#' @example /don't run {}
#'
SED_climate_from_dataframe
<-
function
(
clim_file
,
latitude
,
ref_elev
,
file_prefix
,
clim_dir
,
year_offset
=
0
)
{
# number you want the years to start at
save_clim
<-
function
(
curr_clim
,
min_year
){
curr_year
<-
unique
(
curr_clim
$
year
)
lc_year
<-
curr_year
-
min_year
+
year_offset
curr_file
<-
file.path
(
clim_dir
,
paste0
(
paste
(
file_prefix
,
lc_year
,
sep
=
"_"
),
".txt"
))
cat
(
curr_file
,
"\n"
)
con
<-
file
(
curr_file
,
open
=
"wt"
)
writeLines
(
"#header info#"
,
con
)
writeLines
(
paste
(
latitude
,
"#average latitude of the sites - used for cacluating drought index in model bugmann#"
),
con
)
writeLines
(
paste
(
ref_elev
,
"#reference elevation#"
),
con
)
writeLines
(
"# mean monthly temperature ?C total monthly precipitation mm #"
,
con
)
writeLines
(
"# x y year jan feb marz april mai june july aug sept oct nov dec jan feb marz april mai june july aug sept oct nov dec #"
,
con
)
write.table
(
as.matrix
(
curr_clim
),
#file = file.path(clim_dir, paste0(paste(file_prefix, i-1, sep = "_"), ".txt") ),
file
=
con
,
row.names
=
FALSE
,
col.names
=
FALSE
,
append
=
TRUE
)
close
(
con
)
}
# now just for test to call function
years
<-
unique
(
clim_file
$
year
)
#return(years)
min_year
<-
min
(
years
)
#doParallel::registerDoParallel(cores = 3)
plyr
::
ddply
(
clim_file
,
~
year
,
save_clim
,
min_year
)
#.parallel = TRUE)
return
(
1
)
}
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