SSS
Jens Daniel Müller & Lara Burchardt
16 March, 2020
Last updated: 2020-03-16
Checks: 7 0
Knit directory: Baltic_Productivity/
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Ignored: data/Finnmaid/
Ignored: data/GETM/
Ignored: data/OSTIA/
Ignored: data/_merged_data_files/
Ignored: data/_merged_data_files_2019V1/
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1 Medium Salinity
In the following section, we want to calculate the medium salinity per month and transect section. We will therefore end up with 544 x 12 salinity values.
nc <- nc_open(paste("data/Finnmaid/", "FM_all_2019_on_standard_tracks.nc", sep = ""))
# read required vectors from netcdf file
route <- ncvar_get(nc, "route")
route <- unlist(strsplit(route, ""))
date_time <- ncvar_get(nc, "time")
latitude_east <- ncvar_get(nc, "latitude_east")
longitude_east <-ncvar_get(nc, "longitude_east")
date_time_o <- ncvar_get(nc, "otime_east")
array <- ncvar_get(nc, var) # store the data in a 2-dimensional array
#dim(array) # should have 2 dimensions: 544 coordinate, 2089 time steps
fillvalue <- ncatt_get(nc, var, "_FillValue")
array[array == fillvalue$value] <- NA
rm(fillvalue)
cor_vector <- c(1:544)
for (i in seq(1,length(route),1)){
if(route[i] == select_route) {
slice <- array[i,] #define slice of the data, per row (per measurment day)
value <- slice
date <- ymd("2000-01-01") + date_time[i]
#if detailed date/time information is needed: uncomment that
#date <- as.Date(c(1:544)) # set up "date" variable to be overwritten later, needs to be "Date" object
#for (a in seq(1,length(latitude_east),1)){ # for slice i the corresponding 544 transect steps are
#temp_time <- ymd("2000-01-01") + date_time_o[i,a] # adjoined by corresponding time ("otime_east")
#date[a] <- temp_time
#}
#temp <- bind_cols(value = value, lon = longitude_east, lat = latitude_east,
#corvector = cor_vector, date_time = date)
#temp$date_time <- as.POSIXct(temp$date_time)
#when detailed time/date information is needed, comment the following
temp <- bind_cols(value = value, lon = longitude_east, lat = latitude_east,
corvector = cor_vector)
temp$date <- date
#
if (exists("fm_sss", inherits = FALSE)){
fm_sss <- bind_rows(fm_sss, temp)
} else{fm_sss <- temp}
rm(temp, value, date)
}
print(i)
}
nc_close(nc)
fm_sss_corvector <- fm_sss %>%
transmute(sss = value,
year = year(date),
month = month(date),
corvector = corvector )
for (cor in 1:544){
temp <- fm_sss_corvector %>%
filter(corvector == cor) %>%
select(month, corvector, sss) %>%
group_by(month, corvector) %>%
summarise_all(mean, na.rm = TRUE)
if (exists("fm_sss_monthly", inherits = FALSE)){
fm_sss_monthly <- bind_rows(fm_sss_monthly, temp)
} else{fm_sss_monthly <- temp}
rm(temp)
}
fm_sss_monthly %>%
vroom_write(here::here("data/_summarized_data_files/", file = "fm_sss_monthly_perTransect.csv"))
rm(fm_sss_monthly, fm_sss_corvector, var, select_route)fm_sss_monthly <- vroom::vroom(
here::here("data/_summarized_data_files","fm_sss_monthly_perTransect.csv"))
fm_sss_monthly <- fm_sss_monthly %>%
mutate(dist.trav = corvector * 2,
month_factor = as.factor(month))
fm_sss_monthly %>%
ggplot(aes(dist.trav, sss, color = month_factor))+
geom_point(size = 0.1)+
labs(x="Distance to Travemuende [km]",
y="Surface Salinity")+
theme_bw()+
scale_colour_brewer(palette = "Paired",
type = "qual",
name = "Month",
labels = c("January", "February", "March", "April", "May", "June", "July", "August", "September", "October", "November", "December"))
rm(fm_sss_monthly)
sessionInfo()R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] metR_0.5.0 here_0.1 xts_0.11-2 zoo_1.8-6
[5] dygraphs_1.1.1.6 geosphere_1.5-10 lubridate_1.7.4 vroom_1.2.0
[9] ncdf4_1.17 forcats_0.4.0 stringr_1.4.0 dplyr_0.8.3
[13] purrr_0.3.3 readr_1.3.1 tidyr_1.0.0 tibble_2.1.3
[17] ggplot2_3.3.0 tidyverse_1.3.0
loaded via a namespace (and not attached):
[1] nlme_3.1-137 bitops_1.0-6 fs_1.3.1
[4] bit64_0.9-7 RColorBrewer_1.1-2 httr_1.4.1
[7] rprojroot_1.3-2 tools_3.5.0 backports_1.1.5
[10] R6_2.4.0 DBI_1.0.0 colorspace_1.4-1
[13] withr_2.1.2 sp_1.3-2 tidyselect_0.2.5
[16] gridExtra_2.3 bit_1.1-14 compiler_3.5.0
[19] git2r_0.26.1 cli_1.1.0 rvest_0.3.5
[22] xml2_1.2.2 labeling_0.3 scales_1.0.0
[25] checkmate_1.9.4 digest_0.6.22 foreign_0.8-70
[28] rmarkdown_2.0 pkgconfig_2.0.3 htmltools_0.4.0
[31] dbplyr_1.4.2 maps_3.3.0 htmlwidgets_1.5.1
[34] rlang_0.4.5 readxl_1.3.1 rstudioapi_0.10
[37] generics_0.0.2 jsonlite_1.6 RCurl_1.95-4.12
[40] magrittr_1.5 Formula_1.2-3 dotCall64_1.0-0
[43] Matrix_1.2-14 Rcpp_1.0.2 munsell_0.5.0
[46] lifecycle_0.1.0 stringi_1.4.3 yaml_2.2.0
[49] plyr_1.8.4 grid_3.5.0 maptools_0.9-8
[52] formula.tools_1.7.1 parallel_3.5.0 promises_1.1.0
[55] crayon_1.3.4 lattice_0.20-35 haven_2.2.0
[58] hms_0.5.2 zeallot_0.1.0 knitr_1.26
[61] pillar_1.4.2 reprex_0.3.0 glue_1.3.1
[64] evaluate_0.14 data.table_1.12.6 modelr_0.1.5
[67] operator.tools_1.6.3 vctrs_0.2.0 spam_2.3-0.2
[70] httpuv_1.5.2 cellranger_1.1.0 gtable_0.3.0
[73] assertthat_0.2.1 xfun_0.10 broom_0.5.3
[76] later_1.0.0 memoise_1.1.0 fields_9.9
[79] workflowr_1.6.0