In ISCN/SOCDRaHR2: Scripts to read in and harmonize different digital soil data archives

library(SOCDRaH2)

library(tidyverse)
library(vroom)

library(ggmap)
library(maps)
library(mapdata)

dataDir <- '~/Documents/Datasets/ISCN'
knitr::opts_chunk$set(eval=FALSE)

layer_raw <- vroom::vroom(file.path(dataDir, 'ISCN3_layer.csv'), col_types = strrep('c', times = 95))
profile_raw <-  vroom::vroom(file.path(dataDir, 'ISCN3_profile.csv'), col_types = strrep('c', times = 44))
dataset_raw <-  vroom::vroom(file.path(dataDir, 'ISCN3_dataset.csv'), col_types = strrep('c', times = 19))
citation_raw <-  vroom::vroom(file.path(dataDir, 'ISCN3_citation.csv'), col_types = strrep('c', times = 12))

Overview

temp <- layer_raw %>%
  filter(dataset_name_sub != 'NRCS Sept/2014') %>%
  select(-'ISCN 1-1 (2015-12-10)') %>%
  group_by(dataset_name_sub) %>% 
  tally(name = 'layer_count')

temp %>% full_join(profile_raw %>%
  filter(dataset_name_sub != 'NRCS Sept/2014') %>%
  select(-'ISCN 1-1 (2015-12-10)') %>%
  group_by(dataset_name_sub) %>% 
  tally(name = 'profile_count')) %>% 
  arrange(-layer_count)

Lu_PIMA

• Lu_PIMA
  • modification date not consistant between citation & dataset?

datasetName <- 'Lu_PIMA'

citation_raw %>% 
  filter(dataset_name == 'Lu_PIMA') %>% 
  select_if(function(xx){!is.na(xx)}) %>%
  full_join( dataset_raw %>% 
      filter(dataset_name == 'Lu_PIMA') %>% 
      select_if(function(xx){!is.na(xx)}),
    by = c("dataset_name", "dataset_type (dataset_type)", "curator_name", "curator_organization", "curator_email"),
    suffix = c('.citation', '.dataset')) %>%
  mutate_at(vars(contains('date')), function(xx){lubridate::as_date(as.numeric(xx), origin = '1900-01-01')}) %>%
  mutate_at(vars(contains('count')), as.numeric) %>%
  t()

Lu_PIMA_profile <- profile_raw %>%
  filter(dataset_name_sub == 'Lu_PIMA') %>%
  select_if(function(xx){any(!is.na(xx))}) %>%
  mutate_if(function(xx){all(grepl('^-?\\d*.?\\d+E?-?\\d*$', xx) | is.na(xx))}, as.numeric) %>%
  mutate(`thaw_depth_profile (cm)` = 
           as.numeric(gsub('none', 'Inf', `thaw_depth_profile (cm)`))) %>%
  mutate_at(vars(contains('date')), function(xx){lubridate::as_date(as.numeric(xx), origin = '1900-01-01')})

str(Lu_PIMA_profile)

dataset_profile <- noNRCS_ISCN3_profile  %>%
  filter(dataset_name_sub == datasetName) %>%
  mutate(`thaw_depth_profile (cm)` = 
           gsub('none', 'Inf', `thaw_depth_profile (cm)`)) %>%
  standardCast() %>%
  rename(dataset_name = 'dataset_name_sub') %>%
  select(`dataset_name`, `site_name`, `profile_name`, 
         `lat (dec. deg)`, `long (dec. deg)`, `datum (datum)`, 
         `state (state_province)`, `country (country)`, 
         `observation_date (YYYY-MM-DD)`, 
         `profile_zero_ref (profile_zero_ref)`, 
         #`layer_top (cm)`, `layer_bot (cm)`, `soc_depth (cm)`, 
         `elevation (m)`, 
         `ecoregion`, `vegclass_local`, 
         `landform (landform)`, `2d_position (2d_position)`, 
         `aspect_deg (degree)`, `slope (percent)`, 
         `drainagecl (drainage)`, `thaw_depth_profile (cm)`,
         `site_note`)

dataset_layer <- noNRCS_ISCN3_layer %>%
  filter(dataset_name_sub == datasetName) %>%
  standardCast() %>% 
  rename(dataset_name = 'dataset_name_sub') %>%
  select(`dataset_name`, `site_name`, `profile_name`, `layer_name`,
         `lat (dec. deg)`, `long (dec. deg)`, `datum (datum)`, 
         #`state (state_province)`, `country (country)`,  `observation_date (YYYY-MM-DD)`,  `vegclass_local`, 
         `layer_top (cm)`, `layer_bot (cm)`, 
         `hzn`, `hzn_desgn`, `color`, 
         `bd_samp (g cm-3)`, `c_tot (percent)`, `n_tot (percent)`, 
         `ph_h2o`, `sand_tot_psa (percent)`, 
         `silt_tot_psa (percent)`, `clay_tot_psa (percent)`, 
         `wpg2 (percent)`, `root_quant_size`)

all_study <- bind_rows(dataset_study, all_study)
all_profile <- bind_rows(dataset_profile, all_profile)
all_layer <- bind_rows(dataset_layer, all_layer)

ggplot(data =  map_data('world') %>%
         filter(region %in% c('Canada', 'USA', 'Mexico'))) + 
  geom_polygon(aes(x=long, y = lat, group = group), 
               fill = 'grey', color = 'black') + 
  geom_point(data=dataset_profile, 
             aes(x = `long (dec. deg)`, y = `lat (dec. deg)`),
             shape = 'x', color = 'red') +
  coord_fixed(1.3) +
  xlim(-180, -50) +
  theme_nothing() 

dataset_layer %>%
  pivot_longer(cols = intersect(names(.), type_cols$num_cols), values_drop_na = TRUE) %>%
  group_by(name) %>% summarize(n = length(value), unique_n = length(unique(value))) %>%
  bind_rows(
    dataset_layer %>%
      pivot_longer(cols = intersect(names(.), type_cols$factor_cols), values_drop_na = TRUE) %>%
      group_by(name) %>% summarize(n = length(value), unique_n = length(unique(value))) ) %>%
  arrange(n) %>%
  knitr::kable()

ggplot(dataset_layer %>% 
         pivot_longer( cols=c('layer_top (cm)', 'layer_bot (cm)'),
                       values_to='depth') %>%
         pivot_longer(cols = `bd_samp (g cm-3)`:`wpg2 (percent)`, 
                      values_to = 'measurement', names_to = 'type')) +
         geom_line(aes(x=depth, y= measurement, group = profile_name)) +
  facet_wrap(~type, scales='free')

ISCN/SOCDRaHR2 documentation built on May 26, 2023, 6:44 a.m.