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sfn_data classes

Victor Granda (Sapfluxnet Team)

2023-01-25

`sfn_data`

sfn_data is an S4 class designed for store and interact with sap flow data at individual plant level (not raw data), primarily from Sapfluxnet project sites data and metadata.

S4 Slots

sfn_data class has twelve different slots:

sapf_data: Tibble containing the sap flow data, each column representing an individual tree, without any TIMESTAMP variable.
env_data: Tibble containing the environmental data, each column an environmental variable, without any TIMESTAMP variable. It must have the same nrow thet sapf_data, in order to be able to combine both in further analyses or aggregations.
sapf_flags: Tibble with the same dimensions as sapf_data, containing the flags (special remarks indicating possible outliers or any annotation of interest) for each observation in sapf_data.
env_flags: Tibble with the same dimensions as env_data, containing the flags for each observation in env_data.
si_code: Character vector of length 1 with the site code. Useful for further analyses or aggregations in order to identify the site when working with more then one.
timestamp: POSIXct vector of length equal to nrow(sapf_data) with the timestamp values.
solar_timestamp: POSIXct vector of length equal to nrow(sapf_data) with the apparent solar timestamp.
site_md: Tibble with the site metadata. See sfn_vars_to_filter() for a list of possible metadata variables. This variables are not mandatory, and new ones can be added.
stand_md: Tibble with the stand metadata. See sfn_vars_to_filter() for a list of possible metadata variables. This variables are not mandatory, and new ones can be added.
species_md: Tibble with the species metadata. See sfn_vars_to_filter() for a list of possible metadata variables. This variables are not mandatory, and new ones can be added.
plant_md: Tibble with the plant metadata. See sfn_vars_to_filter() for a list of possible metadata variables. This variables are not mandatory, and new ones can be added.
env_md: Tibble with the environmental metadata. See sfn_vars_to_filter() for a list of possible metadata variables. This variables are not mandatory, and new ones can be added.

`sfn_data` design

The schematics of the class are summarised in Fig 1.

sfn_data schematics

This design have some characteristics:

Dimensions: Dimensions must comply:

nrow(sapf_data) == nrow(env_data) == nrow(sapf_flags) == nrow(env_flags) == length(timestamp) == length(solar_timestamp)

ncol(sapf_data) == ncol(sapf_flags)

ncol(env_data) == ncol(env_flags)

In the case of differences in the dimensions between environmental and sap flow data, NAs must be added in the corresponding places when equalising both TIMESTAMPs (i.e. if env data is longer then sapf data, rows are added to the later with NAs to make them equal, and flags (“NA_ADDED”) are raised to indicate the adding).
si_code slot: This slot indicates the site. This is useful for identifying the site in the metrics functions results.
Compartmentalization: timestamp and solar_timestamp are isolated from data (sapf and env) in their own slot. This made easier subsetting the object and open the possibility of working with the timestamps only.
Flags: Two slots are used for storing data flags. As the flag slots have the same dimensions as the corresponding dataset slot, selection of flagged data is straightforward:

sapf_data[flag_data == "flag", ]

Methods

Some methods are included in the class:

show: calling a sfn_data object shows info about it

library(sapfluxnetr)
data('ARG_TRE', package = 'sapfluxnetr')
ARG_TRE
#> sfn_data object
#> Data from ARG_TRE site
#> 
#> Data kindly provided by  Seabstian Pfautsch  from  University of Sydney
#> and  Pablo Peri  from  Instituto Nacional de Tecnología Agropecuaria 
#> 
#> Site related literature:  DOI 10.1007/s00468-013-0935-4 
#> 
#> Sapflow data:  312  observations of  4  trees/plants
#> Species present:  Nothofagus antarctica 
#> 
#> Environmental data:  312  observations.
#> Variables present:
#>   ta rh vpd sw_in ws precip swc_shallow ppfd_in ext_rad 
#> 
#> Biome:  Woodland/Shrubland 
#> 
#> TIMESTAMP span:  2009-11-18 -03--2009-11-30 23:00:00 -03 
#> 
#> Solar TIMESTAMP span:  2009-11-17 22:24:58 UTC--2009-11-30 21:20:48 UTC 
#> 
#> Sapflow data flags:
#> No flags present
#> 
#> Environmental data flags:
#> RANGE_WARN   OUT_WARN CALCULATED 
#>         18         24        624

get methods: methods to get any slot outside the object. In the case of sapf and env data, TIMESTAMP is added (based on the solar argument) in order to obtain fully functional datasets. See ?sfn_get_methods for more details.

get_sapf_data(ARG_TRE, solar = FALSE)
#> # A tibble: 312 × 5
#>    TIMESTAMP           ARG_TRE_Nan_Jt_1 ARG_TRE_Nan_Jt_2 ARG_TRE_Nan_J…¹ ARG_T…²
#>    <dttm>                         <dbl>            <dbl>           <dbl>   <dbl>
#>  1 2009-11-18 00:00:00             322.             190.            313.    218.
#>  2 2009-11-18 01:00:00             293.             157.            293.    293.
#>  3 2009-11-18 02:00:00             298.             178.            331.    309.
#>  4 2009-11-18 03:00:00             298.             168.            299.    258.
#>  5 2009-11-18 04:00:00             301.             170.            292.    301.
#>  6 2009-11-18 05:00:00             320.             198.            295.    261.
#>  7 2009-11-18 06:00:00             343.             196.            301.    285.
#>  8 2009-11-18 07:00:00             324.             194.            292.    282.
#>  9 2009-11-18 08:00:00             353.             284.            323.    374.
#> 10 2009-11-18 09:00:00             433.             340.            352.    372.
#> # … with 302 more rows, and abbreviated variable names ¹ARG_TRE_Nan_Jt_3,
#> #   ²ARG_TRE_Nan_Jt_4
get_sapf_data(ARG_TRE, solar = TRUE)
#> # A tibble: 312 × 5
#>    TIMESTAMP           ARG_TRE_Nan_Jt_1 ARG_TRE_Nan_Jt_2 ARG_TRE_Nan_J…¹ ARG_T…²
#>    <dttm>                         <dbl>            <dbl>           <dbl>   <dbl>
#>  1 2009-11-17 22:24:58             322.             190.            313.    218.
#>  2 2009-11-17 23:24:58             293.             157.            293.    293.
#>  3 2009-11-18 00:24:43             298.             178.            331.    309.
#>  4 2009-11-18 01:24:43             298.             168.            299.    258.
#>  5 2009-11-18 02:24:43             301.             170.            292.    301.
#>  6 2009-11-18 03:24:43             320.             198.            295.    261.
#>  7 2009-11-18 04:24:43             343.             196.            301.    285.
#>  8 2009-11-18 05:24:43             324.             194.            292.    282.
#>  9 2009-11-18 06:24:43             353.             284.            323.    374.
#> 10 2009-11-18 07:24:43             433.             340.            352.    372.
#> # … with 302 more rows, and abbreviated variable names ¹ARG_TRE_Nan_Jt_3,
#> #   ²ARG_TRE_Nan_Jt_4
get_env_data(ARG_TRE) # solar default is FALSE
#> # A tibble: 312 × 10
#>    TIMESTAMP              ta    rh   vpd sw_in    ws precip swc_shallow ppfd_in
#>    <dttm>              <dbl> <dbl> <dbl> <dbl> <dbl>  <dbl>       <dbl>   <dbl>
#>  1 2009-11-18 00:00:00  1     41.7 0.383   0   13.6       0       0.396      0 
#>  2 2009-11-18 01:00:00  1.2   41.5 0.389   0   15.8       0       0.396      0 
#>  3 2009-11-18 02:00:00  1.4   41.4 0.396   0   22.5       0       0.395      0 
#>  4 2009-11-18 03:00:00  1     38.9 0.401   0   13.6       0       0.394      0 
#>  5 2009-11-18 04:00:00  0.6   36.5 0.405   0    6.72      0       0.394      0 
#>  6 2009-11-18 05:00:00  1.65  37.5 0.430   0   20.3       0       0.394      0 
#>  7 2009-11-18 06:00:00  2.7   38.5 0.456   0    4.48      0       0.393      0 
#>  8 2009-11-18 07:00:00  4     38.2 0.503   0    2.24      0       0.392      0 
#>  9 2009-11-18 08:00:00  5.3   37.8 0.554  99.4  2.24      0       0.391    210.
#> 10 2009-11-18 09:00:00  6.75  33.0 0.660 245    4.48      0       0.391    518.
#> # … with 302 more rows, and 1 more variable: ext_rad <dbl>
get_sapf_flags(ARG_TRE) # solar default is FALSE
#> # A tibble: 312 × 5
#>    TIMESTAMP           ARG_TRE_Nan_Jt_1 ARG_TRE_Nan_Jt_2 ARG_TRE_Nan_J…¹ ARG_T…²
#>    <dttm>              <chr>            <chr>            <chr>           <chr>  
#>  1 2009-11-18 00:00:00 ""               ""               ""              ""     
#>  2 2009-11-18 01:00:00 ""               ""               ""              ""     
#>  3 2009-11-18 02:00:00 ""               ""               ""              ""     
#>  4 2009-11-18 03:00:00 ""               ""               ""              ""     
#>  5 2009-11-18 04:00:00 ""               ""               ""              ""     
#>  6 2009-11-18 05:00:00 ""               ""               ""              ""     
#>  7 2009-11-18 06:00:00 ""               ""               ""              ""     
#>  8 2009-11-18 07:00:00 ""               ""               ""              ""     
#>  9 2009-11-18 08:00:00 ""               ""               ""              ""     
#> 10 2009-11-18 09:00:00 ""               ""               ""              ""     
#> # … with 302 more rows, and abbreviated variable names ¹ARG_TRE_Nan_Jt_3,
#> #   ²ARG_TRE_Nan_Jt_4
get_env_flags(ARG_TRE) # solar default is FALSE
#> # A tibble: 312 × 10
#>    TIMESTAMP           ta    rh    vpd   sw_in ws    precip swc_shallow ppfd_in 
#>    <dttm>              <chr> <chr> <chr> <chr> <chr> <chr>  <chr>       <chr>   
#>  1 2009-11-18 00:00:00 ""    ""    ""    ""    ""    ""     ""          CALCULA…
#>  2 2009-11-18 01:00:00 ""    ""    ""    ""    ""    ""     ""          CALCULA…
#>  3 2009-11-18 02:00:00 ""    ""    ""    ""    ""    ""     ""          CALCULA…
#>  4 2009-11-18 03:00:00 ""    ""    ""    ""    ""    ""     ""          CALCULA…
#>  5 2009-11-18 04:00:00 ""    ""    ""    ""    ""    ""     ""          CALCULA…
#>  6 2009-11-18 05:00:00 ""    ""    ""    ""    ""    ""     ""          CALCULA…
#>  7 2009-11-18 06:00:00 ""    ""    ""    ""    ""    ""     ""          CALCULA…
#>  8 2009-11-18 07:00:00 ""    ""    ""    ""    ""    ""     ""          CALCULA…
#>  9 2009-11-18 08:00:00 ""    ""    ""    ""    ""    ""     ""          CALCULA…
#> 10 2009-11-18 09:00:00 ""    ""    ""    ""    ""    ""     ""          CALCULA…
#> # … with 302 more rows, and 1 more variable: ext_rad <chr>
get_si_code(ARG_TRE)
#> [1] "ARG_TRE"
get_timestamp(ARG_TRE)[1:10]
#>  [1] "2009-11-18 00:00:00 -03" "2009-11-18 01:00:00 -03"
#>  [3] "2009-11-18 02:00:00 -03" "2009-11-18 03:00:00 -03"
#>  [5] "2009-11-18 04:00:00 -03" "2009-11-18 05:00:00 -03"
#>  [7] "2009-11-18 06:00:00 -03" "2009-11-18 07:00:00 -03"
#>  [9] "2009-11-18 08:00:00 -03" "2009-11-18 09:00:00 -03"
get_solar_timestamp(ARG_TRE)[1:10]
#>  [1] "2009-11-17 22:24:58 UTC" "2009-11-17 23:24:58 UTC"
#>  [3] "2009-11-18 00:24:43 UTC" "2009-11-18 01:24:43 UTC"
#>  [5] "2009-11-18 02:24:43 UTC" "2009-11-18 03:24:43 UTC"
#>  [7] "2009-11-18 04:24:43 UTC" "2009-11-18 05:24:43 UTC"
#>  [9] "2009-11-18 06:24:43 UTC" "2009-11-18 07:24:43 UTC"
get_site_md(ARG_TRE)
#> # A tibble: 1 × 24
#>   si_addcontr_…¹ si_ad…² si_ad…³ si_ad…⁴ si_code si_co…⁵ si_co…⁶ si_co…⁷ si_co…⁸
#>   <chr>          <chr>   <chr>   <chr>   <chr>   <chr>   <chr>   <chr>   <chr>  
#> 1 <NA>           Pablo   Instit… Peri    ARG_TRE <NA>    Seabst… Univer… Pfauts…
#> # … with 15 more variables: si_country <chr>, si_dendro_network <lgl>,
#> #   si_dist_mgmt <chr>, si_elev <int>, si_flux_network <lgl>, si_igbp <chr>,
#> #   si_lat <dbl>, si_long <dbl>, si_name <chr>, si_paper <chr>,
#> #   si_remarks <lgl>, is_inside_country <lgl>, si_mat <dbl>, si_map <dbl>,
#> #   si_biome <chr>, and abbreviated variable names ¹si_addcontr_email,
#> #   ²si_addcontr_firstname, ³si_addcontr_institution, ⁴si_addcontr_lastname,
#> #   ⁵si_contact_email, ⁶si_contact_firstname, ⁷si_contact_institution, …
get_stand_md(ARG_TRE)
#> # A tibble: 1 × 18
#>   st_age st_asp…¹ st_ba…² st_cl…³ st_de…⁴ st_gr…⁵ st_he…⁶ st_lai st_name st_re…⁷
#>    <int> <chr>      <dbl> <lgl>     <int> <chr>     <int> <lgl>  <lgl>   <lgl>  
#> 1    140 Flat        19.4 NA          512 Natura…       6 NA     NA      NA     
#> # … with 8 more variables: st_sand_perc <lgl>, st_silt_perc <lgl>,
#> #   st_soil_depth <int>, st_soil_texture <chr>, st_terrain <chr>,
#> #   st_treatment <lgl>, si_code <chr>, st_USDA_soil_texture <chr>, and
#> #   abbreviated variable names ¹st_aspect, ²st_basal_area, ³st_clay_perc,
#> #   ⁴st_density, ⁵st_growth_condition, ⁶st_height, ⁷st_remarks
get_species_md(ARG_TRE)
#> # A tibble: 1 × 5
#>   sp_basal_area_perc sp_leaf_habit  sp_name               sp_ntrees si_code
#>                <int> <chr>          <chr>                     <int> <chr>  
#> 1                100 cold deciduous Nothofagus antarctica         4 ARG_TRE
get_plant_md(ARG_TRE)
#> # A tibble: 4 × 26
#>   pl_age pl_azi…¹ pl_ba…² pl_code pl_dbh pl_he…³ pl_le…⁴ pl_name pl_ra…⁵ pl_re…⁶
#>    <int> <chr>      <dbl> <chr>    <dbl> <lgl>     <dbl> <chr>   <chr>   <lgl>  
#> 1    140 Correct…    23.5 ARG_TR…   23.6 NA         29.7 Na-1    Correc… NA     
#> 2    140 No azim…    22.5 ARG_TR…   20.2 NA         13.0 Na-2    Correc… NA     
#> 3    140 No azim…    22   ARG_TR…   23.8 NA         29.8 Na-3    Correc… NA     
#> 4    140 No azim…    23.5 ARG_TR…   19.5 NA         15.1 Na-4    Correc… NA     
#> # … with 16 more variables: pl_sap_units <chr>, pl_sapw_area <dbl>,
#> #   pl_sapw_depth <dbl>, pl_sens_calib <lgl>, pl_sens_cor_grad <chr>,
#> #   pl_sens_cor_zero <chr>, pl_sens_hgt <dbl>, pl_sens_length <int>,
#> #   pl_sens_man <chr>, pl_sens_meth <chr>, pl_sens_timestep <int>,
#> #   pl_social <chr>, pl_species <chr>, pl_treatment <lgl>, si_code <chr>,
#> #   pl_sap_units_orig <chr>, and abbreviated variable names ¹pl_azimut_int,
#> #   ²pl_bark_thick, ³pl_height, ⁴pl_leaf_area, ⁵pl_radial_int, ⁶pl_remarks
get_env_md(ARG_TRE)
#> # A tibble: 1 × 17
#>   env_l…¹ env_n…² env_p…³ env_p…⁴ env_p…⁵ env_r…⁶ env_rh env_s…⁷ env_s…⁸ env_s…⁹
#>   <lgl>   <chr>   <chr>   <chr>   <chr>   <lgl>   <chr>  <lgl>     <int> <chr>  
#> 1 NA      Not pr… leaf: … Not pr… Cleari… NA      Clear… NA           15 Cleari…
#> # … with 7 more variables: env_ta <chr>, env_time_daylight <lgl>,
#> #   env_timestep <int>, env_time_zone <chr>, env_vpd <chr>, env_ws <chr>,
#> #   si_code <chr>, and abbreviated variable names ¹env_leafarea_seasonal,
#> #   ²env_netrad, ³env_plant_watpot, ⁴env_ppfd_in, ⁵env_precip, ⁶env_remarks,
#> #   ⁷env_swc_deep_depth, ⁸env_swc_shallow_depth, ⁹env_sw_in

assignation: methods for "<-" are implemented, allowing transformation of the slots. This is used internally in some functions but is not recommended except for updating metadata slots. In data slots this changes are not reflected in the flags, so the reproducibility and traceability will be lost if used without care. See ?sfn_replacement_methods for more details.

# extraction and modification
foo_site_md <- get_site_md(ARG_TRE)
foo_site_md[['si_biome']]
#> [1] "Woodland/Shrubland"
foo_site_md[['si_biome']] <- 'Temperate forest'
# assignation
get_site_md(ARG_TRE) <- foo_site_md
# check it worked
get_site_md(ARG_TRE)[['si_biome']]
#> [1] "Temperate forest"

validation: a validation method is implemented in order to avoid creation of invalid sfn_data objects (i.e objects with different data dimensions, objects without metadata…)

# get sap flow data
foo_bad_sapf <- get_sapf_data(ARG_TRE)
# pull a row, now it has diferent dimensions then
foo_bad_sapf <- foo_bad_sapf[-1,]
# try to assign the incorrect data fails
get_sapf_data(ARG_TRE) <- foo_bad_sapf[,-1] # ERROR

#> Error in validObject(object) : 
#>   invalid class "sfn_data" object: 1: nrow(sapf_data) != nrow(env_data)
#> invalid class "sfn_data" object: 2: nrow(sapf_data) != length(timestamp) | nrow(env_data) != length(timestamp)
#> invalid class "sfn_data" object: 3: nrow(*_flags) =! nrow(*_flags) | nrow(*_flags) =! nrow(*_data)

#> Error in `get_sapf_data<-`(`*tmp*`, value = structure(list(ARG_TRE_Nan_Jt_1 = c(292.9710029771, : new data is not valid: Error in validObject(object) : 
#>   invalid class "sfn_data" object: 1: nrow(sapf_data) != nrow(env_data)
#> invalid class "sfn_data" object: 2: nrow(sapf_data) != length(timestamp) | nrow(env_data) != length(timestamp)
#> invalid class "sfn_data" object: 3: nrow(*_flags) =! nrow(*_flags) | nrow(*_flags) =! nrow(*_data)

# try to build a new object also fails
sfn_data(
  sapf_data = foo_bad_sapf[,-1], # remember to remove timestamp column
  env_data = get_env_data(ARG_TRE)[,-1],
  sapf_flags = get_env_flags(ARG_TRE)[,-1],
  env_flags = get_env_flags(ARG_TRE)[,-1],
  si_code = get_si_code(ARG_TRE),
  timestamp = get_timestamp(ARG_TRE),
  solar_timestamp = get_solar_timestamp(ARG_TRE),
  site_md = get_site_md(ARG_TRE),
  stand_md = get_stand_md(ARG_TRE),
  species_md = get_species_md(ARG_TRE),
  plant_md = get_plant_md(ARG_TRE),
  env_md = get_env_md(ARG_TRE)
)

#> Error in validObject(.Object): invalid class "sfn_data" object: 1: nrow(sapf_data) != nrow(env_data)
#> invalid class "sfn_data" object: 2: nrow(sapf_data) != length(timestamp) | nrow(env_data) != length(timestamp)
#> invalid class "sfn_data" object: 3: nrow(*_flags) =! nrow(*_flags) | nrow(*_flags) =! nrow(*_data)

Utilities

sapfluxnetr package offers some utilities to visualize and work with sfn_data objects:

`sfn_plot`

This function allows to plot sfn_data objects. See ?sfn_plot for more details.

library(ggplot2)

sfn_plot(ARG_TRE, type = 'env') +
  facet_wrap(~ Variable, ncol = 3, scales = 'free_y') +
  theme(legend.position = 'none')


sfn_plot(ARG_TRE, formula_env = ~ vpd) +
  theme(legend.position = 'none')

`sfn_filter`

This function emulates filter function from dplyr package for sfn_data objects. Useful to filter by some specific timestamp. Be advised, using this function to filter by sap flow or environmental variables can create TIMESTAMP gaps. See sfn_filter for more details.

library(lubridate)
library(dplyr)

# get only the values for november
sfn_filter(ARG_TRE, month(TIMESTAMP) == 11)
#> sfn_data object
#> Data from ARG_TRE site
#> 
#> Data kindly provided by  Seabstian Pfautsch  from  University of Sydney
#> and  Pablo Peri  from  Instituto Nacional de Tecnología Agropecuaria 
#> 
#> Site related literature:  DOI 10.1007/s00468-013-0935-4 
#> 
#> Sapflow data:  312  observations of  4  trees/plants
#> Species present:  Nothofagus antarctica 
#> 
#> Environmental data:  312  observations.
#> Variables present:
#>   ta rh vpd sw_in ws precip swc_shallow ppfd_in ext_rad 
#> 
#> Biome:  Temperate forest 
#> 
#> TIMESTAMP span:  2009-11-18 -03--2009-11-30 23:00:00 -03 
#> 
#> Solar TIMESTAMP span:  2009-11-17 22:24:58 UTC--2009-11-30 21:20:48 UTC 
#> 
#> Sapflow data flags:
#> No flags present
#> 
#> Environmental data flags:
#> RANGE_WARN   OUT_WARN CALCULATED 
#>         18         24        624

`sfn_mutate`

This function allows mutation of data variables inside the sfn_data object. Useful when you need to transform a variable to another units or similar. A flag (‘USER_MODF’) will be added to all values in the mutated variable. See sfn_mutate for more details.

At this moment, mutate does not allows creating new variables, only mutate existing variables

# transform ws from m/s to km/h
foo_mutated <- sfn_mutate(ARG_TRE, ws = ws * 3600/1000)
get_env_data(foo_mutated)[['ws']][1:10]
#>  [1] 48.888 56.952 81.144 48.888 24.192 73.080 16.128  8.064  8.064 16.128

`sfn_mutate_at`

This function mutates all variables declared with the function provided. Useful when you need to conditionally transform the data, i.e. converting to NA sap flow values when an environmental variable exceeds some threshold. See sfn_mutate_at for more details.

foo_mutated_2 <- sfn_mutate_at(
  ARG_TRE,
  vars(one_of(names(get_sapf_data(ARG_TRE)[,-1]))),
  list(~ case_when(
    ws > 25 ~ NA_real_,
    TRUE ~ .
  ))
)

# see the difference between ARG_TRE and foo_mutated_2
get_sapf_data(ARG_TRE)
#> # A tibble: 312 × 5
#>    TIMESTAMP           ARG_TRE_Nan_Jt_1 ARG_TRE_Nan_Jt_2 ARG_TRE_Nan_J…¹ ARG_T…²
#>    <dttm>                         <dbl>            <dbl>           <dbl>   <dbl>
#>  1 2009-11-18 00:00:00             322.             190.            313.    218.
#>  2 2009-11-18 01:00:00             293.             157.            293.    293.
#>  3 2009-11-18 02:00:00             298.             178.            331.    309.
#>  4 2009-11-18 03:00:00             298.             168.            299.    258.
#>  5 2009-11-18 04:00:00             301.             170.            292.    301.
#>  6 2009-11-18 05:00:00             320.             198.            295.    261.
#>  7 2009-11-18 06:00:00             343.             196.            301.    285.
#>  8 2009-11-18 07:00:00             324.             194.            292.    282.
#>  9 2009-11-18 08:00:00             353.             284.            323.    374.
#> 10 2009-11-18 09:00:00             433.             340.            352.    372.
#> # … with 302 more rows, and abbreviated variable names ¹ARG_TRE_Nan_Jt_3,
#> #   ²ARG_TRE_Nan_Jt_4
get_sapf_data(foo_mutated_2)
#> # A tibble: 312 × 5
#>    TIMESTAMP           ARG_TRE_Nan_Jt_1 ARG_TRE_Nan_Jt_2 ARG_TRE_Nan_J…¹ ARG_T…²
#>    <dttm>                         <dbl>            <dbl>           <dbl>   <dbl>
#>  1 2009-11-18 00:00:00             322.             190.            313.    218.
#>  2 2009-11-18 01:00:00             293.             157.            293.    293.
#>  3 2009-11-18 02:00:00             298.             178.            331.    309.
#>  4 2009-11-18 03:00:00             298.             168.            299.    258.
#>  5 2009-11-18 04:00:00             301.             170.            292.    301.
#>  6 2009-11-18 05:00:00             320.             198.            295.    261.
#>  7 2009-11-18 06:00:00             343.             196.            301.    285.
#>  8 2009-11-18 07:00:00             324.             194.            292.    282.
#>  9 2009-11-18 08:00:00             353.             284.            323.    374.
#> 10 2009-11-18 09:00:00             433.             340.            352.    372.
#> # … with 302 more rows, and abbreviated variable names ¹ARG_TRE_Nan_Jt_3,
#> #   ²ARG_TRE_Nan_Jt_4

`*_metrics` functions

Family of functions to aggregate and summarise the site data. See ?metrics for more details.

foo_daily <- daily_metrics(ARG_TRE)
#> [1] "Crunching data for ARG_TRE. In large datasets this could take a while"
#> [1] "General data for ARG_TRE"
foo_daily[['sapf']][['sapf_gen']]
#> NULL

For full control of metrics and custom aggregations see vignette('custom-aggregation', package = 'sapfluxnetr')

`sfn_data_multi`

sfn_data_multi is an S4 class designed to store multiple sfn_data objects. It inherits from list so, in a nutshell, sfn_data_multi is a list of sfn_data objects.

Methods

sfn_data_multi has the following methods declared.

show: it shows the number, codes and combined timestamp span of sites in the multi object.

# creating a sfn_data_multi object
data(ARG_MAZ, package = 'sapfluxnetr')
data(AUS_CAN_ST2_MIX, package = 'sapfluxnetr')
multi_sfn <- sfn_data_multi(ARG_TRE, ARG_MAZ, AUS_CAN_ST2_MIX)

# show method
multi_sfn
#> sfn_data_multi object
#> 3 sites: ARG_TRE ARG_MAZ AUS_CAN_ST2_MIX
#> Approximate time span (UTC) for the combined sites: 2006-06-20 10:54:42 UTC--2009-11-18 22:24:18 UTC

get methods: they work the same as in the sfn_data objects, except they return a list, with the corresponding data for the sites in the sfn_data_multi object as elements.

# get sap flow data
get_sapf_data(multi_sfn)
#> $ARG_TRE
#> # A tibble: 312 × 5
#>    TIMESTAMP           ARG_TRE_Nan_Jt_1 ARG_TRE_Nan_Jt_2 ARG_TRE_Nan_J…¹ ARG_T…²
#>    <dttm>                         <dbl>            <dbl>           <dbl>   <dbl>
#>  1 2009-11-18 00:00:00             322.             190.            313.    218.
#>  2 2009-11-18 01:00:00             293.             157.            293.    293.
#>  3 2009-11-18 02:00:00             298.             178.            331.    309.
#>  4 2009-11-18 03:00:00             298.             168.            299.    258.
#>  5 2009-11-18 04:00:00             301.             170.            292.    301.
#>  6 2009-11-18 05:00:00             320.             198.            295.    261.
#>  7 2009-11-18 06:00:00             343.             196.            301.    285.
#>  8 2009-11-18 07:00:00             324.             194.            292.    282.
#>  9 2009-11-18 08:00:00             353.             284.            323.    374.
#> 10 2009-11-18 09:00:00             433.             340.            352.    372.
#> # … with 302 more rows, and abbreviated variable names ¹ARG_TRE_Nan_Jt_3,
#> #   ²ARG_TRE_Nan_Jt_4
#> 
#> $ARG_MAZ
#> # A tibble: 288 × 6
#>    TIMESTAMP           ARG_MAZ_Npu_Jt_1 ARG_MAZ_Npu_Jt_2 ARG_M…¹ ARG_M…² ARG_M…³
#>    <dttm>                         <dbl>            <dbl>   <dbl>   <dbl>   <dbl>
#>  1 2009-11-19 00:00:00            1955.             754.    742.   2679.   1494.
#>  2 2009-11-19 01:00:00            1833.             752.    631.   2527.   1504.
#>  3 2009-11-19 02:00:00            1817.             795.    597.   2514.   1446.
#>  4 2009-11-19 03:00:00            1598.             788.    579.   1938.   1265.
#>  5 2009-11-19 04:00:00            1419.             780.    518.   2061.   1181.
#>  6 2009-11-19 05:00:00            1506.             735.    430.   1977.   1231.
#>  7 2009-11-19 06:00:00            1649.             720.    539.   1984.   1310.
#>  8 2009-11-19 07:00:00            1630.             882.    542.   2371.   1506.
#>  9 2009-11-19 08:00:00            1909.            1015.    655.   2926.   1690.
#> 10 2009-11-19 09:00:00            2849.            1459.    930.   3802.   2265.
#> # … with 278 more rows, and abbreviated variable names ¹ARG_MAZ_Npu_Jt_3,
#> #   ²ARG_MAZ_Npu_Jt_4, ³ARG_MAZ_Npu_Jt_5
#> 
#> $AUS_CAN_ST2_MIX
#> # A tibble: 17,808 × 35
#>    TIMESTAMP           AUS_CAN…¹ AUS_C…² AUS_C…³ AUS_C…⁴ AUS_C…⁵ AUS_C…⁶ AUS_C…⁷
#>    <dttm>                  <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>
#>  1 2006-06-20 11:00:00        NA      NA      NA      NA      NA      NA      NA
#>  2 2006-06-20 11:30:00        NA      NA      NA      NA      NA      NA      NA
#>  3 2006-06-20 12:00:00        NA      NA      NA      NA      NA      NA      NA
#>  4 2006-06-20 12:30:00        NA      NA      NA      NA      NA      NA      NA
#>  5 2006-06-20 13:00:00        NA      NA      NA      NA      NA      NA      NA
#>  6 2006-06-20 13:30:00        NA      NA      NA      NA      NA      NA      NA
#>  7 2006-06-20 14:00:00        NA      NA      NA      NA      NA      NA      NA
#>  8 2006-06-20 14:30:00        NA      NA      NA      NA      NA      NA      NA
#>  9 2006-06-20 15:00:00        NA      NA      NA      NA      NA      NA      NA
#> 10 2006-06-20 15:30:00        NA      NA      NA      NA      NA      NA      NA
#> # … with 17,798 more rows, 27 more variables: AUS_CAN_ST2_MIX_Egl_Js_8 <dbl>,
#> #   AUS_CAN_ST2_MIX_Egl_Js_9 <dbl>, AUS_CAN_ST2_MIX_Ame_Js_10 <dbl>,
#> #   AUS_CAN_ST2_MIX_Ame_Js_11 <dbl>, AUS_CAN_ST2_MIX_Egl_Js_12 <dbl>,
#> #   AUS_CAN_ST2_MIX_Ame_Js_13 <dbl>, AUS_CAN_ST2_MIX_Egl_Js_14 <dbl>,
#> #   AUS_CAN_ST2_MIX_Egl_Js_15 <dbl>, AUS_CAN_ST2_MIX_Ame_Js_16 <dbl>,
#> #   AUS_CAN_ST2_MIX_Egl_Js_17 <dbl>, AUS_CAN_ST2_MIX_Ame_Js_18 <dbl>,
#> #   AUS_CAN_ST2_MIX_Ame_Js_19 <dbl>, AUS_CAN_ST2_MIX_Egl_Js_20 <dbl>, …
# get plant metadata
get_plant_md(multi_sfn)
#> $ARG_TRE
#> # A tibble: 4 × 26
#>   pl_age pl_azi…¹ pl_ba…² pl_code pl_dbh pl_he…³ pl_le…⁴ pl_name pl_ra…⁵ pl_re…⁶
#>    <int> <chr>      <dbl> <chr>    <dbl> <lgl>     <dbl> <chr>   <chr>   <lgl>  
#> 1    140 Correct…    23.5 ARG_TR…   23.6 NA         29.7 Na-1    Correc… NA     
#> 2    140 No azim…    22.5 ARG_TR…   20.2 NA         13.0 Na-2    Correc… NA     
#> 3    140 No azim…    22   ARG_TR…   23.8 NA         29.8 Na-3    Correc… NA     
#> 4    140 No azim…    23.5 ARG_TR…   19.5 NA         15.1 Na-4    Correc… NA     
#> # … with 16 more variables: pl_sap_units <chr>, pl_sapw_area <dbl>,
#> #   pl_sapw_depth <dbl>, pl_sens_calib <lgl>, pl_sens_cor_grad <chr>,
#> #   pl_sens_cor_zero <chr>, pl_sens_hgt <dbl>, pl_sens_length <int>,
#> #   pl_sens_man <chr>, pl_sens_meth <chr>, pl_sens_timestep <int>,
#> #   pl_social <chr>, pl_species <chr>, pl_treatment <lgl>, si_code <chr>,
#> #   pl_sap_units_orig <chr>, and abbreviated variable names ¹pl_azimut_int,
#> #   ²pl_bark_thick, ³pl_height, ⁴pl_leaf_area, ⁵pl_radial_int, ⁶pl_remarks
#> 
#> $ARG_MAZ
#> # A tibble: 5 × 26
#>   pl_age pl_azi…¹ pl_ba…² pl_code pl_dbh pl_he…³ pl_le…⁴ pl_name pl_ra…⁵ pl_re…⁶
#>    <int> <chr>      <dbl> <chr>    <dbl> <lgl>     <dbl> <chr>   <chr>   <lgl>  
#> 1    180 Correct…    14.7 ARG_MA…   41.1 NA        109.  Np-1    Correc… NA     
#> 2    180 No azim…    13   ARG_MA…   33.2 NA         58.4 Np-2    Correc… NA     
#> 3    180 No azim…     6   ARG_MA…   23.2 NA         35.0 Np-3    Correc… NA     
#> 4    180 No azim…    21   ARG_MA…   55.6 NA        174.  Np-4    Correc… NA     
#> 5    180 No azim…    10   ARG_MA…   38   NA         88   Np-5    Correc… NA     
#> # … with 16 more variables: pl_sap_units <chr>, pl_sapw_area <dbl>,
#> #   pl_sapw_depth <dbl>, pl_sens_calib <lgl>, pl_sens_cor_grad <chr>,
#> #   pl_sens_cor_zero <chr>, pl_sens_hgt <dbl>, pl_sens_length <int>,
#> #   pl_sens_man <chr>, pl_sens_meth <chr>, pl_sens_timestep <int>,
#> #   pl_social <chr>, pl_species <chr>, pl_treatment <lgl>, si_code <chr>,
#> #   pl_sap_units_orig <chr>, and abbreviated variable names ¹pl_azimut_int,
#> #   ²pl_bark_thick, ³pl_height, ⁴pl_leaf_area, ⁵pl_radial_int, ⁶pl_remarks
#> 
#> $AUS_CAN_ST2_MIX
#> # A tibble: 34 × 26
#>    pl_age pl_az…¹ pl_ba…² pl_code pl_dbh pl_he…³ pl_le…⁴ pl_name pl_ra…⁵ pl_re…⁶
#>     <dbl> <chr>   <lgl>   <chr>    <dbl>   <dbl> <lgl>   <chr>   <chr>   <chr>  
#>  1   14.5 No azi… NA      AUS_CA…   13.1    14.3 NA      CRR4AE5 Measur… The tr…
#>  2   14.5 No azi… NA      AUS_CA…   10.4    12.9 NA      CRR2AE… Measur… <NA>   
#>  3   14.5 No azi… NA      AUS_CA…   12.8    14.1 NA      CRR3AE… Measur… <NA>   
#>  4   14.5 No azi… NA      AUS_CA…   17.1    19.4 NA      CRR3EA… Measur… <NA>   
#>  5   14.5 No azi… NA      AUS_CA…   11.6    13.6 NA      CRR3AE… Measur… <NA>   
#>  6   14.5 No azi… NA      AUS_CA…   19.2    20.5 NA      CRR3EA… Measur… <NA>   
#>  7   14.5 No azi… NA      AUS_CA…   12.8    16.6 NA      CRR3EA… Measur… <NA>   
#>  8   14.5 No azi… NA      AUS_CA…   12.5    14.1 NA      CRR3AE… Measur… <NA>   
#>  9   14.5 No azi… NA      AUS_CA…   13.6    17.2 NA      CRR4EA… Measur… <NA>   
#> 10   14.5 No azi… NA      AUS_CA…   13.8    14.7 NA      CRR4AE… Measur… <NA>   
#> # … with 24 more rows, 16 more variables: pl_sap_units <chr>,
#> #   pl_sapw_area <dbl>, pl_sapw_depth <dbl>, pl_sens_calib <lgl>,
#> #   pl_sens_cor_grad <lgl>, pl_sens_cor_zero <chr>, pl_sens_hgt <dbl>,
#> #   pl_sens_length <lgl>, pl_sens_man <lgl>, pl_sens_meth <chr>,
#> #   pl_sens_timestep <int>, pl_social <lgl>, pl_species <chr>,
#> #   pl_treatment <chr>, si_code <chr>, pl_sap_units_orig <chr>, and abbreviated
#> #   variable names ¹pl_azimut_int, ²pl_bark_thick, ³pl_height, ⁴pl_leaf_area, …
# with metadata, we can collapse
get_plant_md(multi_sfn, collapse = TRUE)
#> # A tibble: 43 × 26
#>    pl_age pl_az…¹ pl_ba…² pl_code pl_dbh pl_he…³ pl_le…⁴ pl_name pl_ra…⁵ pl_re…⁶
#>     <dbl> <chr>     <dbl> <chr>    <dbl>   <dbl>   <dbl> <chr>   <chr>   <chr>  
#>  1  140   Correc…    23.5 ARG_TR…   23.6    NA      29.7 Na-1    Correc… <NA>   
#>  2  140   No azi…    22.5 ARG_TR…   20.2    NA      13.0 Na-2    Correc… <NA>   
#>  3  140   No azi…    22   ARG_TR…   23.8    NA      29.8 Na-3    Correc… <NA>   
#>  4  140   No azi…    23.5 ARG_TR…   19.5    NA      15.1 Na-4    Correc… <NA>   
#>  5  180   Correc…    14.7 ARG_MA…   41.1    NA     109.  Np-1    Correc… <NA>   
#>  6  180   No azi…    13   ARG_MA…   33.2    NA      58.4 Np-2    Correc… <NA>   
#>  7  180   No azi…     6   ARG_MA…   23.2    NA      35.0 Np-3    Correc… <NA>   
#>  8  180   No azi…    21   ARG_MA…   55.6    NA     174.  Np-4    Correc… <NA>   
#>  9  180   No azi…    10   ARG_MA…   38      NA      88   Np-5    Correc… <NA>   
#> 10   14.5 No azi…    NA   AUS_CA…   13.1    14.3    NA   CRR4AE5 Measur… The tr…
#> # … with 33 more rows, 16 more variables: pl_sap_units <chr>,
#> #   pl_sapw_area <dbl>, pl_sapw_depth <dbl>, pl_sens_calib <lgl>,
#> #   pl_sens_cor_grad <chr>, pl_sens_cor_zero <chr>, pl_sens_hgt <dbl>,
#> #   pl_sens_length <int>, pl_sens_man <chr>, pl_sens_meth <chr>,
#> #   pl_sens_timestep <int>, pl_social <chr>, pl_species <chr>,
#> #   pl_treatment <chr>, si_code <chr>, pl_sap_units_orig <chr>, and abbreviated
#> #   variable names ¹pl_azimut_int, ²pl_bark_thick, ³pl_height, ⁴pl_leaf_area, …

Utilities

All the utilities thet exists for sfn_data work for sfn_data_multi objects, executing the function for all the sites contained in the sfn_data_multi object:

`sfn_plot`

multi_plot <- sfn_plot(multi_sfn, formula = ~ vpd)
multi_plot[['ARG_TRE']] + theme(legend.position = 'none')
multi_plot[['AUS_CAN_ST2_MIX']] + theme(legend.position = 'none')
#> Warning: Removed 526066 rows containing missing values (`geom_point()`).

`sfn_filter`

multi_filtered <- sfn_filter(multi_sfn, month(TIMESTAMP) == 11)
get_timestamp(multi_filtered[['AUS_CAN_ST2_MIX']])[1:10]
#>  [1] "2006-11-01 00:00:00 +10" "2006-11-01 00:30:00 +10"
#>  [3] "2006-11-01 01:00:00 +10" "2006-11-01 01:30:00 +10"
#>  [5] "2006-11-01 02:00:00 +10" "2006-11-01 02:30:00 +10"
#>  [7] "2006-11-01 03:00:00 +10" "2006-11-01 03:30:00 +10"
#>  [9] "2006-11-01 04:00:00 +10" "2006-11-01 04:30:00 +10"

`sfn_mutate`

multi_mutated <- sfn_mutate(multi_sfn, ws = ws * 3600/1000)
get_env_data(multi_mutated[['AUS_CAN_ST2_MIX']])[['ws']][1:10]
#>  [1] 0.00 0.00 0.00 0.00 0.36 0.36 0.00 0.00 0.00 0.36

`sfn_mutate_at`

vars_to_not_mutate <- c(
  "TIMESTAMP", "ta", "rh", "vpd", "sw_in", "ws",
  "precip", "swc_shallow", "ppfd_in", "ext_rad"
)

multi_mutated_2 <- sfn_mutate_at(
  multi_sfn,
  vars(-one_of(vars_to_not_mutate)),
  list(~ case_when(
    ws > 25 ~ NA_real_,
    TRUE ~ .
  ))
)
#> Warning: Unknown columns: `swc_shallow`

multi_mutated_2[['ARG_TRE']]
#> sfn_data object
#> Data from ARG_TRE site
#> 
#> Data kindly provided by  Seabstian Pfautsch  from  University of Sydney
#> and  Pablo Peri  from  Instituto Nacional de Tecnología Agropecuaria 
#> 
#> Site related literature:  DOI 10.1007/s00468-013-0935-4 
#> 
#> Sapflow data:  312  observations of  4  trees/plants
#> Species present:  Nothofagus antarctica 
#> 
#> Environmental data:  312  observations.
#> Variables present:
#>   ta rh vpd sw_in ws precip swc_shallow ppfd_in ext_rad 
#> 
#> Biome:  Temperate forest 
#> 
#> TIMESTAMP span:  2009-11-18 -03--2009-11-30 23:00:00 -03 
#> 
#> Solar TIMESTAMP span:  2009-11-17 22:24:58 UTC--2009-11-30 21:20:48 UTC 
#> 
#> Sapflow data flags:
#> USER_MODF 
#>      1248 
#> 
#> Environmental data flags:
#> RANGE_WARN   OUT_WARN CALCULATED 
#>         18         24        624

`*_metrics`

multi_metrics <- daily_metrics(multi_sfn)
#> [1] "Crunching data for ARG_TRE. In large datasets this could take a while"
#> [1] "General data for ARG_TRE"
#> [1] "Crunching data for ARG_MAZ. In large datasets this could take a while"
#> [1] "General data for ARG_MAZ"
#> [1] "Crunching data for AUS_CAN_ST2_MIX. In large datasets this could take a while"
#> [1] "General data for AUS_CAN_ST2_MIX"
multi_metrics[['ARG_TRE']][['sapf']]
#> # A tibble: 14 × 21
#>    TIMESTAMP           ARG_TRE…¹ ARG_T…² ARG_T…³ ARG_T…⁴ ARG_T…⁵ ARG_T…⁶ ARG_T…⁷
#>    <dttm>                  <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl>
#>  1 2009-11-17 00:00:00      308.    173.    303.    255.    20.7    23.2    14.0
#>  2 2009-11-18 00:00:00      507.    376.    432.    490.   170.    174.    130. 
#>  3 2009-11-19 00:00:00      541.    380.    391.    524.   262.    169.    150. 
#>  4 2009-11-20 00:00:00      330.    218.    272.    334.   139.     67.2    74.6
#>  5 2009-11-21 00:00:00      338.    219.    278.    351.   190.    108.    113. 
#>  6 2009-11-22 00:00:00      384.    243.    310.    383.   268.    172.    184. 
#>  7 2009-11-23 00:00:00      492.    300.    390.    513.   327.    200.    228. 
#>  8 2009-11-24 00:00:00      573.    389.    497.    626.   313.    222.    261. 
#>  9 2009-11-25 00:00:00      601.    400.    484.    644.   193.    133.    170. 
#> 10 2009-11-26 00:00:00      502.    360.    450.    613.   277.    233.    308. 
#> 11 2009-11-27 00:00:00      544.    411.    506.    740.   271.    221.    285. 
#> 12 2009-11-28 00:00:00      573.    451.    589.    840.   180.    169.    249. 
#> 13 2009-11-29 00:00:00      371.    285.    357.    547.   233.    220.    197. 
#> 14 2009-11-30 00:00:00      386.    293.    381.    602.   273.    209.    288. 
#> # … with 13 more variables: ARG_TRE_Nan_Jt_4_sd <dbl>,
#> #   ARG_TRE_Nan_Jt_1_coverage <dbl>, ARG_TRE_Nan_Jt_2_coverage <dbl>,
#> #   ARG_TRE_Nan_Jt_3_coverage <dbl>, ARG_TRE_Nan_Jt_4_coverage <dbl>,
#> #   ARG_TRE_Nan_Jt_1_q_95 <dbl>, ARG_TRE_Nan_Jt_2_q_95 <dbl>,
#> #   ARG_TRE_Nan_Jt_3_q_95 <dbl>, ARG_TRE_Nan_Jt_4_q_95 <dbl>,
#> #   ARG_TRE_Nan_Jt_1_centroid <dbl>, ARG_TRE_Nan_Jt_2_centroid <dbl>,
#> #   ARG_TRE_Nan_Jt_3_centroid <dbl>, ARG_TRE_Nan_Jt_4_centroid <dbl>, and …

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.

sfn_data classes

Victor Granda (Sapfluxnet Team)

2023-01-25

sfn_data

S4 Slots

sfn_data design

Methods

Utilities

sfn_plot

sfn_filter

sfn_mutate

sfn_mutate_at

*_metrics functions

sfn_data_multi

Methods

Utilities

sfn_plot

sfn_filter

sfn_mutate

sfn_mutate_at

*_metrics

`sfn_data`

`sfn_data` design

`sfn_plot`

`sfn_filter`

`sfn_mutate`

`sfn_mutate_at`

`*_metrics` functions

`sfn_data_multi`

`sfn_plot`

`sfn_filter`

`sfn_mutate`

`sfn_mutate_at`

`*_metrics`