R: Complete metrics wrappers

metrics {sapfluxnetr}

R Documentation

Complete metrics wrappers

Description

This set of functions returns a complete set of statistics for a site (using sfn_data) or several sites (using sfn_data_multi)

Usage

daily_metrics(
  sfn_data,
  solar = TRUE,
  probs = c(0.95),
  tidy = FALSE,
  metadata = NULL,
  ...
)

monthly_metrics(
  sfn_data,
  solar = TRUE,
  probs = c(0.95),
  tidy = FALSE,
  metadata = NULL,
  ...
)

nightly_metrics(
  sfn_data,
  period = c("1 day", "1 month"),
  solar = TRUE,
  int_start = 20,
  int_end = 6,
  probs = c(0.95),
  tidy = FALSE,
  metadata = NULL,
  ...
)

daylight_metrics(
  sfn_data,
  period = c("1 day", "1 month"),
  solar = TRUE,
  int_start = 6,
  int_end = 20,
  probs = c(0.95),
  tidy = FALSE,
  metadata = NULL,
  ...
)

predawn_metrics(
  sfn_data,
  period = c("1 day", "1 month"),
  solar = TRUE,
  int_start = 4,
  int_end = 6,
  probs = c(0.95),
  tidy = FALSE,
  metadata = NULL,
  ...
)

midday_metrics(
  sfn_data,
  period = c("1 day", "1 month"),
  solar = TRUE,
  int_start = 11,
  int_end = 13,
  probs = c(0.95),
  tidy = FALSE,
  metadata = NULL,
  ...
)

Arguments

`sfn_data`	`sfn_data` or `sfn_data_multi` object to obtain the metrics from
`solar`	Logical indicating if the solarTIMESTAMP must be used instead of the site local TIMESTAMP. Default to TRUE (use solarTIMESTAMP).
`probs`	numeric vector of probabilities for `quantile`
`tidy`	Logical indicating if the metrics must be returned in a tidy format (a long tibble, each observation in its own row)
`metadata`	metadata object, usually the result of `read_sfn_metadata`. Only used if tidy is TRUE.
`...`	additional arguments to be passed to `.collapse_timestamp` or `floor_date` or `ceiling_date`.
`period`	Time period to aggregate data by. See period section for an explanation about the periods ('3 hours', '1 day', '1 month', '1 year', ...)
`int_start`	Integer value indicating the starting hour of the special interval in 24h format. See Interval section in details.
`int_end`	Integer value indicating the ending hour of the special interval in 24h format. See Interval section in details.

Details

*_metrics functions are wrappers for sfn_metrics with a set of fixed arguments.

*_metrics functions return all or some of the following statistics:

mean: mean of variable (tree or environmental variable) for the given period. NAs are removed
sd: standard deviation of the variable for the given period. NAs are removed
coverage: Data coverage percentage (percentage of measures without NAs)
q_XX: 0.XX quantile value for the period
centroid: Diurnal centroid value (hours passed until the half of the summed daily value was reached). Only returned for sapflow measures when period is '1 day'
accumulated: Accumulated values for precipitation only

Value

If tidy is TRUE, a tibble with the metrics for sapflow and environmental data, with all the metadata included. If tidy is FALSE (default), a list of tibbles with the calculated metrics.

daily_metrics

daily_metrics summarise daily data for all hours in the day

monthly_metrics

monthly_metrics summarise monthly data for all hours in the day.

nightly_metrics

nightly_metrics will return the metrics for night periods, summarised daily or monthly

Night for daily period starts in DOY x and ends in DOY x+1 (i.e. if night_start = 20, night_end = 6 values for the night starting at 2018-03-28 20:00:00 and ending at 2018-03-29 06:00:00 are summarised).

Night for monthly period summarises all night periods in the month, that includes from 00:00:00 of the first month night to 23:59:59 of the last month night.

daylight_metrics

daylight_metrics will return the metrics for daylight periods, summarised daily or monthly. Daylight interval is selected by start and end hours.

predawn_metrics

predawn_metrics will always return the metrics for predawn period, summarised daily or monthly. Predawn interval is selected by start and end hours.

Predawn metrics did not return the centroid metric.

midday_metrics

midday_metrics will always return the metrics for midday period, summarised daily or monthly. midday interval is selected by start and end hours.

Midday metrics did not return the centroid metric.

Examples

## daily_metrics
# data load
data('ARG_TRE', package = 'sapfluxnetr')
data('sfn_metadata_ex', package = 'sapfluxnetr')

# non tidy raw metrics (default)
ARG_TRE_raw_daily <- daily_metrics(ARG_TRE)
str(ARG_TRE_raw_daily)


# tidy daily metrics
ARG_TRE_daily <- daily_metrics(
  ARG_TRE, tidy = TRUE, metadata = sfn_metadata_ex
)
ARG_TRE_daily


## monthly_metrics
# data load
data('ARG_TRE', package = 'sapfluxnetr')
data('sfn_metadata_ex', package = 'sapfluxnetr')

# non tidy raw metrics (default)
ARG_TRE_raw_monthly <- monthly_metrics(ARG_TRE)
str(ARG_TRE_raw_monthly)


# tidy monthly metrics
ARG_TRE_monthly <- monthly_metrics(
  ARG_TRE, tidy = TRUE, metadata = sfn_metadata_ex
)
ARG_TRE_monthly



## nightly_metrics
# data load
data('AUS_CAN_ST2_MIX', package = 'sapfluxnetr')

# non tidy daily night metrics (default)
AUS_CAN_ST2_MIX_night <- nightly_metrics(AUS_CAN_ST2_MIX)

str(AUS_CAN_ST2_MIX_night)
AUS_CAN_ST2_MIX_night[['sapf']]
AUS_CAN_ST2_MIX_night[['env']]

# change the night interval
AUS_CAN_ST2_MIX_night_short <- nightly_metrics(
  AUS_CAN_ST2_MIX, int_start = 21, int_end = 4 # night starting and ending hour
)
AUS_CAN_ST2_MIX_night_short[['env']]

# tidy nightly metrics
data('sfn_metadata_ex', package = 'sapfluxnetr')
AUS_CAN_ST2_MIX_night_tidy <- nightly_metrics(
  AUS_CAN_ST2_MIX,
  tidy = TRUE, metadata = sfn_metadata_ex
)
AUS_CAN_ST2_MIX_night_tidy



## daylight_metrics
# data load
data('AUS_CAN_ST2_MIX', package = 'sapfluxnetr')

# non tidy daily daylight metrics (default)
AUS_CAN_ST2_MIX_daylight <- daylight_metrics(AUS_CAN_ST2_MIX)

str(AUS_CAN_ST2_MIX_daylight)
AUS_CAN_ST2_MIX_daylight[['sapf']]
AUS_CAN_ST2_MIX_daylight[['env']]

# change the daylight interval
AUS_CAN_ST2_MIX_daylight_short <- daylight_metrics(
  AUS_CAN_ST2_MIX, int_start = 8, int_end = 18 # night starting and ending hour
)
AUS_CAN_ST2_MIX_daylight_short[['env']]

# tidy daylight metrics
data('sfn_metadata_ex', package = 'sapfluxnetr')
AUS_CAN_ST2_MIX_daylight_tidy <- daylight_metrics(
  AUS_CAN_ST2_MIX,
  tidy = TRUE, metadata = sfn_metadata_ex
)
AUS_CAN_ST2_MIX_daylight_tidy



## predawn_metrics
# data load
data('AUS_CAN_ST2_MIX', package = 'sapfluxnetr')

# non tidy daily predawn metrics (default)
AUS_CAN_ST2_MIX_predawn <- predawn_metrics(AUS_CAN_ST2_MIX)

str(AUS_CAN_ST2_MIX_predawn)
AUS_CAN_ST2_MIX_predawn[['sapf']]
AUS_CAN_ST2_MIX_predawn[['env']]

# change the predawn interval
AUS_CAN_ST2_MIX_predawn_short <- predawn_metrics(
  AUS_CAN_ST2_MIX, int_start = 8, int_end = 18 # night starting and ending hour
)
AUS_CAN_ST2_MIX_predawn_short[['env']]

# tidy daylight metrics
data('sfn_metadata_ex', package = 'sapfluxnetr')
AUS_CAN_ST2_MIX_predawn_tidy <- predawn_metrics(
  AUS_CAN_ST2_MIX,
  tidy = TRUE, metadata = sfn_metadata_ex
)
AUS_CAN_ST2_MIX_predawn_tidy



## midday_metrics
# data load
data('AUS_CAN_ST2_MIX', package = 'sapfluxnetr')

# non tidy daily midday metrics (default)
AUS_CAN_ST2_MIX_midday <- midday_metrics(AUS_CAN_ST2_MIX)

str(AUS_CAN_ST2_MIX_midday)
AUS_CAN_ST2_MIX_midday[['sapf']]
AUS_CAN_ST2_MIX_midday[['env']]

# change the midday interval
AUS_CAN_ST2_MIX_midday_short <- midday_metrics(
  AUS_CAN_ST2_MIX, int_start = 8, int_end = 18 # night starting and ending hour
)
AUS_CAN_ST2_MIX_midday_short[['env']]

# tidy daylight metrics
data('sfn_metadata_ex', package = 'sapfluxnetr')
AUS_CAN_ST2_MIX_midday_tidy <- midday_metrics(
  AUS_CAN_ST2_MIX,
  tidy = TRUE, metadata = sfn_metadata_ex
)
AUS_CAN_ST2_MIX_midday_tidy

[Package sapfluxnetr version 0.1.4 Index]