A function that both checks and prepares a data.frame for use in
the trackSpp function.
Usage
checkDat(
dat,
inv = NULL,
species = "Species",
site = "Site",
quad = "Quad",
year = "Year",
geometry = "geometry",
reformatDat = FALSE,
...
)Arguments
- dat
An sf data.frame of the same format as
grasslandData. It must have columns that contain...a unique identification for each research site in character format with no NAs (the default column name is "Site")
species name in character format with no NAs (the default column name is "Species")
unique quadrat identifier in character format with no NAs (the default column name is "Quad")
year of data collection in integer format with no NAs (the default column name is "Year")
an s.f 'geometry' column that contains a polygon or multipolygon data type for each individual observation (the default column name is "geometry")
- inv
The name of each element of the list is a quadrat name in 'dat', and the contents of that list element is a numeric vector of all of the years in which that quadrat (or other unique spatial area) was sampled. Make sure this is the years the quadrat was actually sampled, not just the years that have data in the 'dat' argument! This argument allows the function to differentiate between years when the quadrat wasn't sampled and years when there just weren't any individuals of a species present in that quadrat.
- species
An optional character string argument. Indicates the name of the column in 'dat' that contains species name data. It is unnecessary to include a value for this argument if the column name is "Species" (default value is 'Species').
- site
An optional character string argument. Indicates the name of the column in 'dat' that contains site name data. It is unnecessary to include a value for this argument if the column name is "Site" (default value is 'Site').
- quad
An optional character string argument. Indicates the name of the column in 'dat' that contains quadrat name data. It is unnecessary to include a value for this argument if the column name is "Quad" (default is 'Quad').
- year
An optional character string argument. Indicates the name of the column in 'dat' that contains data for year of sampling. It is unnecessary to include a value for this argument if the column name is "Year" (default is 'Year').
- geometry
An optional character string argument. Indicates the name of the column in 'dat' that contains sf geometry data. It is unnecessary to include a value for this argument if the column name is "geometry" (default is 'geometry').
- reformatDat
A TRUE/FALSE argument. If 'FALSE', which is the default value, then
checkDat()prints a message that says the 'dat' and 'inv' datasets are ready for use in thetrackSpp()function. This message includes any column name arguments that must be included in thetrackSpp()function call for these datasets. If 'TRUE',checkDat()returns a list with three elements: a version of 'dat' that has been checked for errors and is ready to be input directly into thetrackSpporassignfunctions, a version of 'inv' that is checked and ready for input intotrackSpp()orassign(), and a character vector called 'userColNames' that has all of the user-defined column names that were used in the original version of 'dat'.- ...
Other arguments passed on to methods. Not currently used.
Value
If the 'reformatDat' argument is FALSE (the default), the return of
this function is a message that says the 'dat' and 'inv' datasets are ready
for use in the trackSpp() function. This message includes any column name
arguments that must be included in the trackSpp() function call for these
datasets.
If the 'reformatDat' argument is TRUE, then checkDat() returns a list that
contains versions of 'dat' and 'inv' that are ready to go directly into the
trackSpp() or assign() functions. The list has the following elements:
- dat
An sf data.frame that has five columns called 'Species', 'Site', 'Quad', 'Year', and 'geometry'. Any additional columns that were present in the version of 'dat' input into the
checkDat()function will also be included in this version, although the column names will be appended with "_USER".- inv
A named list. The name of each element of the list is a quadrat name in 'dat', and the contents of that list element is a numeric vector of all of the years in which that quadrat (or other unique spatial area) was sampled. For each list element, the vector of years is in sequential order from oldest to most recent.
- userColNames
A named character vector. This vector contains the column names provided by the user for all of the required data columns in the original version of 'dat'. The name of each vector element indicates the type of data that is contained in the column with the name in that vector element. For example, if the 'dat' data.frame input into
checkDat()has the names 'Species','location' 'quadrat', 'Year', and 'geometry', then this list element will be a character vector of these values with the names 'species', 'site', 'quad', 'year', and 'geometry'.
Details
This function is used internally in trackSpp and other
plantTracker functions to check the 'dat' and 'inv' arguments and ensure that
they are in the correct format with the correct column names. checkDat()
can also be used independently to check that a data.frame is in the correct
format and contains the correct data to be used in the trackSpp() or other
plantTracker functions.
Examples
checkDat(dat = grasslandData,
inv = grasslandInventory)
#> The data you put into the 'checkDat()' function for the 'dat' and
#> 'inv' arguments are ready to be used in the 'trackSpp()' function! You
#> do not need to include any values for the 'species', 'site', 'quad',
#> 'year', and 'geometry' arguments in 'trackSpp()
checkDat(dat = grasslandData,
inv = grasslandInventory,
reformatDat = TRUE)
#> $dat
#> Simple feature collection with 1242 features and 12 fields
#> Geometry type: GEOMETRY
#> Dimension: XY
#> Bounding box: xmin: -0.001386579 ymin: -0.001470638 xmax: 1.000536 ymax: 1.001267
#> CRS: NA
#> First 10 features:
#> Species Clone_USER Seedling_USER Stems_USER Basal_USER
#> 117603 Heteropogon contortus 0 0 NA NA
#> 117604 Heteropogon contortus 0 0 NA NA
#> 117605 Heteropogon contortus 0 0 NA NA
#> 117606 Heteropogon contortus 0 0 NA NA
#> 117607 Heteropogon contortus 0 0 NA NA
#> 117608 Heteropogon contortus 0 0 NA NA
#> 117609 Heteropogon contortus 0 0 NA NA
#> 117610 Heteropogon contortus 0 0 NA NA
#> 117611 Heteropogon contortus 0 0 NA NA
#> 117612 Heteropogon contortus 0 0 NA NA
#> Type_USER Site Quad Year sp_code_4_USER sp_code_6_USER Area_USER
#> 117603 poly AZ SG2 1922 HECO HETCON 0.0006140896
#> 117604 poly AZ SG2 1922 HECO HETCON 0.0014183352
#> 117605 poly AZ SG2 1922 HECO HETCON 0.0005743856
#> 117606 poly AZ SG2 1922 HECO HETCON 0.0009549092
#> 117607 poly AZ SG2 1922 HECO HETCON 0.0016950661
#> 117608 poly AZ SG2 1922 HECO HETCON 0.0037240299
#> 117609 poly AZ SG2 1922 HECO HETCON 0.0012574011
#> 117610 poly AZ SG2 1922 HECO HETCON 0.0019521166
#> 117611 poly AZ SG2 1922 HECO HETCON 0.0011659233
#> 117612 poly AZ SG2 1922 HECO HETCON 0.0009111819
#> geometry
#> 117603 POLYGON ((0.237747 0.908835...
#> 117604 POLYGON ((0.2833037 0.85959...
#> 117605 POLYGON ((0.008583123 0.449...
#> 117606 POLYGON ((0.1480142 0.46983...
#> 117607 POLYGON ((0.03573306 0.5259...
#> 117608 POLYGON ((0.2441894 0.52689...
#> 117609 POLYGON ((0.2888257 0.51815...
#> 117610 POLYGON ((0.3527891 0.45648...
#> 117611 POLYGON ((0.6749071 0.82646...
#> 117612 POLYGON ((0.4604686 0.76526...
#>
#> $inv
#> $inv$C5
#> [1] 1936 1937 1938 1939 1940
#>
#> $inv$D1
#> [1] 1936 1937 1938 1939 1940
#>
#> $inv$SG2
#> [1] 1922 1923 1924 1925 1926 1927
#>
#> $inv$SG4
#> [1] 1922 1923 1924 1925 1926 1927
#>
#>
#> $userColNames
#> species site quad year geometry
#> "Species" "Site" "Quad" "Year" "geometry"
#>