Function removes cases to produce desired missingness patterns and proportions.
amputeScaleScore( ampute.data, additional.data = NULL, compact.results = FALSE, growth.config = NULL, status.config = NULL, default.vars = c("CONTENT_AREA", "GRADE", "SCALE_SCORE", "ACHIEVEMENT_LEVEL"), demographics = NULL, institutions = NULL, ampute.vars = NULL, ampute.var.weights = NULL, reverse.weight = "SCALE_SCORE", ampute.args = list(prop=0.3, type="RIGHT"), complete.cases.only = TRUE, partial.fill = TRUE, invalidate.repeater.dups = TRUE, seed = 4224L, M = 10)
| ampute.data | The complete dataset in which to create missing values. |
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| additional.data | the function will return only data that is required for a SGP analysis (based on growth.config). This allows for the addition of more data (e.g. 2019 grades not used as priors) |
| compact.results | By default (FALSE), the function will return a list of longitudinal datassets with the current (amputed) and prior (unchanged) student records. This is helpful for diagnostics and ease of use, but also produces more redundant prior data than needed. Setting this argument to TRUE returns a single data.table object with a TRUE/FALSE indicator column added for each requested amputation. This flag can be used to make the SCALE_SCORE (and/or other variables) NA in subsequent use cases. |
| growth.config | An elongated SGP config script with an entry for each grade/content_area/year cohort that will be analyzed in subsequent simulations. |
| status.config | An elongated SGP config script. This needs to have an entry for each grade/content_area/year cohort that will be analyzed in subsequent simulations. Unlike a growth.config entry, status.config entries use data from the same grade, but from a prior year (i.e. not individual variables). For example you might predict 2021 3rd grade ELA missingness from 2019 3rd grade school mean scale score, FRL status, etc. |
| default.vars | Variables that will be used in extracting cohort records (subject and grade) and other variables from the data that the user may want returned in the amputed data. |
| demographics | Demographic (factor/character) variables to use and/or return in the final dataset. |
| institutions | Institution IDs that will be used/or returned in the amputed data |
| ampute.vars | Intersection of default.vars, demographics and institutions that will be used in the construction of the weighted scores that define the probability of being missing. Any institution included will be used to construct institution level means of other student level ampute.vars. For example, with c("SCHOOL_NUMBER", "SCALE_SCORE", "FREE_REDUCED_LUNCH_STATUS"), student level scores and demographics will be used along with their associated school level mean scores and proportion FRL (4 total factors). The default (NULL) means that no factors are considered, creating a "missing completely at random" (MCAR) missingness pattern. |
| ampute.var.weights | Relative weights assigned to the ampute vars. Default is NULL meaning the weighted sum scores will be calculated with equal weight (=1). A named list can be provided with the desired relative weights. For example, 'list(SCALE_SCORE=3, FREE_REDUCED_LUNCH_STATUS=2, SCHOOL_NUMBER=1)' will weight a student's scale scores by a factor of 3 and FRL by 2, with all (any other ampute.vars) remaining at the default of 1. This includes school level aggregates in this example. Note that differential weights for institutions should be placed at the end of the list. If institution IDs (e.g., SCHOOL_NUMBER) are omitted from the list, the aggregates will be given the same weight as the associated student level variable. In the given example, SCALE_SCORE and school mean scale score would be given a relative weight of 3. This argument is ignored when `ampute.vars = NULL`. |
| reverse.weight | The current default for ampute.args$type is "RIGHT", which means that students with high weighted scores have the highest probability for amputation. This makes sense for high students and/or students in high achieving schools. This function inverses the variable(s) individual (and institutional mean) value(s) so that higher weight is given to lower scores/means. This argument is ignored when `ampute.vars = NULL`. |
| ampute.args | Variables to be used in the mice:ampute.continuous function. Currenly only `prop` and `type` can be modified. See ?mice::ampute.continuous and ?mice::ampute for more information. The `prop` piece is inexact and has required some modification on my part. Its still imprecise, particularly for values away from 0.5 (50 to set prop=0.95 or greater. Note that the prop gives a total proportion missing, which accounts for missingness already included in the data due to students with incomplete longitudinal data histories. For example, if a cohort starts with 5 students missing due to incomplete histories, an additional 25 missing to get to the 30 with in some regards with the next argument, which removes these cases first. |
| complete.cases.only | Should cases without the most recent prior and current score be removed? This removes students with partial longitudinal histories from the most recent prior (e.g., 2019) to the current year (e.g., 2021), producing a "complete" dataset that is easier to interpret. |
| partial.fill | Should an attempt be made to fill in some of the demographic and institution ID information based on students previous values? Part of the process of the amputeScaleScore function is to take the long data (ampute.data) and then first widen and then re-lengthen the data, which creates holes for students with incomplete longitudinal records. This part of the function fills in these holes for students with existing missing data. |
| invalidate.repeater.dups | Students who repeat a grade will get missing data rows inserted for the grade that they "should" be in in 2021. This leads to duplicated cases that can lead to problems in the SGP analyses. This argument returns those cases with the VALID_CASE variable set to "INVALID_CASE". |
| seed | A random seed set for the amputation process to allow for replication of results, or for alternative results using the same code. |
| M | The number of amputed datasets to return. The default is 10. |
From the amputation process specified, the function returns either a list (default) of M amputed datasets or a single data set with M columns of missing record indicators. The datasets will exclude data for students not used in any of the specified growth.config or status.config cohorts, unless the additional.data argument has been included.
Function returns either a list (default) of amputed longitudinal data sets or a single data set containing additional columns of indicators for records to be removed.
not_run({ data_to_ampute <- SGPdata::sgpData_LONG_COVID ### Read in STEP 0 SGP configuration scripts source("SGP_CONFIG/STEP_0/Ampute_2021/Growth.R") source("SGP_CONFIG/STEP_0/Ampute_2021/Status.R") ### NOTE: the amputeScaleScore function requires the "mice" package! Test_Data_LONG <- amputeScaleScore( ampute.data = data_to_ampute, growth.config = growth_config_2021, status.config = status_config_2021, M = 1) })