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Number comment fix #104

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merged 2 commits into from
Mar 15, 2024
Merged

Number comment fix #104

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fedf291
remove # from comments
jsocolar Mar 15, 2024
c1d0735
standardize
jsocolar Mar 15, 2024
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54 changes: 27 additions & 27 deletions R/make_occupancy_lpmf.R
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Original file line number Diff line number Diff line change
Expand Up @@ -15,8 +15,8 @@ make_occupancy_single_lpmf <- function (max_rep) {
array[] int y, // detection data
vector mu, // lin pred for detection
vector occ, // lin pred for occupancy. Elements after vint1[1] irrelevant.
array[] int vint1, // # units (n_unit). Elements after 1 irrelevant.
array[] int vint2, // # sampling events per unit (n_rep). Elements after vint1[1] irrelevant.
array[] int vint1, // n units (n_unit). Elements after 1 irrelevant.
array[] int vint2, // n sampling events per unit (n_rep). Elements after vint1[1] irrelevant.
array[] int vint3, // Indicator for > 0 detections (Q). Elements after vint1[1] irrelevant.

// indices for jth repeated sampling event to each unit (elements after vint1[1] irrelevant):"
Expand Down Expand Up @@ -96,11 +96,11 @@ make_occupancy_augmented_lpmf <- function (max_rep) {
vector mu, // lin pred for detection
vector occ, // lin pred for occupancy. Elements after vint1[1] irrelevant.
vector Omega, // lin pred for availability. Elements after 1 irrelevant.
array[] int vint1, // # units (n_unit). Elements after 1 irrelevant.
array[] int vint2, // # sampling events per unit (n_rep). Elements after vint1[1] irrelevant.
array[] int vint1, // n units (n_unit). Elements after 1 irrelevant.
array[] int vint2, // n sampling events per unit (n_rep). Elements after vint1[1] irrelevant.
array[] int vint3, // Indicator for > 0 detections (Q). Elements after vint1[1] irrelevant.

array[] int vint4, // # species (observed + augmented). Elements after 1 irrelevant.
array[] int vint4, // n species (observed + augmented). Elements after 1 irrelevant.
array[] int vint5, // Indicator for species was observed. Elements after vint4[1] irrelevant

array[] int vint6, // species
Expand Down Expand Up @@ -337,10 +337,10 @@ make_occupancy_multi_colex_lpmf <- function (max_rep, max_year) {
vector occ, // linear predictor for initial occupancy. Elements after vint1[1] irrelevant.
vector colo, // linear predictor for colonization. Elements after vint2[1] irrelevant.
vector ex, // linear predictor for extinction. Elements after vint2[1] irrelevant.
array[] int vint1, // # of series (# of HMMs). Elements after 1 irrelevant.
array[] int vint2, // # units (series-years). Elements after 1 irrelevant.
array[] int vint3, // # years per series. Elements after vint1[1] irrelevant.
array[] int vint4, // # sampling events per unit (n_rep). Elements after vint2[1] irrelevant.
array[] int vint1, // n series (n HMMs). Elements after 1 irrelevant.
array[] int vint2, // n units (series-years). Elements after 1 irrelevant.
array[] int vint3, // n years per series. Elements after vint1[1] irrelevant.
array[] int vint4, // n sampling events per unit (n_rep). Elements after vint2[1] irrelevant.
array[] int vint5, // Indicator for > 0 detections (Q). Elements after vint2[1] irrelevant.

// indices for jth unit (first rep) for each series. Elements after vint1[1] irrelevant."
Expand Down Expand Up @@ -431,10 +431,10 @@ make_occupancy_multi_colex_eq_lpmf <- function (max_rep, max_year) {
vector mu, // linear predictor for detection
vector colo, // linear predictor for colonization. Elements after vint2[1] irrelevant.
vector ex, // linear predictor for extinction. Elements after vint2[1] irrelevant.
array[] int vint1, // # of series (# of HMMs). Elements after 1 irrelevant.
array[] int vint2, // # units (series-years). Elements after 1 irrelevant.
array[] int vint3, // # years per series. Elements after vint1[1] irrelevant.
array[] int vint4, // # sampling events per unit (n_rep). Elements after vint2[1] irrelevant.
array[] int vint1, // n series (n HMMs). Elements after 1 irrelevant.
array[] int vint2, // n units (series-years). Elements after 1 irrelevant.
array[] int vint3, // n years per series. Elements after vint1[1] irrelevant.
array[] int vint4, // n sampling events per unit (n_rep). Elements after vint2[1] irrelevant.
array[] int vint5, // Indicator for > 0 detections (Q). Elements after vint2[1] irrelevant.

// indices for jth unit (first rep) for each series. Elements after vint1[1] irrelevant."
Expand Down Expand Up @@ -528,10 +528,10 @@ make_occupancy_multi_autologistic_lpmf <- function (max_rep, max_year) {
vector occ, // linear predictor for initial occupancy. Elements after vint1[1] irrelevant.
vector colo, // linear predictor for colonization. Elements after vint2[1] irrelevant.
vector autologistic, // logit-scale offset for persistence. Elements after vint2[1] irrelevant.
array[] int vint1, // # of series (# of HMMs). Elements after 1 irrelevant.
array[] int vint2, // # units (series-years). Elements after 1 irrelevant.
array[] int vint3, // # years per series. Elements after vint1[1] irrelevant.
array[] int vint4, // # sampling events per unit (n_rep). Elements after vint2[1] irrelevant.
array[] int vint1, // n series (n HMMs). Elements after 1 irrelevant.
array[] int vint2, // n units (series-years). Elements after 1 irrelevant.
array[] int vint3, // n years per series. Elements after vint1[1] irrelevant.
array[] int vint4, // n sampling events per unit (n_rep). Elements after vint2[1] irrelevant.
array[] int vint5, // Indicator for > 0 detections (Q). Elements after vint2[1] irrelevant.

// indices for jth unit (first rep) for each series. Elements after vint1[1] irrelevant."
Expand Down Expand Up @@ -624,10 +624,10 @@ make_occupancy_multi_autologistic_eq_lpmf <- function (max_rep, max_year) {
vector mu, // linear predictor for detection
vector colo, // linear predictor for colonization. Elements after vint2[1] irrelevant.
vector autologistic, // logit-scale offset for persistence. Elements after vint2[1] irrelevant.
array[] int vint1, // # of series (# of HMMs). Elements after 1 irrelevant.
array[] int vint2, // # units (series-years). Elements after 1 irrelevant.
array[] int vint3, // # years per series. Elements after vint1[1] irrelevant.
array[] int vint4, // # sampling events per unit (n_rep). Elements after vint2[1] irrelevant.
array[] int vint1, // n series (n HMMs). Elements after 1 irrelevant.
array[] int vint2, // n units (series-years). Elements after 1 irrelevant.
array[] int vint3, // n years per series. Elements after vint1[1] irrelevant.
array[] int vint4, // n sampling events per unit (n_rep). Elements after vint2[1] irrelevant.
array[] int vint5, // Indicator for > 0 detections (Q). Elements after vint2[1] irrelevant.

// indices for jth unit (first rep) for each series. Elements after vint1[1] irrelevant."
Expand Down Expand Up @@ -714,8 +714,8 @@ make_occupancy_single_threaded_lpmf <- function (max_rep, grainsize) {
array[] int y, // detection data
vector occ,
vector mu, // lin pred for detection
array[] int vint1, // # units (n_unit). Elements after 1 irrelevant.
array[] int vint2, // # sampling events per unit (n_rep). Elements after vint1[1] irrelevant.
array[] int vint1, // n units (n_unit). Elements after 1 irrelevant.
array[] int vint2, // n sampling events per unit (n_rep). Elements after vint1[1] irrelevant.
array[] int vint3, // Indicator for > 0 detections (Q). Elements after vint1[1] irrelevant.

// indices for jth repeated sampling event to each unit (elements after vint1[1] irrelevant):"
Expand All @@ -734,8 +734,8 @@ make_occupancy_single_threaded_lpmf <- function (max_rep, grainsize) {
sf_text1.2 <- paste0(" ", grainsize, ", // grainsize")
sf_text1.3 <- " y, // detection data
mu, // lin pred for detection
vint1, // # units (n_unit). Elements after 1 irrelevant.
vint2, // # sampling events per unit (n_rep). Elements after vint1[1] irrelevant.
vint1, // n units (n_unit). Elements after 1 irrelevant.
vint2, // n sampling events per unit (n_rep). Elements after vint1[1] irrelevant.
vint3, // Indicator for > 0 detections (Q). Elements after vint1[1] irrelevant.

// indices for jth repeated sampling event to each unit (elements after vint1[1] irrelevant):"
Expand Down Expand Up @@ -770,8 +770,8 @@ make_occupancy_single_partial_sum <- function (max_rep) {
int end,
array[] int y, // detection data
vector mu, // lin pred for detection
array[] int vint1, // # units (n_unit). Elements after 1 irrelevant.
array[] int vint2, // # sampling events per unit (n_rep). Elements after vint1[1] irrelevant.
array[] int vint1, // n units (n_unit). Elements after 1 irrelevant.
array[] int vint2, // n sampling events per unit (n_rep). Elements after vint1[1] irrelevant.
array[] int vint3, // Indicator for > 0 detections (Q). Elements after vint1[1] irrelevant.

// indices for jth repeated sampling event to each unit (elements after vint1[1] irrelevant):"
Expand Down
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